This section describes how to unpack, make, and run LAMMPS, for both -new and experienced users. +
This section describes how to build and run LAMMPS, for both new and +experienced users.
2.1 What's in the LAMMPS distributionRead this first: +
This section has the following sub-sections:
+Building LAMMPS can be non-trivial. You will likely need to edit a makefile, there are compiler options, additional libraries can be used (MPI, FFT), etc. Please read this section carefully. If you are not @@ -74,8 +84,10 @@ there isn't a similar Makefile for in the distribution), send it to the developers and we'll include it in future LAMMPS releases.
-Building a LAMMPS executable: -
+The src directory contains the C++ source and header files for LAMMPS. It also contains a top-level Makefile and a MAKE sub-directory with low-level Makefile.* files for several machines. From within the src @@ -93,8 +105,10 @@
If you get no errors and an executable like lmp_linux or lmp_mac is produced, you're done; it's your lucky day.
-Errors that can occur when making LAMMPS: -
+(1) If the make command breaks immediately with errors that indicate it can't find files with a "*" in their names, this can be because your machine's make doesn't support wildcard expansion in a makefile. @@ -116,16 +130,29 @@ whatever existing file is closest to your platform as a starting point. See the next section for more instructions.
-Editing a new low-level Makefile.foo: +
(3) If you get a link-time error about missing libraries or missing +dependencies, then it can be because:
+The first issue is discussed below. The other two issue mean you need +to edit your low-level Makefile.foo, as discussed in the next +sub-section. +
+These are the issues you need to address when editing a low-level -Makefile for your machine. With a couple exceptions, the only portion -of the file you should need to edit is the "System-specific Settings" +Makefile for your machine. The only portion of the file you should +need to edit is the first line and the "System-specific Settings" section.
-(1) Change the first line of Makefile.foo to include the word "foo" -and whatever other options you set. This is the line you will see if -you just type "make". +
(1) Change the first line of Makefile.foo to list the word "foo" after +the "#", and whatever other options you set. This is the line you +will see if you just type "make".
(2) Set the paths and flags for your C++ compiler, including optimization flags. You can use g++, the open-source GNU compiler, @@ -210,6 +237,17 @@ create a Makefile.foo patterned after Makefile.tflop, which uses different rules that do not involve dependency files.
+(9) The comments after the "System-specific Settings" heading refer to +Fortran, BLAS, GPU, etc system libraries. You only need to include +these settings if you intend to build LAMMPS with the optional +packages that use add-on LAMMPS libraries that need these system +libraries. See the section below for more details. If you +are not using these packages and their associated LAMMPS libraries, +then you can either comment out the relevant lines in the Makefile, or +leave the setting blank. If you do not do this, and your system does +not have the specified system library (e.g. a BLAS or CUDA library) +then you will get an error when you build LAMMPS. +
That's it. Once you have a correct Makefile.foo and you have pre-built the MPI and FFT libraries it will use, all you need to do from the src directory is type one of these 2 commands: @@ -219,8 +257,10 @@
You should get the executable lmp_foo when the build is complete.
-Additional build tips: -
+(1) Building LAMMPS for multiple platforms.
You can make LAMMPS for multiple platforms from the same src @@ -259,7 +299,7 @@
On a Macintosh, try compiling the pair "long" files without the -fast compiler option.
-(4) Building for a Macintosh. +
(4) Building for a Mac.
OS X is BSD Unix, so it already works. See the Makefile.mac file.
@@ -277,12 +317,23 @@This section has the following sub-sections: +
+The source code for LAMMPS is structured as a large set of core files -which are always used, plus optional packages, which are groups of -files that enable a specific set of features. For example, force -fields for molecular systems or granular systems are in packages. You -can see the list of both standard and user-contributed packages by -typing "make package". +which are always included, plus optional packages. Packages are +groups of files that enable a specific set of features. For example, +force fields for molecular systems or granular systems are in +packages. You can see the list of all packages by typing "make +package".
The current list of standard packages is as follows:
@@ -307,8 +358,10 @@There are also user-contributed packages which may be as simple as a single additional file or many files grouped together which add a -specific functionality to the code. The difference between a -standard package versus a user package is as follows. +specific functionality to the code. +
+The difference between a standard package versus a user package is +as follows.
Standard packages are supported by the LAMMPS developers and are written in a syntax and style consistent with the rest of LAMMPS. @@ -324,11 +377,13 @@
Any or all packages can be included or excluded independently when +Including/excluding packages: + +
Any or all packages can be included or excluded independently BEFORE LAMMPS is built.
-The two exceptions to this are the "gpu" and "opt" packages. Some of -the files in these packages require other packages to also be +
Note: The two exceptions to this are the "gpu" and "opt" packages. +Some of the files in these packages require other packages to also be included. If this is not the case, then those subsidiary files in "gpu" and "opt" will not be installed either. To install all the files in package "gpu", the "asphere" package must also be installed. @@ -350,103 +405,136 @@ no-user", "make yes-all" or "make no-all" to include/exclude various sets of packages. Type "make package" to see the various options.
-These make commands work by simply moving files back and forth between -the main src directory and sub-directories with the package name, so -that the files are seen or not seen when LAMMPS is built. After you -have included or excluded a package, you must re-build LAMMPS. +
IMPORTANT NOTE: These make commands work by simply moving files back +and forth between the main src directory and sub-directories with the +package name, so that the files are seen or not seen when LAMMPS is +built. After you have included or excluded a package, you must +re-build LAMMPS.
Additional make options exist to help manage LAMMPS files that exist in both the src directory and in package sub-directories. You do not normally need to use these commands unless you are editing LAMMPS -files or have downloaded a patch from the LAMMPS WWW site. Typing -"make package-update" will overwrite src files with files from the -package directories if the package has been included. It should be -used after a patch is installed, since patches only update the master -package version of a file. Typing "make package-overwrite" will -overwrite files in the package directories with src files. Typing -"make package-check" will list differences between src and package -versions of the same files. Again, type "make package" to see the -various options. -
-A few packages require that additional libraries be compiled first, -which LAMMPS will link to when it builds. These are stored under -under the lammps/lib directory of the distribution. Currently, these -include libraries for the "gpu", "meam", "poems", and "reax" packages. -You should look at the README files in the lib directories +files or have downloaded a patch from the LAMMPS WWW site. +
+Typing "make package-update" will overwrite src files with files from +the package directories if the package has been included. It should +be used after a patch is installed, since patches only update the +master package version of a file. Typing "make package-overwrite" +will overwrite files in the package directories with src files. +Typing "make package-check" will list differences between src and +package versions of the same files. Again, type "make package" to see +the various options. +
+A few packages (standard or user) require that add-on libraries be +compiled first, which LAMMPS will link to when it builds. The source +code for these libraries are included in the LAMMPS distribution under +the "lib" directory. Look at the README files in the lib directories (e.g. lib/reax/README) for instructions on how to build each library.
-The "gpu" library in lib/gpu contains code to enable portions of -LAMMPS to run on a GPU chip associated with your CPU. Currently, only -NVIDIA GPUs are supported. Building this library requires NVIDIA Cuda -tools to be installed on your system. See the Running on GPUs -section below for more info about installing and using Cuda. -
-The "meam" library in lib/meam computes the modified embedded atom -method potential, which is a generalization of EAM potentials that can -be used to model a wider variety of materials. This MEAM -implementation was written by Greg Wagner at Sandia. It requires a -F90 compiler to build. The C++ to FORTRAN function calls in pair_meam.cpp -assumes that FORTRAN object names are converted to C object names by -appending an underscore character. This is generally the case, but -on machines that do not conform to this convention, you will need to -modify either the C++ code or your compiler settings. -
-The "poems" library in lib/poems computes the constrained rigid-body -motion of articulated (jointed) multibody systems. POEMS was written -and is distributed by Prof Kurt Anderson's group at Rensselaer -Polytechnic Institute (RPI). -
-The "reax" library in lib/reax computes the Reactive Force Field -(ReaxFF) potential, developed by Adri van Duin in Bill Goddard's group -at CalTech. This implementation in LAMMPS uses many of Adri's files -and was developed by Aidan Thompson at Sandia and Hansohl Cho at MIT. -It requires a F77 or F90 compiler to build. -The C++ to FORTRAN function calls in pair_reax.cpp -assume that FORTRAN object names are converted to C object names by -appending an underscore character. This is generally the case, but -on machines that do not conform to this convention, you will need to -modify either the C++ code or your compiler settings. The name conversion -is handled by the preprocessor macro called FORTRAN in pair_reax_fortran.h. -Different definitions of this macro can be obtained by adding a -machine-specific macro definition to the CCFLAGS variable in your Makefile -e.g. -D_IBM. See pair_reax_fortran.h for more info. +
IMPORTANT NOTE: If you have included a package that uses +one of the libraries, then you must build the library BEFORE +building LAMMPS itself, as the LAMMPS build will link with +the library file. +
+Here is a bit of information about each library: +
+The "atc" library in lib/atc is used by the user-atc package. It +provides continuum field estimation and molecular dynamics-finite +element coupling methods. It was written primarily by Reese Jones, +Jeremy Templeton and Jonathan Zimmerman at Sandia. +
+The "gpu" library in lib/gpu is used by the gpu package. It +contains code to enable portions of LAMMPS to run on a GPU chip +associated with your CPU. Currently, only NVIDIA GPUs are supported. +Building this library requires NVIDIA Cuda tools to be installed on +your system. See the Running on GPUs section below for more +info about installing and using Cuda. +
+The "meam" library in lib/meam is used by the meam package. +computes the modified embedded atom method potential, which is a +generalization of EAM potentials that can be used to model a wider +variety of materials. This MEAM implementation was written by Greg +Wagner at Sandia. It requires a F90 compiler to build. The C++ to +FORTRAN function calls in pair_meam.cpp assumes that FORTRAN object +names are converted to C object names by appending an underscore +character. This is generally the case, but on machines that do not +conform to this convention, you will need to modify either the C++ +code or your compiler settings. +
+The "poems" library in lib/poems is used by the poems package. +computes the constrained rigid-body motion of articulated (jointed) +multibody systems. POEMS was written and is distributed by Prof Kurt +Anderson's group at Rensselaer Polytechnic Institute (RPI). +
+The "reax" library in lib/reax is used by the reax package. It +computes the Reactive Force Field (ReaxFF) potential, developed by +Adri van Duin in Bill Goddard's group at CalTech. This implementation +in LAMMPS uses many of Adri's files and was developed by Aidan +Thompson at Sandia and Hansohl Cho at MIT. It requires a F77 or F90 +compiler to build. The C++ to FORTRAN function calls in pair_reax.cpp +assume that FORTRAN object names are converted to C object names by +appending an underscore character. This is generally the case, but on +machines that do not conform to this convention, you will need to +modify either the C++ code or your compiler settings. The name +conversion is handled by the preprocessor macro called FORTRAN in +pair_reax_fortran.h. Different definitions of this macro can be +obtained by adding a machine-specific macro definition to the CCFLAGS +variable in your Makefile e.g. -D_IBM. See pair_reax_fortran.h for +more info.
-As its README file describes, for each library, the library is built -by typing something like +
As described in its README file, each library is built by typing +something like
-make -f Makefile.foo +make -f Makefile.g++in the appropriate directory, e.g. in lib/reax.
You must use a Makefile that is a match for your system. If one of the provided Makefiles is not appropriate for your system you will -need to edit or add one. For example, in the case of libraries of -Fortran code, your system must have a Fortran compiler, the settings -for which will be in the Makefile. -
-Once the desired library or libraries are built, you can build LAMMPS. -From the lammps/src directory type this, for example, to build LAMMPS -with ReaxFF: +need to edit or add one. For example, in the case of Fotran-based +libraries, your system must have a Fortran compiler, the settings for +which will be in the Makefile. +
+
+ +Additional Makefile settings for extra libraries: + +After the desired library or libraries are built, and the package has +been included, you can build LAMMPS itself. For example, from the +lammps/src directory you would type this, to build LAMMPS with ReaxFF. +Note that the library itself, namely lib/reax/libreax.a, must already +have been built, as dicussed in the preceding section, for the +LAMMPS build to be successful.
make yes-reax make g++-Note that simply building the library (reax in this case), which must -be done first, is not sufficient to use it from LAMMPS. You must also -include the package that uses and wraps the library before you build -LAMMPS itself. -
-To use the gpu package and library, the lo-level Makefile in -lammps/src/MAKE, such as Makefile.g++, must typically have settings -for LINKGPU and GPULIB that are specific to the NVIDIA software -installed on your system. -
-To use the meam or reax packages and libraries that are Fortran based, -the lo-level Makefile in lammps/src/MAKE, such as Makefile.g++, must -typically have settings for LINKFORT and FORTLIB that are specific to -the Fortran compiler installed on your system. This is so that the -C++ compiler can perform a cross-language link using the appropriate -Fortran libraries. +
Note that simply building the library is not sufficient to use it from +LAMMPS. You must also include the package that uses and wraps the +library before you build LAMMPS itself. +
+As discussed in point (9) of this section above, there are +settings in the low-level Makefile that specify additional system +libraries needed by individual LAMMPS add-on libraries. These are the +settings you must specify correctly in your low-level Makefile in +lammps/src/MAKE, such as Makefile.foo: +
+To use the user-atc package and library, the settings for LINKBLAS and +BLASLIB must be correct. This is so that the appropriate BLAS and +LAPACK libs, used by the user-atc library, can be found. +
+To use the gpu package and library, the settings for LINKGPU and +GPULIB must be correct. These are specific to the NVIDIA CUDA +software which must be installed on your system. +
+To use the meam or reax packages and their libraries which are Fortran +based, the settings for LINKFORT and FORTLIB must be correct. This is +so that the C++ compiler can perform a cross-language link using the +appropriate system Fortran libraries.
diff -Naur lammps-22Sep09/doc/Section_start.txt lammps-24Sep09/doc/Section_start.txt --- lammps-22Sep09/doc/Section_start.txt 2009-08-14 15:20:35.000000000 -0600 +++ lammps-24Sep09/doc/Section_start.txt 2009-09-24 11:42:17.000000000 -0600 @@ -8,8 +8,8 @@ 2. Getting Started :h3 -This section describes how to unpack, make, and run LAMMPS, for both -new and experienced users. +This section describes how to build and run LAMMPS, for both new and +experienced users. 2.1 "What's in the LAMMPS distribution"_#2_1 2.2 "Making LAMMPS"_#2_2 @@ -48,7 +48,17 @@ 2.2 Making LAMMPS :h4,link(2_2) -[{Read this first:}] +This section has the following sub-sections: + +"Read this first"_#2_2_1 +"Building a LAMMPS executable"_#2_2_2 +"Errors that can occur when making LAMMPS"_#2_2_3 +"Editing a new low-level Makefile"_#2_2_4 +"Additional build tips"_#2_2_5 :ul + +:line + +[{Read this first:}] :link(2_2_1) Building LAMMPS can be non-trivial. You will likely need to edit a makefile, there are compiler options, additional libraries can be used @@ -69,7 +79,9 @@ there isn't a similar Makefile for in the distribution), send it to the developers and we'll include it in future LAMMPS releases. -[{Building a LAMMPS executable:}] +:line + +[{Building a LAMMPS executable:}] :link(2_2_2) The src directory contains the C++ source and header files for LAMMPS. It also contains a top-level Makefile and a MAKE sub-directory with @@ -88,7 +100,9 @@ If you get no errors and an executable like lmp_linux or lmp_mac is produced, you're done; it's your lucky day. -[{Errors that can occur when making LAMMPS:}] +:line + +[{Errors that can occur when making LAMMPS:}] :link(2_2_3) (1) If the make command breaks immediately with errors that indicate it can't find files with a "*" in their names, this can be because @@ -111,16 +125,29 @@ whatever existing file is closest to your platform as a starting point. See the next section for more instructions. -[{Editing a new low-level Makefile.foo:}] +(3) If you get a link-time error about missing libraries or missing +dependencies, then it can be because: + +you have not pre-built the necessary "add-on LAMMPS library"_#2_3_3 +you are linking to a library that doesn't exist on your system +you are not linking to the necessary system library :ul + +The first issue is discussed below. The other two issue mean you need +to edit your low-level Makefile.foo, as discussed in the next +sub-section. + +:line + +[{Editing a new low-level Makefile.foo:}] :link(2_2_4) These are the issues you need to address when editing a low-level -Makefile for your machine. With a couple exceptions, the only portion -of the file you should need to edit is the "System-specific Settings" +Makefile for your machine. The only portion of the file you should +need to edit is the first line and the "System-specific Settings" section. -(1) Change the first line of Makefile.foo to include the word "foo" -and whatever other options you set. This is the line you will see if -you just type "make". +(1) Change the first line of Makefile.foo to list the word "foo" after +the "#", and whatever other options you set. This is the line you +will see if you just type "make". (2) Set the paths and flags for your C++ compiler, including optimization flags. You can use g++, the open-source GNU compiler, @@ -205,6 +232,17 @@ create a Makefile.foo patterned after Makefile.tflop, which uses different rules that do not involve dependency files. +(9) The comments after the "System-specific Settings" heading refer to +Fortran, BLAS, GPU, etc system libraries. You only need to include +these settings if you intend to build LAMMPS with the optional +packages that use add-on LAMMPS libraries that need these system +libraries. See the "section below"_#2_3_3 for more details. If you +are not using these packages and their associated LAMMPS libraries, +then you can either comment out the relevant lines in the Makefile, or +leave the setting blank. If you do not do this, and your system does +not have the specified system library (e.g. a BLAS or CUDA library) +then you will get an error when you build LAMMPS. + That's it. Once you have a correct Makefile.foo and you have pre-built the MPI and FFT libraries it will use, all you need to do from the src directory is type one of these 2 commands: @@ -214,7 +252,9 @@ You should get the executable lmp_foo when the build is complete. -[{Additional build tips:}] +:line + +[{Additional build tips:}] :link(2_2_5) (1) Building LAMMPS for multiple platforms. @@ -254,7 +294,7 @@ On a Macintosh, try compiling the pair "long" files without the -fast compiler option. -(4) Building for a Macintosh. +(4) Building for a Mac. OS X is BSD Unix, so it already works. See the Makefile.mac file. @@ -272,12 +312,23 @@ 2.3 Making LAMMPS with optional packages :h4,link(2_3) +This section has the following sub-sections: + +"Package basics"_#2_3_1 +"Including/excluding packages"_#2_3_2 +"Packages that require extra LAMMPS libraries"_#2_3_3 +"Additional Makefile settings for extra libraries"_#2_3_4 :ul + +:line + +[{Package basics:}] :link(2_3_1) + The source code for LAMMPS is structured as a large set of core files -which are always used, plus optional packages, which are groups of -files that enable a specific set of features. For example, force -fields for molecular systems or granular systems are in packages. You -can see the list of both standard and user-contributed packages by -typing "make package". +which are always included, plus optional packages. Packages are +groups of files that enable a specific set of features. For example, +force fields for molecular systems or granular systems are in +packages. You can see the list of all packages by typing "make +package". The current list of standard packages is as follows: @@ -300,8 +351,10 @@ There are also user-contributed packages which may be as simple as a single additional file or many files grouped together which add a -specific functionality to the code. The difference between a -{standard} package versus a {user} package is as follows. +specific functionality to the code. + +The difference between a {standard} package versus a {user} package is +as follows. Standard packages are supported by the LAMMPS developers and are written in a syntax and style consistent with the rest of LAMMPS. @@ -317,11 +370,13 @@ :line -Any or all packages can be included or excluded independently when +[{Including/excluding packages:}] :link(2_3_2) + +Any or all packages can be included or excluded independently BEFORE LAMMPS is built. -The two exceptions to this are the "gpu" and "opt" packages. Some of -the files in these packages require other packages to also be +Note: The two exceptions to this are the "gpu" and "opt" packages. +Some of the files in these packages require other packages to also be included. If this is not the case, then those subsidiary files in "gpu" and "opt" will not be installed either. To install all the files in package "gpu", the "asphere" package must also be installed. @@ -343,103 +398,136 @@ no-user", "make yes-all" or "make no-all" to include/exclude various sets of packages. Type "make package" to see the various options. -These make commands work by simply moving files back and forth between -the main src directory and sub-directories with the package name, so -that the files are seen or not seen when LAMMPS is built. After you -have included or excluded a package, you must re-build LAMMPS. +IMPORTANT NOTE: These make commands work by simply moving files back +and forth between the main src directory and sub-directories with the +package name, so that the files are seen or not seen when LAMMPS is +built. After you have included or excluded a package, you must +re-build LAMMPS. Additional make options exist to help manage LAMMPS files that exist in both the src directory and in package sub-directories. You do not normally need to use these commands unless you are editing LAMMPS -files or have downloaded a patch from the LAMMPS WWW site. Typing -"make package-update" will overwrite src files with files from the -package directories if the package has been included. It should be -used after a patch is installed, since patches only update the master -package version of a file. Typing "make package-overwrite" will -overwrite files in the package directories with src files. Typing -"make package-check" will list differences between src and package -versions of the same files. Again, type "make package" to see the -various options. - -A few packages require that additional libraries be compiled first, -which LAMMPS will link to when it builds. These are stored under -under the lammps/lib directory of the distribution. Currently, these -include libraries for the "gpu", "meam", "poems", and "reax" packages. -You should look at the README files in the lib directories +files or have downloaded a patch from the LAMMPS WWW site. + +Typing "make package-update" will overwrite src files with files from +the package directories if the package has been included. It should +be used after a patch is installed, since patches only update the +master package version of a file. Typing "make package-overwrite" +will overwrite files in the package directories with src files. +Typing "make package-check" will list differences between src and +package versions of the same files. Again, type "make package" to see +the various options. + +:line + +[{Packages that require extra LAMMPS libraries:}] :link(2_3_3) + +A few packages (standard or user) require that add-on libraries be +compiled first, which LAMMPS will link to when it builds. The source +code for these libraries are included in the LAMMPS distribution under +the "lib" directory. Look at the README files in the lib directories (e.g. lib/reax/README) for instructions on how to build each library. -The "gpu" library in lib/gpu contains code to enable portions of -LAMMPS to run on a GPU chip associated with your CPU. Currently, only -NVIDIA GPUs are supported. Building this library requires NVIDIA Cuda -tools to be installed on your system. See the "Running on GPUs"_#2_8 -section below for more info about installing and using Cuda. - -The "meam" library in lib/meam computes the modified embedded atom -method potential, which is a generalization of EAM potentials that can -be used to model a wider variety of materials. This MEAM -implementation was written by Greg Wagner at Sandia. It requires a -F90 compiler to build. The C++ to FORTRAN function calls in pair_meam.cpp -assumes that FORTRAN object names are converted to C object names by -appending an underscore character. This is generally the case, but -on machines that do not conform to this convention, you will need to -modify either the C++ code or your compiler settings. - -The "poems" library in lib/poems computes the constrained rigid-body -motion of articulated (jointed) multibody systems. POEMS was written -and is distributed by Prof Kurt Anderson's group at Rensselaer -Polytechnic Institute (RPI). - -The "reax" library in lib/reax computes the Reactive Force Field -(ReaxFF) potential, developed by Adri van Duin in Bill Goddard's group -at CalTech. This implementation in LAMMPS uses many of Adri's files -and was developed by Aidan Thompson at Sandia and Hansohl Cho at MIT. -It requires a F77 or F90 compiler to build. -The C++ to FORTRAN function calls in pair_reax.cpp -assume that FORTRAN object names are converted to C object names by -appending an underscore character. This is generally the case, but -on machines that do not conform to this convention, you will need to -modify either the C++ code or your compiler settings. The name conversion -is handled by the preprocessor macro called FORTRAN in pair_reax_fortran.h. -Different definitions of this macro can be obtained by adding a -machine-specific macro definition to the CCFLAGS variable in your Makefile -e.g. -D_IBM. See pair_reax_fortran.h for more info. +IMPORTANT NOTE: If you have included a package that uses +one of the libraries, then you must build the library BEFORE +building LAMMPS itself, as the LAMMPS build will link with +the library file. + +Here is a bit of information about each library: + +The "atc" library in lib/atc is used by the user-atc package. It +provides continuum field estimation and molecular dynamics-finite +element coupling methods. It was written primarily by Reese Jones, +Jeremy Templeton and Jonathan Zimmerman at Sandia. + +The "gpu" library in lib/gpu is used by the gpu package. It +contains code to enable portions of LAMMPS to run on a GPU chip +associated with your CPU. Currently, only NVIDIA GPUs are supported. +Building this library requires NVIDIA Cuda tools to be installed on +your system. See the "Running on GPUs"_#2_8 section below for more +info about installing and using Cuda. + +The "meam" library in lib/meam is used by the meam package. +computes the modified embedded atom method potential, which is a +generalization of EAM potentials that can be used to model a wider +variety of materials. This MEAM implementation was written by Greg +Wagner at Sandia. It requires a F90 compiler to build. The C++ to +FORTRAN function calls in pair_meam.cpp assumes that FORTRAN object +names are converted to C object names by appending an underscore +character. This is generally the case, but on machines that do not +conform to this convention, you will need to modify either the C++ +code or your compiler settings. + +The "poems" library in lib/poems is used by the poems package. +computes the constrained rigid-body motion of articulated (jointed) +multibody systems. POEMS was written and is distributed by Prof Kurt +Anderson's group at Rensselaer Polytechnic Institute (RPI). + +The "reax" library in lib/reax is used by the reax package. It +computes the Reactive Force Field (ReaxFF) potential, developed by +Adri van Duin in Bill Goddard's group at CalTech. This implementation +in LAMMPS uses many of Adri's files and was developed by Aidan +Thompson at Sandia and Hansohl Cho at MIT. It requires a F77 or F90 +compiler to build. The C++ to FORTRAN function calls in pair_reax.cpp +assume that FORTRAN object names are converted to C object names by +appending an underscore character. This is generally the case, but on +machines that do not conform to this convention, you will need to +modify either the C++ code or your compiler settings. The name +conversion is handled by the preprocessor macro called FORTRAN in +pair_reax_fortran.h. Different definitions of this macro can be +obtained by adding a machine-specific macro definition to the CCFLAGS +variable in your Makefile e.g. -D_IBM. See pair_reax_fortran.h for +more info. -As its README file describes, for each library, the library is built -by typing something like +As described in its README file, each library is built by typing +something like -make -f Makefile.foo :pre +make -f Makefile.g++ :pre in the appropriate directory, e.g. in lib/reax. You must use a Makefile that is a match for your system. If one of the provided Makefiles is not appropriate for your system you will -need to edit or add one. For example, in the case of libraries of -Fortran code, your system must have a Fortran compiler, the settings -for which will be in the Makefile. - -Once the desired library or libraries are built, you can build LAMMPS. -From the lammps/src directory type this, for example, to build LAMMPS -with ReaxFF: +need to edit or add one. For example, in the case of Fotran-based +libraries, your system must have a Fortran compiler, the settings for +which will be in the Makefile. + +:line + +[{Additional Makefile settings for extra libraries:}] :link(2_3_4) + +After the desired library or libraries are built, and the package has +been included, you can build LAMMPS itself. For example, from the +lammps/src directory you would type this, to build LAMMPS with ReaxFF. +Note that the library itself, namely lib/reax/libreax.a, must already +have been built, as dicussed in the preceding section, for the +LAMMPS build to be successful. make yes-reax make g++ :pre -Note that simply building the library (reax in this case), which must -be done first, is not sufficient to use it from LAMMPS. You must also -include the package that uses and wraps the library before you build -LAMMPS itself. - -To use the gpu package and library, the lo-level Makefile in -lammps/src/MAKE, such as Makefile.g++, must typically have settings -for LINKGPU and GPULIB that are specific to the NVIDIA software -installed on your system. - -To use the meam or reax packages and libraries that are Fortran based, -the lo-level Makefile in lammps/src/MAKE, such as Makefile.g++, must -typically have settings for LINKFORT and FORTLIB that are specific to -the Fortran compiler installed on your system. This is so that the -C++ compiler can perform a cross-language link using the appropriate -Fortran libraries. +Note that simply building the library is not sufficient to use it from +LAMMPS. You must also include the package that uses and wraps the +library before you build LAMMPS itself. + +As discussed in point (9) of "this section"_#2_2_4 above, there are +settings in the low-level Makefile that specify additional system +libraries needed by individual LAMMPS add-on libraries. These are the +settings you must specify correctly in your low-level Makefile in +lammps/src/MAKE, such as Makefile.foo: + +To use the user-atc package and library, the settings for LINKBLAS and +BLASLIB must be correct. This is so that the appropriate BLAS and +LAPACK libs, used by the user-atc library, can be found. + +To use the gpu package and library, the settings for LINKGPU and +GPULIB must be correct. These are specific to the NVIDIA CUDA +software which must be installed on your system. + +To use the meam or reax packages and their libraries which are Fortran +based, the settings for LINKFORT and FORTLIB must be correct. This is +so that the C++ compiler can perform a cross-language link using the +appropriate system Fortran libraries. :line diff -Naur lammps-22Sep09/doc/USER/atc/man_atom_element_map.html lammps-24Sep09/doc/USER/atc/man_atom_element_map.html --- lammps-22Sep09/doc/USER/atc/man_atom_element_map.html 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/doc/USER/atc/man_atom_element_map.html 2009-09-24 11:42:17.000000000 -0600 @@ -0,0 +1,26 @@ + + +ATC: fix_modify AtC transfer atom_element_map + + + +fix_modify AtC transfer atom_element_map
+syntax
+fix_modify AtC transfer atom_element_map <eulerian|lagrangian> <frequency>
+
fix_modify atc transfer atom_element_map eulerian 100 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_boundary_integral.html lammps-24Sep09/doc/USER/atc/man_boundary_integral.html
--- lammps-22Sep09/doc/USER/atc/man_boundary_integral.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_boundary_integral.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,26 @@
+
+
+ fix_modify AtC transfer boundary_integral stress faceset loop1 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_contour_integral.html lammps-24Sep09/doc/USER/atc/man_contour_integral.html
--- lammps-22Sep09/doc/USER/atc/man_contour_integral.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_contour_integral.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,26 @@
+
+
+ fix_modify AtC transfer contour_integral stress faceset loop1 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_disp_control.html lammps-24Sep09/doc/USER/atc/man_disp_control.html
--- lammps-22Sep09/doc/USER/atc/man_disp_control.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_disp_control.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,40 @@
+
+
+
+fix_modify AtC transfer momentum control rescale <frequency>
+
+fix_modify AtC transfer momentum control glc_displacement
+
+fix_modify AtC transfer momentum control glc_velocity
+
+fix_modify AtC transfer momentum control flux [faceset face_set_id, interpolate]
1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_electron_integration.html lammps-24Sep09/doc/USER/atc/man_electron_integration.html
--- lammps-22Sep09/doc/USER/atc/man_electron_integration.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_electron_integration.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,30 @@
+
+
++num_subcycle_steps (int), optional = number of subcycle steps for the electron time integration
fix_modify AtC extrinsic electron_integration implicit fix_modify AtC extrinsic electron_integration explicit 100 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_equilibrium_start.html lammps-24Sep09/doc/USER/atc/man_equilibrium_start.html
--- lammps-22Sep09/doc/USER/atc/man_equilibrium_start.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_equilibrium_start.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,24 @@
+
+
+ fix_modify atc transfer equilibrium_start on 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_extrinsic_exchange.html lammps-24Sep09/doc/USER/atc/man_extrinsic_exchange.html
--- lammps-22Sep09/doc/USER/atc/man_extrinsic_exchange.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_extrinsic_exchange.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,24 @@
+
+
+ fix_modify AtC extrinsic exchange on 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_fem_mesh.html lammps-24Sep09/doc/USER/atc/man_fem_mesh.html
--- lammps-22Sep09/doc/USER/atc/man_fem_mesh.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_fem_mesh.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,25 @@
+
+
+ fix_modify AtC fem create mesh 10 1 1 feRegion p p p 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_filter_scale.html lammps-24Sep09/doc/USER/atc/man_filter_scale.html
--- lammps-22Sep09/doc/USER/atc/man_filter_scale.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_filter_scale.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,28 @@
+
+
+ fix_modify AtC transfer filter scale 10.0 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_fix_atc.html lammps-24Sep09/doc/USER/atc/man_fix_atc.html
--- lammps-22Sep09/doc/USER/atc/man_fix_atc.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_fix_atc.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,119 @@
+
+
+ fix_modify AtC transfer thermal Ar_thermal.dat fix_modify AtC transfer hardy
+The following coupling example is typical, but non-exhaustive:
+
+ # ... commands to create and initialize the MD system
+
+ # initial fix to designate coupling type and group to apply it to
+ # tag group physics material_file
+ fix AtC internal atc thermal Ar_thermal.mat
+
+ # create a uniform 12 x 2 x 2 mesh that covers region contain the group
+ # nx ny nz region periodicity
+ fix_modify AtC fem create mesh 12 2 2 mdRegion f p p
+
+ # specify the control method for the type of coupling
+ # physics control_type
+ fix_modify AtC transfer thermal control flux
+
+ # specify the initial values for the empirical field "temperature"
+ # field node_group value
+ fix_modify AtC transfer initial temperature all 30.
+
+ # create an output stream for nodal fields
+ # filename output_frequency
+ fix_modify AtC transfer output atc_fe_output 100
+
+
+ run 1000
+
+likewise for this post-processing example:
+
+ # ... commands to create and initialize the MD system
+
+ # initial fix to designate post-processing and the group to apply it to
+ # no material file is allowed nor required
+ fix AtC internal atc hardy
+
+ # create a uniform 1 x 1 x 1 mesh that covers region contain the group
+ # with periodicity this effectively creats a system average
+ fix_modify AtC fem create mesh 1 1 1 box p p p
+
+ # change from default lagrangian map to eulerian
+ # refreshed every 100 steps
+ fix_modify AtC atom_element_map eulerian 100
+
+ # start with no field defined
+ fix_modify AtC transfer fields none
+
+ # add mass density, potential energy density, stress and temperature
+ fix_modify AtC transfer fields add density energy stress temperature
+
+ # create an output stream for nodal fields
+ # filename output_frequency
+ fix_modify AtC transfer output nvtFE 100 text
+
+ run 1000
+
+Note coupling and post-processing can be combined in the same simulations using separate fixes.
+ For detailed exposition of the theory and algorithms please see:
+
+Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes The finite element method , Dover 2003, for the basics of FE simulation.
+Currently,
+fix_modify commands for boundary and initial conditions:
+
+fix_modify commands for control and filtering:
+
+fix_modify commands for output:
+
+fix_modify commands for post-processing:
+
+miscellaneous fix_modify commands:
+
+Note: a set of example input files with the attendant material files are included with this package
1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_fix_flux.html lammps-24Sep09/doc/USER/atc/man_fix_flux.html
--- lammps-22Sep09/doc/USER/atc/man_fix_flux.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_fix_flux.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,26 @@
+
+
+ fix_modify atc transfer fix_flux temperature faceSet 10.0 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_fix_nodes.html lammps-24Sep09/doc/USER/atc/man_fix_nodes.html
--- lammps-22Sep09/doc/USER/atc/man_fix_nodes.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_fix_nodes.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,27 @@
+
+
+ fix_modify AtC transfer fix temperature groupNAME 10. fix_modify AtC transfer fix temperature groupNAME 0 0 0 10.0 0 0 1.0 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_hardy_computes.html lammps-24Sep09/doc/USER/atc/man_hardy_computes.html
--- lammps-22Sep09/doc/USER/atc/man_hardy_computes.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_hardy_computes.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,38 @@
+
+
+ compute virial all stress/atom fix_modify AtC transfer computes add virial volume fix_modify AtC transfer computes delete virial compute centrosymmetry all centro/atom fix_modify AtC transfer computes add centrosymmetry number 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_hardy_fields.html lammps-24Sep09/doc/USER/atc/man_hardy_fields.html
--- lammps-22Sep09/doc/USER/atc/man_hardy_fields.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_hardy_fields.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,46 @@
+
+
+ fix_modify AtC transfer fields add velocity temperature fix_modify AtC transfer fields none fix_modify AtC transfer fields add velocity temperature 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_hardy_gradients.html lammps-24Sep09/doc/USER/atc/man_hardy_gradients.html
--- lammps-22Sep09/doc/USER/atc/man_hardy_gradients.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_hardy_gradients.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,30 @@
+
+
+ fix_modify AtC transfer gradients add temperature velocity stress fix_modify AtC transfer gradients delete velocity 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_hardy_kernel.html lammps-24Sep09/doc/USER/atc/man_hardy_kernel.html
--- lammps-22Sep09/doc/USER/atc/man_hardy_kernel.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_hardy_kernel.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,36 @@
+
+
+ 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_hardy_on_the_fly.html lammps-24Sep09/doc/USER/atc/man_hardy_on_the_fly.html
--- lammps-22Sep09/doc/USER/atc/man_hardy_on_the_fly.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_hardy_on_the_fly.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,34 @@
+
+
+ fix_modify AtC transfer on_the_fly bond on fix_modify AtC transfer on_the_fly kernel fix_modify AtC transfer on_the_fly kernel off 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_hardy_rates.html lammps-24Sep09/doc/USER/atc/man_hardy_rates.html
--- lammps-22Sep09/doc/USER/atc/man_hardy_rates.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_hardy_rates.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,31 @@
+
+
+ fix_modify AtC transfer rates add temperature velocity stress fix_modify AtC transfer rates delete stress 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_hardy_set.html lammps-24Sep09/doc/USER/atc/man_hardy_set.html
--- lammps-22Sep09/doc/USER/atc/man_hardy_set.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_hardy_set.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,27 @@
+
+
+ fix_modify AtC transfer set reference_potential_energy fix_modify AtC transfer set reference_potential_energy -0.05 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_initial.html lammps-24Sep09/doc/USER/atc/man_initial.html
--- lammps-22Sep09/doc/USER/atc/man_initial.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_initial.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,25 @@
+
+
+ fix_modify atc transfer initial temperature groupNAME 10. 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_internal_quadrature.html lammps-24Sep09/doc/USER/atc/man_internal_quadrature.html
--- lammps-22Sep09/doc/USER/atc/man_internal_quadrature.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_internal_quadrature.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,23 @@
+
+
+ fix_modify atc transfer internal_quadrature off 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_mesh_delete_elements.html lammps-24Sep09/doc/USER/atc/man_mesh_delete_elements.html
--- lammps-22Sep09/doc/USER/atc/man_mesh_delete_elements.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_mesh_delete_elements.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,25 @@
+
+
+ fix_modify AtC delete_elements gap 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_mesh_elemset.html lammps-24Sep09/doc/USER/atc/man_mesh_elemset.html
--- lammps-22Sep09/doc/USER/atc/man_mesh_elemset.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_mesh_elemset.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,25 @@
+
+
+ fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_mesh_faceset.html lammps-24Sep09/doc/USER/atc/man_mesh_faceset.html
--- lammps-22Sep09/doc/USER/atc/man_mesh_faceset.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_mesh_faceset.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,25 @@
+
+
+ fix_modify AtC mesh create_faceset obndy -4.0 4.0 -12 12 -12 12 out 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_mesh_nodeset.html lammps-24Sep09/doc/USER/atc/man_mesh_nodeset.html
--- lammps-22Sep09/doc/USER/atc/man_mesh_nodeset.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_mesh_nodeset.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,25 @@
+
+
+ fix_modify AtC mesh create_faceset left -4.1 3.9 -100 100 -100 100 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_mesh_output.html lammps-24Sep09/doc/USER/atc/man_mesh_output.html
--- lammps-22Sep09/doc/USER/atc/man_mesh_output.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_mesh_output.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,24 @@
+
+
+ fix_modify AtC mesh output meshData 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_neighbor_reset_frequency.html lammps-24Sep09/doc/USER/atc/man_neighbor_reset_frequency.html
--- lammps-22Sep09/doc/USER/atc/man_neighbor_reset_frequency.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_neighbor_reset_frequency.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,25 @@
+
+
+ fix_modify AtC transfer neighbor_reset_frequency 1000 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_read_restart.html lammps-24Sep09/doc/USER/atc/man_read_restart.html
--- lammps-22Sep09/doc/USER/atc/man_read_restart.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_read_restart.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,25 @@
+
+
+ fix_modify AtC transfer read_restart ATC_state 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_remove_source.html lammps-24Sep09/doc/USER/atc/man_remove_source.html
--- lammps-22Sep09/doc/USER/atc/man_remove_source.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_remove_source.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,25 @@
+
+
+ fix_modify atc transfer remove_source temperature groupNAME 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_source.html lammps-24Sep09/doc/USER/atc/man_source.html
--- lammps-22Sep09/doc/USER/atc/man_source.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_source.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,25 @@
+
+
+ fix_modify atc transfer source temperature middle temporal_ramp 10. 0. 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_thermal_control.html lammps-24Sep09/doc/USER/atc/man_thermal_control.html
--- lammps-22Sep09/doc/USER/atc/man_thermal_control.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_thermal_control.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,47 @@
+
+
+
+fix_modify AtC transfer thermal control rescale <frequency>
+
+fix_modify AtC transfer thermal control hoover
+
+fix_modify AtC transfer thermal control flux <boundary_integration_type> <face_set_id(optional)>
+
fix_modify AtC transfer thermal control none fix_modify AtC transfer thermal control rescale 10 fix_modify AtC transfer thermal control hoover fix_modify AtC transfer thermal control flux bndy_faces 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_time_filter.html lammps-24Sep09/doc/USER/atc/man_time_filter.html
--- lammps-22Sep09/doc/USER/atc/man_time_filter.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_time_filter.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,29 @@
+
+
+ fix_modify atc transfer filter on 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_time_integration.html lammps-24Sep09/doc/USER/atc/man_time_integration.html
--- lammps-22Sep09/doc/USER/atc/man_time_integration.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_time_integration.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,23 @@
+
+
+ fix_modify atc transfer pmfc on 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_transfer_atomic_output.html lammps-24Sep09/doc/USER/atc/man_transfer_atomic_output.html
--- lammps-22Sep09/doc/USER/atc/man_transfer_atomic_output.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_transfer_atomic_output.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,27 @@
+
+
+ fix_modify AtC transfer atomic_output heatMD 100 fix_modify AtC transfer atomic_output nanoMD 1 text 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_transfer_boundary.html lammps-24Sep09/doc/USER/atc/man_transfer_boundary.html
--- lammps-22Sep09/doc/USER/atc/man_transfer_boundary.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_transfer_boundary.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,25 @@
+
+
+ fix_modify AtC transfer boundary type ghost_atoms 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_transfer_internal.html lammps-24Sep09/doc/USER/atc/man_transfer_internal.html
--- lammps-22Sep09/doc/USER/atc/man_transfer_internal.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_transfer_internal.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,25 @@
+
+
+ fix_modify AtC transfer internal type internal_atoms 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_transfer_output.html lammps-24Sep09/doc/USER/atc/man_transfer_output.html
--- lammps-22Sep09/doc/USER/atc/man_transfer_output.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_transfer_output.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,31 @@
+
+
+ fix_modify AtC transfer output heatFE 100 fix_modify AtC transfer output hardyFE 1 text tensor_components 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_unfix_flux.html lammps-24Sep09/doc/USER/atc/man_unfix_flux.html
--- lammps-22Sep09/doc/USER/atc/man_unfix_flux.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_unfix_flux.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,26 @@
+
+
+ fix_modify atc transfer unfix_flux temperature faceSet 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_unfix_nodes.html lammps-24Sep09/doc/USER/atc/man_unfix_nodes.html
--- lammps-22Sep09/doc/USER/atc/man_unfix_nodes.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_unfix_nodes.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,25 @@
+
+
+ fix_modify AtC transfer unfix temperature groupNAME 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/USER/atc/man_write_restart.html lammps-24Sep09/doc/USER/atc/man_write_restart.html
--- lammps-22Sep09/doc/USER/atc/man_write_restart.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/USER/atc/man_write_restart.html 2009-09-24 11:42:17.000000000 -0600
@@ -0,0 +1,25 @@
+
+
+ fix_modify AtC transfer write_restart restart.mydata 1.3.9.1
+
+
diff -Naur lammps-22Sep09/doc/fix_atc.html lammps-24Sep09/doc/fix_atc.html
--- lammps-22Sep09/doc/fix_atc.html 1969-12-31 17:00:00.000000000 -0700
+++ lammps-24Sep09/doc/fix_atc.html 2009-09-24 11:49:17.000000000 -0600
@@ -0,0 +1,231 @@
+
+Syntax: +
+fix ID groupID atc type paramfile ++
Examples: +
+fix AtC atc_atoms atc thermal Ar_thermal.dat +fix AtC atc_atoms atc transfer hardy ++
Description: +
+This fix creates a coupled finite element (FE) and molecular dynamics +(MD) simulation and/or an on-the-fly estimation of continuum fields. +Interscale operators are defined that construct continuum fields from +atomic data. Coupled simulations use FE projection approximated on a +discrete field. Currently, coupling is restricted to thermal physics. +The Hardy module can use either FE projection or integration Kernels +evaluated at mesh points. +
+Coupling methods enable appropriate corrections to the atomic data to +be made based on the FE field. For example, a Gaussian isokinetic +thermostat can apply heat sources to the atoms that varies in space on +the same scale as the FE element size. Meshes are not created +automatically and must be specified on LAMMPS regions with prescribed +element sizes. Note that mesh computations and storage run in serial +(not parallelized) so performance will degrade when large element +counts are used. +
+Note that coupling and post-processing can be combined in the same +simulations using separate fix atc commands. +
+For detailed exposition of the theory and algorithms implemented in +this fix, please see the papers here and here. +Please refer to the standard finite element (FE) texts, such as this +book, for the basics of FE simulation. +
+Thermal and two_temperature (coupling) types use a Verlet +time-integration algorithm. The hardy type does not contain its own +time-integrator and must be used with a separate fix that does contain +one, e.g. fix nve, fix nvt, etc. +
+A set of example input files with the attendant material files are +included in the examples/USER/atc directory of the LAMMPS +distribution. +
+An extensive set of additional documentation pages for the options +turned on via the fix_modify command for this fix +are inlcluded in the doc/USER/atc directory of the LAMMPS +distribution. Individual doc pages are listed and linked to below. +
+The following commands are typical of a coupling problem: +
+# ... commands to create and initialize the MD system ++
# initial fix to designate coupling type and group to apply it to + # tag group physics material_file + fix AtC internal atc thermal Ar_thermal.mat ++
# create a uniform 12 x 2 x 2 mesh that covers region contain the group + # nx ny nz region periodicity + fix_modify AtC fem create mesh 12 2 2 mdRegion f p p ++
# specify the control method for the type of coupling + # physics control_type + fix_modify AtC transfer thermal control flux ++
# specify the initial values for the empirical field "temperature" + # field node_group value + fix_modify AtC transfer initial temperature all 30.0 ++
# create an output stream for nodal fields + # filename output_frequency + fix_modify AtC transfer output atc_fe_output 100 ++
run 1000 ++
The following commands are typical of a post-processing (Hardy) problem: +
+# ... commands to create and initialize the MD system ++
# initial fix to designate post-processing and the group to apply it to + # no material file is allowed nor required + fix AtC internal atc hardy ++
# create a uniform 1 x 1 x 1 mesh that covers region contain the group + # with periodicity this effectively creats a system average + fix_modify AtC fem create mesh 1 1 1 box p p p ++
# change from default lagrangian map to eulerian + # refreshed every 100 steps + fix_modify AtC atom_element_map eulerian 100 ++
# start with no field defined + fix_modify AtC transfer fields none ++
# add mass density, potential energy density, stress and temperature + fix_modify AtC transfer fields add density energy stress temperature ++
# create an output stream for nodal fields + # filename output_frequency + fix_modify AtC transfer output nvtFE 100 text ++
run 1000 ++
Restart, fix_modify, output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. The fix_modify options +relevant to this fix are listed below. No global scalar or vector or +per-atom quantities are stored by this fix for access by various +output commands. No parameter of this fix +can be used with the start/stop keywords of the run +command. This fix is not invoked during energy +minimization. +
+Restrictions: +
+This fix is part of the "user-atc" package. It is only enabled if +LAMMPS was built with that package, which also requires the ATC +library be built and linked with LAMMPS. See the Making +LAMMPS section for more info. +
+Related commands: +
+After specifying this fix in your input script, several other +fix_modify commands are used to setup the problem, +e.g. define the finite element mesh and prescribe initial and boundary +conditions. +
+fix_modify commands for setup: +
+fix_modify commands for boundary and initial conditions: +
+fix_modify commands for control and filtering: +
+fix_modify commands for output: +
+fix_modify commands for post-processing: +
+miscellaneous fix_modify commands: +
+ +Default: none +
+(Wagner) Wagner, Jones, Templeton, Parks, Special Issue of +Computer Methods and Applied Mechanics, 197, 3351-3365 (2008). +
+ + +(Zimmerman) Zimmerman, Webb, Hoyt, Jones, Klein, Bammann, Special +Issue of Modelling and Simulation in Materials Science and +Engineering, 12, S319 (2004). +
+ + +(Hughes) T.J.R Hughes, "The Finite Element Method," Dover (2003). +
+ diff -Naur lammps-22Sep09/doc/fix_atc.txt lammps-24Sep09/doc/fix_atc.txt --- lammps-22Sep09/doc/fix_atc.txt 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/doc/fix_atc.txt 2009-09-24 11:49:17.000000000 -0600 @@ -0,0 +1,220 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix atc command :h3 + +[Syntax:] + +fix ID groupID atc type paramfile :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +atc = style name of this fix command :l +type = {thermal} or {two_temperature} or {hardy} :l + {thermal} = thermal coupling with field: temperature + {two_temperature} = electron-phonon coupling with field, temperature and electron_temperature + {hardy} = Hardy on-the-fly post-processing +paramfile = file with material parameters (not specified for {hardy} type) :l,ule + +[Examples:] + +fix AtC atc_atoms atc thermal Ar_thermal.dat +fix AtC atc_atoms atc transfer hardy :pre + +[Description:] + +This fix creates a coupled finite element (FE) and molecular dynamics +(MD) simulation and/or an on-the-fly estimation of continuum fields. +Interscale operators are defined that construct continuum fields from +atomic data. Coupled simulations use FE projection approximated on a +discrete field. Currently, coupling is restricted to thermal physics. +The Hardy module can use either FE projection or integration Kernels +evaluated at mesh points. + +Coupling methods enable appropriate corrections to the atomic data to +be made based on the FE field. For example, a Gaussian isokinetic +thermostat can apply heat sources to the atoms that varies in space on +the same scale as the FE element size. Meshes are not created +automatically and must be specified on LAMMPS regions with prescribed +element sizes. Note that mesh computations and storage run in serial +(not parallelized) so performance will degrade when large element +counts are used. + +Note that coupling and post-processing can be combined in the same +simulations using separate fix atc commands. + +For detailed exposition of the theory and algorithms implemented in +this fix, please see the papers "here"_#Wagner and "here"_#Zimmerman. +Please refer to the standard finite element (FE) texts, such as "this +book"_#Hughes, for the basics of FE simulation. + +:line + +{Thermal} and {two_temperature} (coupling) types use a Verlet +time-integration algorithm. The {hardy} type does not contain its own +time-integrator and must be used with a separate fix that does contain +one, e.g. "fix nve"_fix_nve.html, "fix nvt"_fix_nvt.html, etc. + +A set of example input files with the attendant material files are +included in the examples/USER/atc directory of the LAMMPS +distribution. + +An extensive set of additional documentation pages for the options +turned on via the "fix_modify"_fix_modify.html command for this fix +are inlcluded in the doc/USER/atc directory of the LAMMPS +distribution. Individual doc pages are listed and linked to below. + +The following commands are typical of a coupling problem: + + # ... commands to create and initialize the MD system :pre + + # initial fix to designate coupling type and group to apply it to + # tag group physics material_file + fix AtC internal atc thermal Ar_thermal.mat :pre + + # create a uniform 12 x 2 x 2 mesh that covers region contain the group + # nx ny nz region periodicity + fix_modify AtC fem create mesh 12 2 2 mdRegion f p p :pre + + # specify the control method for the type of coupling + # physics control_type + fix_modify AtC transfer thermal control flux :pre + + # specify the initial values for the empirical field "temperature" + # field node_group value + fix_modify AtC transfer initial temperature all 30.0 :pre + + # create an output stream for nodal fields + # filename output_frequency + fix_modify AtC transfer output atc_fe_output 100 :pre + + run 1000 :pre + +The following commands are typical of a post-processing (Hardy) problem: + + # ... commands to create and initialize the MD system :pre + + # initial fix to designate post-processing and the group to apply it to + # no material file is allowed nor required + fix AtC internal atc hardy :pre + + # create a uniform 1 x 1 x 1 mesh that covers region contain the group + # with periodicity this effectively creats a system average + fix_modify AtC fem create mesh 1 1 1 box p p p :pre + + # change from default lagrangian map to eulerian + # refreshed every 100 steps + fix_modify AtC atom_element_map eulerian 100 :pre + + # start with no field defined + fix_modify AtC transfer fields none :pre + + # add mass density, potential energy density, stress and temperature + fix_modify AtC transfer fields add density energy stress temperature :pre + + # create an output stream for nodal fields + # filename output_frequency + fix_modify AtC transfer output nvtFE 100 text :pre + + run 1000 :pre + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. The "fix_modify"_fix_modify.html options +relevant to this fix are listed below. No global scalar or vector or +per-atom quantities are stored by this fix for access by various +"output commands"_Section_howto.html#4_15. No parameter of this fix +can be used with the {start/stop} keywords of the "run"_run.html +command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the "user-atc" package. It is only enabled if +LAMMPS was built with that package, which also requires the ATC +library be built and linked with LAMMPS. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. + +[Related commands:] + +After specifying this fix in your input script, several other +"fix_modify"_fix_modify.html commands are used to setup the problem, +e.g. define the finite element mesh and prescribe initial and boundary +conditions. + +fix_modify commands for setup: + +"fix_modify AtC fem create mesh"_USER/atc/man_fem_mesh.html +"fix_modify AtC mesh create_nodeset"_USER/atc/man_mesh_nodeset.html +"fix_modify AtC mesh create_faceset"_USER/atc/man_mesh_faceset.html +"fix_modify AtC mesh create_elementset"_USER/atc/man_mesh_elemset.html +"fix_modify AtC transfer internal"_USER/atc/man_transfer_internal.html +"fix_modify AtC transfer boundary"_USER/atc/man_transfer_boundary.html +"fix_modify AtC transfer internal_quadrature"_USER/atc/man_internal_quadrature.html +"fix_modify AtC transfer pmfc"_USER/atc/man_time_integration.html +"fix_modify AtC extrinsic electron_integration"_USER/atc/man_electron_integration.html :ul + +fix_modify commands for boundary and initial conditions: + +"fix_modify AtC transfer initial"_USER/atc/man_initial.html +"fix_modify AtC transfer fix"_USER/atc/man_fix_nodes.html +"fix_modify AtC transfer unfix"_USER/atc/man_unfix_nodes.html +"fix_modify AtC transfer fix_flux"_USER/atc/man_fix_flux.html +"fix_modify AtC transferunfix_flux"_USER/atc/man_unfix_flux.html +"fix_modify AtC transfer source"_USER/atc/man_source.html +"fix_modify AtC transfer remove_source"_USER/atc/man_remove_source.html :ul + +fix_modify commands for control and filtering: + +"fix_modify AtC transfer thermal control"_USER/atc/man_thermal_control.html +"fix_modify AtC transfer filter"_USER/atc/man_time_filter.html +"fix_modify AtC transfer filter scale"_USER/atc/man_filter_scale.html +"fix_modify AtC transfer equilibrium_start"_USER/atc/man_equilibrium_start.html +"fix_modify AtC extrinsic exchange"_USER/atc/man_extrinsic_exchange.html :ul + +fix_modify commands for output: + +"fix_modify AtC transfer output"_USER/atc/man_transfer_output.html +"fix_modify AtC transfer atomic_output"_USER/atc/man_transfer_atomic_output.html +"fix_modify AtC mesh output"_USER/atc/man_mesh_output.html +"fix_modify AtC transfer write_restart"_USER/atc/man_write_restart.html +"fix_modify AtC transfer read_restart"_USER/atc/man_read_restart.html :ul + +fix_modify commands for post-processing: + +"fix_modify AtC transfer fields"_USER/atc/man_hardy_fields.html +"fix_modify AtC transfer gradients"_USER/atc/man_hardy_gradients.html +"fix_modify AtC transfer rates"_USER/atc/man_hardy_rates.htm +"fix_modify AtC transfer computes"_USER/atc/man_hardy_computes.html +"fix_modify AtC set"_USER/atc/man_hardy_set.html +"fix_modify AtC transfer on_the_fly"_USER/atc/man_hardy_on_the_fly.html +"fix_modify AtC boundary_integral"_USER/atc/man_boundary_integral.html +"fix_modify AtC contour_integral"_USER/atc/man_contour_integral.html :ul + +miscellaneous fix_modify commands: + +"fix_modify AtC transfer atom_element_map"_USER/atc/man_atom_element_map.htm +"fix_modify AtC transfer neighbor_reset_frequency"_USER/atc/man_neighbor_reset_frequency.html :ul + +[Default:] none + +:line + +:link(Wagner) +[(Wagner)] Wagner, Jones, Templeton, Parks, Special Issue of +Computer Methods and Applied Mechanics, 197, 3351-3365 (2008). + +:link(Zimmerman) +[(Zimmerman)] Zimmerman, Webb, Hoyt, Jones, Klein, Bammann, Special +Issue of Modelling and Simulation in Materials Science and +Engineering, 12, S319 (2004). + +:link(Hughes) +[(Hughes)] T.J.R Hughes, "The Finite Element Method," Dover (2003). diff -Naur lammps-22Sep09/examples/USER/atc/README lammps-24Sep09/examples/USER/atc/README --- lammps-22Sep09/examples/USER/atc/README 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/README 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,110 @@ +ATC (Atom To Continuum methods) + +Reese Jones, Jeremy Templeton, Jonathan Zimmerman +rjones@sandia.gov +September 2009 + +-------------- + +This directory contains examples run using the AtC library in LAMMPS +in its various coupling and post-processing modes. Descriptions of +the files in each are provided below. In addition to the included +output these examples will "dump" mesh-based data either in binary +(Ensight) format or simple column-based text format (for gnuplot, for +example). + +bar1d_thermal: + input files: + in.bar1d - Atoms comprise a subset of a 1D finite element bar, + heated at the left end and cooled at the right end. + A Gaussian isokinetic thermostat is used to keep the atomic + kinetic temperature equal to the finite element temperature + at the boundaries. + in.bar1d_flux - Same setup and geometry as in.bar1d. + A Gaussian isokinetic thermostat is used to transfer + the FE heat flux to the atoms at the boundaries. + Ar_thermal.mat - Material parameter file specifying + the thermal properties of argon. + temp.init - Initial set of atomic positions and velocities. + + output files: + bar1d.log - LAMMPS log file generated by running in.bar1d. + bar1d_flux.log - LAMMPS log file generated by running in.bar1d_flux. + +bar1d_two_temperature: + input files: + in.bar1d_ttm - Atoms comprise a subset of a 1D finite element bar, + with a high fixed electron temperature on the left end + and low fixed phonon and electron temperatures on the right end. + A Gaussian isokinetic thermostat is used to transfer energy + from the electron temperature field to the atoms. + in.gaussianIC_ttm - Atoms fully overlap an FE mesh with an initially + elevated electron temperature having a Gaussian distribution. + in.no_atoms - Heating followed by relaxation is simulated on a FE mesh. + in.uniform_exchange - Electron and kinetic temperatures are initially + spatially uniform but out of equilibrium, followed by relaxation. + in.uniform_heating - Initially equal electron and kinetic temperatures + are subjected to heating of the kinetic temperature only. The kinetic + temperature is fixed at both ends while the electrons are insulated. + Ar_ttm.mat - Material parameter file specifying + the kinetic and electric thermal properties of argon. + Cu_ttm.mat - Material parameter file specifying + the kinetic and electric thermal properties of copper. + temp.init - Initial set of atomic positions and velocities for most cases. + uniform_exchange_init.data - Initial set of atomic positions and velocities + for in.uniform_exchange + uniform_heating_init.data - Initial set of atomic positions and velocities + for in.uniform_heating + + output files: + bar1d_ttm.log - LAMMPS log file generated by running in.bar1d_ttm. + gaussianIC_ttm.log - log file generated by running in.gaussianIC_ttm. + no_atoms.log - LAMMPS log file generated by running in.no_atoms. + uniform_exchange.log - log file generated by running in.uniform_exchange. + uniform_heating.log - LAMMPS log file generated by running in.uniform_heating. + +hardy: + input files: + in.consistency - Small block of EAM Copper is used to confirm the + consistency between the atc calculations of 1st Piola-Kirchhoff (P-K) + stress, displacment gradient, and strain energy density for various + amounts of uniaxial strain. + in.eam_kernel_convergence - Block of EAM Gold is used to examine the + variation of the atc estimate of 1st P-K stress with size of localization + (averaging) volume. Volume is spherical, and kernel function + is quartic depending on radial distance from sphere center. + in.eam_unistrain_xxxx - Long block of EAM Copper is subjected to uniaxial + stretching and estimates of 1st P-K stress, energy density, displacement + and displacement gradient are calculated. The end-suffix denotes the + localization volume shape and kernel function type: + cell - 3D rectangular elements with step-functions at cell boundary + mesh - 3D rectangular elements with linear "tent" functions + qcylinder - cylindrical volume with quartic function dependent on + distance from cylinder axis + qsphere - spherical volume with quartic function dependent on + distance from sphere center + step - spherical volume with step-function at sphere boundary + in.eam_volume_stretch - Small block of EAM Copper is equitriaxially + stretched and estimates of 1st P-K stress, energy density, and mass + density are calculated. + in.nvt - Block of Lennard-Jones Argon is simulated at 30K for 1000 timesteps. + + output files: + consistency.log - LAMMPS log file generated by running in.consistency + consistency.screen - Screen/console output generated by running + in.consistency + eam_kernel_convergence.log - LAMMPS log file generated by running + in.eam_kernel_convergence + eam_kernel_convergence.screen - Screen/console output generated by running + in.eam_kernel_convergence + eam_unistrain_xxxx.log - LAMMPS log file generated by running + in.eam_unistrain_xxxx + eam_unistrain_xxxx.screen - Screen/console output generated by running + in.eam_unistrain_xxxx ( xxxx = cell, mesh, qcylinder, qsphere, step ) + eam_volume_stretch.log - LAMMPS log file generated by running + in.eam_volume_stretch + eam_volume_stretchscreen - Screen/console output generated by running + in.eam_volume_stretch + nvt.log - LAMMPS log file generated by running in.nvt + nvt.screen - Screen/console output generated by running in.nvt + diff -Naur lammps-22Sep09/examples/USER/atc/bar1d_thermal/Ar_thermal.mat lammps-24Sep09/examples/USER/atc/bar1d_thermal/Ar_thermal.mat --- lammps-22Sep09/examples/USER/atc/bar1d_thermal/Ar_thermal.mat 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_thermal/Ar_thermal.mat 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,11 @@ +material Ar + heat_flux linear + conductivity .00000000168 + end +end + +material Ar2 + heat_flux linear + conductivity .00000000316 + end +end diff -Naur lammps-22Sep09/examples/USER/atc/bar1d_thermal/bar1d.log lammps-24Sep09/examples/USER/atc/bar1d_thermal/bar1d.log --- lammps-22Sep09/examples/USER/atc/bar1d_thermal/bar1d.log 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_thermal/bar1d.log 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,286 @@ +LAMMPS (7 Jul 2009) +#AtC Thermal Coupling +# This benchmark tests heat conducting into and out of the MD region. The +# temperature is intially 20 everywhere and the left boundary BC is fixed at 40. +# The result should show heat diffusing through the FEM to the MD and back out +# to the FEM on the right. Insufficient time is captured to reach the linear +# steady state, but heat crossing both boundaries should be observed. + + +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init + orthogonal box = (-27.025 -16.215 -16.215) to (27.025 16.215 16.215) + 1 by 1 by 1 processor grid + 1440 atoms + 1440 velocities +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region simRegion block -12 12 -3 3 -3 3 + +# create atoms, NOTE commented out for restart +#region mdRegion block -5 5 -3 3 -3 3 +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 + +# specify interal/ghost atoms +region mdInternal block -4 4 -3 3 -3 3 +group internal region mdInternal +1152 atoms in group internal +group ghost subtract all internal +288 atoms in group ghost + +# velocities have Vcm = 0, NOTE next four lines commented out for restart +#velocity internal create 40. 87287 mom yes loop geom + +#pair_style lj/cut 13.5 +##pair_coeff 1 1 0.010323166 3.405 13.5 +#pair_coeff 1 1 .238 3.405 13.5 + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc thermal Ar_thermal.mat + +# ID part keywords nx ny nz region +#fix_modify AtC fem create mesh 12 2 2 simRegion f p p +fix_modify AtC fem create mesh 12 1 1 simRegion f p p + +# specify atom types +#fix_modify AtC transfer internal type internal +fix_modify AtC transfer boundary type ghost + +# fix a temperature +fix_modify AtC transfer fix temperature all 20. + +# turn on thermostat +fix_modify AtC transfer thermal control rescale 10 + +# equilibrate MD field +#dump D1 all atom 100 dump.bar1d +#fix_modify AtC transfer output bar1dfe 100 +timestep 5 +variable xdof equal 3*count(ghost) +compute_modify thermo_temp extra ${xdof} +compute_modify thermo_temp extra 864 +thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] +thermo_modify format 1 %6i format 2 %7.2g +thermo 100 +run 400 +Memory usage per processor = 8.7506 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -2573.6428 -2710.8793 412.06718 39.965279 20 + 100 2.7 -2537.6764 -2606.3542 412.06718 20 20 + 200 5.5 -2584.8754 -2653.5532 412.06718 20 20 + 300 8.2 -2575.3126 -2643.9904 412.06718 20 20 + 400 11 -2573.4199 -2642.0977 412.06718 20 20 +Loop time of 10.9925 on 1 procs for 400 steps with 1440 atoms + +Pair time (%) = 4.30201 (39.1358) +Neigh time (%) = 1.867 (16.9842) +Comm time (%) = 0.0373757 (0.34001) +Outpt time (%) = 0.00606346 (0.0551598) +Other time (%) = 4.78008 (43.4848) + +Nlocal: 1440 ave 1440 max 1440 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5320 ave 5320 max 5320 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 419459 ave 419459 max 419459 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 838918 ave 838918 max 838918 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 838918 +Ave neighs/atom = 582.582 +Neighbor list builds = 40 +Dangerous builds = 0 + +# change thermostat to hoover +fix_modify AtC transfer unfix temperature all +fix_modify AtC transfer thermal control hoover +fix_modify AtC transfer filter type exponential +fix_modify AtC transfer filter scale 10000.0 +fix_modify AtC transfer filter on +fix_modify AtC transfer internal_quadrature off + +# add nodesets +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12 +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -12 12 -12 12 +fix_modify AtC transfer fix temperature lbc 40. +fix_modify AtC transfer fix temperature rbc 20. + +# initialize filter +#thermo 1 +run 100 +Memory usage per processor = 8.97948 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 400 0 -2573.4199 -2642.0977 274.71145 20 20 + 500 2.7 -2573.7738 -2643.7447 295.61002 20.376549 21.713472 +Loop time of 2.67287 on 1 procs for 100 steps with 1440 atoms + +Pair time (%) = 1.07427 (40.1917) +Neigh time (%) = 0.466434 (17.4507) +Comm time (%) = 0.00930166 (0.348003) +Outpt time (%) = 0.00103688 (0.0387928) +Other time (%) = 1.12183 (41.9709) + +Nlocal: 1440 ave 1440 max 1440 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5320 ave 5320 max 5320 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 419059 ave 419059 max 419059 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 838118 ave 838118 max 838118 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 838118 +Ave neighs/atom = 582.026 +Neighbor list builds = 10 +Dangerous builds = 0 + +# set up output, should be before a "run" +fix_modify AtC transfer output bar1dFE 100 text + +# ouput command +#dump D1 all atom 1000 dump.bar1d +fix_modify AtC transfer atomic_output bar1dMD 100 + +# run with FE +reset_timestep 0 +thermo 100 +run 10000 +Memory usage per processor = 8.97948 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -2573.7738 -2643.7447 295.61002 20.376549 21.713472 + 100 2.7 -2573.654 -2645.0562 298.997 20.793359 21.86901 + 200 5.4 -2574.0035 -2642.057 302.05784 19.818184 22.007349 + 300 8 -2573.5186 -2646.5507 304.88852 21.268004 22.143129 + 400 11 -2573.2662 -2641.032 307.48549 19.734394 22.262531 + 500 13 -2573.5673 -2644.7553 309.92162 20.730998 22.376015 + 600 16 -2572.9368 -2641.5818 312.18796 19.990452 22.483808 + 700 19 -2573.2457 -2642.9406 314.3431 20.296183 22.586025 + 800 21 -2573.215 -2642.7311 316.37915 20.244129 22.681635 + 900 24 -2572.7227 -2643.5215 318.29866 20.617655 22.772405 + 1000 27 -2572.411 -2644.5969 320.08215 21.021606 22.85772 + 1100 29 -2571.4099 -2642.08 321.74721 20.580181 22.940424 + 1200 32 -2570.5495 -2641.7296 323.29152 20.728698 23.01806 + 1300 35 -2570.2491 -2640.8115 324.79381 20.548784 23.09183 + 1400 37 -2570.159 -2641.2853 326.14846 20.713008 23.158731 + 1500 40 -2569.5061 -2642.2055 327.46482 21.171117 23.230527 + 1600 43 -2568.7522 -2639.5246 328.68994 20.609988 23.295442 + 1700 45 -2569.1809 -2642.0975 329.85636 21.234392 23.355365 + 1800 48 -2568.7484 -2643.2103 330.95066 21.684387 23.414458 + 1900 51 -2568.258 -2641.5017 332.02069 21.329638 23.476702 + 2000 54 -2568.192 -2641.4646 333.04827 21.338079 23.534077 + 2100 56 -2568.0746 -2639.9335 334.04476 20.926349 23.588633 + 2200 59 -2567.2717 -2642.2868 334.99014 21.84549 23.639739 + 2300 62 -2566.7209 -2639.9022 335.89195 21.311463 23.692327 + 2400 64 -2566.6054 -2638.8118 336.73569 21.02756 23.743177 + 2500 67 -2565.7629 -2639.6423 337.51835 21.514764 23.792702 + 2600 70 -2565.9251 -2642.5797 338.26277 22.322947 23.837067 + 2700 72 -2564.9995 -2640.0503 339.00006 21.855897 23.885327 + 2800 75 -2565.2468 -2638.033 339.72187 21.196396 23.929976 + 2900 78 -2565.0496 -2639.4905 340.4486 21.678289 23.975728 + 3000 80 -2565.1382 -2637.5132 341.15766 21.076651 24.018275 + 3100 83 -2564.4793 -2636.786 341.85076 21.056788 24.060818 + 3200 86 -2564.1799 -2637.5024 342.51347 21.352563 24.105465 + 3300 88 -2564.4531 -2641.3463 343.13584 22.392438 24.145599 + 3400 91 -2564.2323 -2641.0072 343.75483 22.357976 24.184764 + 3500 94 -2563.378 -2635.3819 344.36945 20.968577 24.22365 + 3600 96 -2563.5014 -2637.8324 345.00242 21.646292 24.265399 + 3700 99 -2563.4092 -2638.0479 345.63031 21.73589 24.302306 + 3800 1e+02 -2563.0307 -2637.5397 346.23705 21.698125 24.340069 + 3900 1e+02 -2562.1415 -2637.2704 346.79157 21.878655 24.379583 + 4000 1.1e+02 -2561.9968 -2637.3928 347.2934 21.956417 24.413166 + 4100 1.1e+02 -2560.7688 -2636.0902 347.76126 21.934696 24.449405 + 4200 1.1e+02 -2561.3033 -2638.2325 348.21187 22.402893 24.48165 + 4300 1.2e+02 -2560.9897 -2637.0909 348.67188 22.161792 24.517482 + 4400 1.2e+02 -2561.1676 -2638.5003 349.1221 22.52042 24.551399 + 4500 1.2e+02 -2560.4797 -2637.3716 349.57016 22.392068 24.58389 + 4600 1.2e+02 -2560.5787 -2637.0577 350.03085 22.2718 24.616821 + 4700 1.3e+02 -2560.9645 -2639.5114 350.46283 22.874034 24.648359 + 4800 1.3e+02 -2560.445 -2637.6681 350.93668 22.488484 24.682119 + 4900 1.3e+02 -2559.5243 -2635.9383 351.38797 22.252882 24.713605 + 5000 1.3e+02 -2559.4948 -2637.7238 351.82736 22.781448 24.746433 + 5100 1.4e+02 -2559.6822 -2636.169 352.25581 22.274077 24.77752 + 5200 1.4e+02 -2559.6398 -2637.3169 352.67163 22.620718 24.810244 + 5300 1.4e+02 -2558.6285 -2634.5293 353.06226 22.103426 24.836256 + 5400 1.4e+02 -2558.6394 -2637.9486 353.46662 23.096021 24.869663 + 5500 1.5e+02 -2558.1403 -2636.176 353.85792 22.725147 24.897758 + 5600 1.5e+02 -2558.0703 -2635.1367 354.27521 22.442874 24.929906 + 5700 1.5e+02 -2558.0656 -2636.7197 354.66462 22.905238 24.956168 + 5800 1.6e+02 -2557.3776 -2634.8266 355.06619 22.554271 24.987034 + 5900 1.6e+02 -2557.2526 -2635.9743 355.44501 22.924934 25.016353 + 6000 1.6e+02 -2557.3833 -2637.2292 355.80121 23.252296 25.043949 + 6100 1.6e+02 -2556.0263 -2633.5408 356.13412 22.573353 25.072447 + 6200 1.7e+02 -2555.7442 -2634.4378 356.46167 22.916748 25.100704 + 6300 1.7e+02 -2555.855 -2635.6231 356.75569 23.22965 25.127725 + 6400 1.7e+02 -2555.933 -2634.2031 357.04516 22.793407 25.152406 + 6500 1.7e+02 -2555.6529 -2635.6086 357.33016 23.28426 25.178081 + 6600 1.8e+02 -2554.8702 -2633.8043 357.60713 22.986754 25.203066 + 6700 1.8e+02 -2555.4594 -2637.4198 357.91044 23.868096 25.228913 + 6800 1.8e+02 -2555.1344 -2633.0306 358.23055 22.684511 25.254519 + 6900 1.8e+02 -2555.203 -2635.8935 358.56704 23.498239 25.281995 + 7000 1.9e+02 -2554.4151 -2634.9963 358.89735 23.466408 25.305952 + 7100 1.9e+02 -2555.5652 -2636.9959 359.27174 23.713819 25.334106 + 7200 1.9e+02 -2554.6218 -2632.7376 359.62885 22.748439 25.361455 + 7300 2e+02 -2553.7347 -2633.5173 359.96531 23.233845 25.386903 + 7400 2e+02 -2553.6833 -2632.7482 360.28731 23.024868 25.412373 + 7500 2e+02 -2554.1584 -2634.2224 360.62311 23.31579 25.437173 + 7600 2e+02 -2553.7146 -2636.4165 360.95078 24.084027 25.461273 + 7700 2.1e+02 -2553.0976 -2633.1652 361.2731 23.316874 25.488376 + 7800 2.1e+02 -2553.7234 -2633.641 361.58496 23.273177 25.51462 + 7900 2.1e+02 -2553.1572 -2635.2359 361.88331 23.902505 25.537243 + 8000 2.1e+02 -2553.0069 -2632.9284 362.20064 23.274304 25.562883 + 8100 2.2e+02 -2552.2172 -2632.9342 362.5047 23.505977 25.58597 + 8200 2.2e+02 -2552.6328 -2633.7047 362.84446 23.609337 25.610996 + 8300 2.2e+02 -2553.0514 -2636.536 363.15344 24.311943 25.634632 + 8400 2.3e+02 -2551.9163 -2634.5593 363.4457 24.066867 25.656569 + 8500 2.3e+02 -2551.1621 -2632.5819 363.73408 23.710645 25.680723 + 8600 2.3e+02 -2551.3228 -2631.8791 364.03489 23.459181 25.706041 + 8700 2.3e+02 -2551.3997 -2634.1928 364.32604 24.110586 25.728322 + 8800 2.4e+02 -2551.5524 -2635.9592 364.60259 24.58049 25.751881 + 8900 2.4e+02 -2550.9861 -2634.5125 364.87711 24.324098 25.772874 + 9000 2.4e+02 -2550.3983 -2630.9444 365.15409 23.456228 25.797098 + 9100 2.4e+02 -2550.2259 -2632.4851 365.42126 23.955067 25.819654 + 9200 2.5e+02 -2549.7275 -2633.251 365.67315 24.323271 25.84363 + 9300 2.5e+02 -2549.2312 -2632.0116 365.91463 24.106861 25.865763 + 9400 2.5e+02 -2549.1796 -2631.7916 366.12014 24.057833 25.884164 + 9500 2.5e+02 -2549.3237 -2632.8582 366.34704 24.326456 25.907195 + 9600 2.6e+02 -2548.7761 -2630.2005 366.56572 23.711991 25.926896 + 9700 2.6e+02 -2548.5538 -2631.9243 366.75569 24.278711 25.946464 + 9800 2.6e+02 -2548.3631 -2632.4881 366.94867 24.498431 25.965165 + 9900 2.7e+02 -2548.2213 -2631.2185 367.15325 24.169994 25.986899 + 10000 2.7e+02 -2547.7789 -2631.2241 367.37155 24.30047 26.007162 +Loop time of 267.8 on 1 procs for 10000 steps with 1440 atoms + +Pair time (%) = 107.528 (40.1525) +Neigh time (%) = 46.6868 (17.4335) +Comm time (%) = 0.952441 (0.355655) +Outpt time (%) = 0.106937 (0.0399319) +Other time (%) = 112.525 (42.0184) + +Nlocal: 1440 ave 1440 max 1440 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5320 ave 5320 max 5320 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 419294 ave 419294 max 419294 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 838588 ave 838588 max 838588 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 838588 +Ave neighs/atom = 582.353 +Neighbor list builds = 1000 +Dangerous builds = 0 diff -Naur lammps-22Sep09/examples/USER/atc/bar1d_thermal/bar1d_flux.log lammps-24Sep09/examples/USER/atc/bar1d_thermal/bar1d_flux.log --- lammps-22Sep09/examples/USER/atc/bar1d_thermal/bar1d_flux.log 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_thermal/bar1d_flux.log 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,334 @@ +LAMMPS (7 Jul 2009) +#AtC Thermal Coupling +# This benchmark tests heat conducting into and out of the MD region. The +# temperature is intially 20 everywhere and the left boundary BC is fixed at +# 40.# The result should show heat diffusing through the FEM to the MD and back +# out # to the FEM on the right. Insufficient time is captured to reach the +# linear # steady state, but heat crossing both boundaries should be observed. +#echo both +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init + orthogonal box = (-27.025 -16.215 -16.215) to (27.025 16.215 16.215) + 1 by 1 by 1 processor grid + 1440 atoms + 1440 velocities +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region simRegion block -12 12 -3 3 -3 3 + +# create atoms, NOTE commented out for restart +#region mdRegion block -5 5 -3 3 -3 3 +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 + +# specify interal/ghost atoms +region mdInternal block -4 4 -3 3 -3 3 +group internal region mdInternal +1152 atoms in group internal +group ghost subtract all internal +288 atoms in group ghost + +# velocities have Vcm = 0, NOTE next four lines commented out for restart +#velocity internal create 40. 87287 mom yes loop geom + +#pair_style lj/cut 13.5 +##pair_coeff 1 1 0.010323166 3.405 13.5 +#pair_coeff 1 1 .238 3.405 13.5 + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +#write_restart tinit.dat + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc thermal Ar_thermal.mat + +# ID part keywords nx ny nz region +#fix_modify AtC fem create mesh 12 2 2 simRegion f p p +fix_modify AtC fem create mesh 12 1 1 simRegion f p p +fix_modify AtC mesh create_faceset ibndy box -4.0 4.0 -12 12 -12 12 in +fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 outward + +# specify atom types +#fix_modify AtC transfer internal type internal +fix_modify AtC transfer boundary type ghost + +# fix a temperature +fix_modify AtC transfer fix temperature all 20. +#fix_modify AtC transfer fix temperature all linear 0 0 0 -0.154 0 0 30. + +# turn on thermostat +fix_modify AtC transfer thermal control rescale 10 + +variable xdof equal 3*count(ghost) +compute_modify thermo_temp extra ${xdof} +compute_modify thermo_temp extra 864 +thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] +thermo_modify format 1 %6i format 2 %7.2g + +# equilibrate MD field +#fix_modify AtC transfer output bar1dfe_flux_init 100 +timestep 5 +thermo 10 +run 400 +Memory usage per processor = 8.7506 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -2573.6428 -2710.8793 412.06718 39.965279 20 + 10 0.28 -2626.7498 -2695.4276 412.06718 20 20 + 20 0.56 -2600.7022 -2669.38 412.06718 20 20 + 30 0.84 -2570.0142 -2638.6921 412.06718 20 20 + 40 1.1 -2548.1494 -2616.8273 412.06718 20 20 + 50 1.4 -2541.6409 -2610.3188 412.06718 20 20 + 60 1.7 -2539.3355 -2608.0134 412.06718 20 20 + 70 2 -2534.3684 -2603.0463 412.06718 20 20 + 80 2.2 -2530.2415 -2598.9194 412.06718 20 20 + 90 2.5 -2531.3411 -2600.019 412.06718 20 20 + 100 2.8 -2537.6764 -2606.3542 412.06718 20 20 + 110 3.1 -2546.506 -2615.1838 412.06718 20 20 + 120 3.4 -2555.0937 -2623.7716 412.06718 20 20 + 130 3.6 -2562.4178 -2631.0957 412.06718 20 20 + 140 3.9 -2568.7827 -2637.4606 412.06718 20 20 + 150 4.2 -2574.6292 -2643.307 412.06718 20 20 + 160 4.5 -2579.7542 -2648.432 412.06718 20 20 + 170 4.8 -2583.6629 -2652.3408 412.06718 20 20 + 180 5 -2585.9113 -2654.5892 412.06718 20 20 + 190 5.3 -2586.1786 -2654.8565 412.06718 20 20 + 200 5.6 -2584.8754 -2653.5532 412.06718 20 20 + 210 5.9 -2582.8956 -2651.5734 412.06718 20 20 + 220 6.2 -2580.6882 -2649.366 412.06718 20 20 + 230 6.5 -2578.24 -2646.9179 412.06718 20 20 + 240 6.7 -2575.9058 -2644.5836 412.06718 20 20 + 250 7 -2574.2875 -2642.9654 412.06718 20 20 + 260 7.3 -2573.8273 -2642.5052 412.06718 20 20 + 270 7.6 -2574.3017 -2642.9796 412.06718 20 20 + 280 7.8 -2574.7059 -2643.3838 412.06718 20 20 + 290 8.1 -2574.7745 -2643.4524 412.06718 20 20 + 300 8.4 -2575.3126 -2643.9904 412.06718 20 20 + 310 8.7 -2576.5002 -2645.178 412.06718 20 20 + 320 9 -2577.7411 -2646.419 412.06718 20 20 + 330 9.3 -2578.2283 -2646.9061 412.06718 20 20 + 340 9.5 -2577.7485 -2646.4263 412.06718 20 20 + 350 9.8 -2576.9631 -2645.6409 412.06718 20 20 + 360 10 -2576.0309 -2644.7088 412.06718 20 20 + 370 10 -2574.9309 -2643.6088 412.06718 20 20 + 380 11 -2573.7943 -2642.4721 412.06718 20 20 + 390 11 -2573.0353 -2641.7132 412.06718 20 20 + 400 11 -2573.4199 -2642.0977 412.06718 20 20 +Loop time of 11.2102 on 1 procs for 400 steps with 1440 atoms + +Pair time (%) = 4.45575 (39.7474) +Neigh time (%) = 1.86555 (16.6416) +Comm time (%) = 0.0379353 (0.338401) +Outpt time (%) = 0.0610819 (0.54488) +Other time (%) = 4.78984 (42.7277) + +Nlocal: 1440 ave 1440 max 1440 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5320 ave 5320 max 5320 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 419459 ave 419459 max 419459 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 838918 ave 838918 max 838918 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 838918 +Ave neighs/atom = 582.582 +Neighbor list builds = 40 +Dangerous builds = 0 + + +# change thermostat to hoover +fix_modify AtC transfer unfix temperature all +fix_modify AtC transfer thermal control flux faceset obndy +fix_modify AtC transfer filter type exponential +fix_modify AtC transfer filter scale 10000.0 +fix_modify AtC transfer filter on + +# add nodesets +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12 +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -12 12 -12 12 +fix_modify AtC transfer fix temperature lbc 40. +fix_modify AtC transfer fix temperature rbc 20. + +# initialize filter +run 100 +Memory usage per processor = 8.97948 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 400 0 -2573.4199 -2642.0977 412.06718 20 20 + 410 0.3 -2573.399 -2643.8456 429.61396 20.515068 21.555366 + 420 0.6 -2573.4225 -2646.1086 430.028 21.16726 21.573916 + 430 0.91 -2573.4498 -2647.2056 430.455 21.478791 21.593046 + 440 1.2 -2573.4565 -2646.2695 430.87731 21.204227 21.611967 + 450 1.5 -2573.4725 -2644.3172 431.27891 20.631017 21.62996 + 460 1.8 -2573.4862 -2643.0051 431.65927 20.244924 21.647001 + 470 2.1 -2573.4906 -2642.6175 432.02801 20.130768 21.663521 + 480 2.4 -2573.5014 -2642.5644 432.3911 20.112138 21.679788 + 490 2.7 -2573.5132 -2642.9216 432.75177 20.212768 21.695947 + 500 3 -2573.5326 -2643.6695 433.11495 20.424906 21.712218 +Loop time of 3.0217 on 1 procs for 100 steps with 1440 atoms + +Pair time (%) = 1.11102 (36.7679) +Neigh time (%) = 0.465189 (15.3949) +Comm time (%) = 0.0091815 (0.303852) +Outpt time (%) = 0.0152943 (0.506148) +Other time (%) = 1.42102 (47.0272) + +Nlocal: 1440 ave 1440 max 1440 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5320 ave 5320 max 5320 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 419046 ave 419046 max 419046 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 838092 ave 838092 max 838092 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 838092 +Ave neighs/atom = 582.008 +Neighbor list builds = 10 +Dangerous builds = 0 + +# set up output, should be before a "run" +fix_modify AtC transfer output bar1d_fluxFE 100 text + +# ouput command +#dump D1 all atom 1000 dump.bar1d +fix_modify AtC transfer atomic_output bar1d_fluxMD 100 + +# run with FE +reset_timestep 0 +thermo 100 +run 10000 +Memory usage per processor = 8.97948 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -2573.5326 -2643.6695 433.11495 20.424906 21.712218 + 100 3 -2573.4996 -2644.68 436.56595 20.728783 21.866831 + 200 6 -2573.6452 -2641.8181 439.65242 19.852963 22.005112 + 300 8.9 -2573.7003 -2646.4622 442.67272 21.189339 22.140428 + 400 12 -2573.8123 -2641.5274 445.34109 19.719609 22.259977 + 500 15 -2573.523 -2644.2791 447.87899 20.605203 22.373681 + 600 18 -2573.5066 -2641.7526 450.30082 19.874234 22.482184 + 700 21 -2573.1755 -2642.9899 452.59197 20.330998 22.584833 + 800 24 -2572.7532 -2642.4538 454.74808 20.297842 22.681431 + 900 27 -2572.4242 -2643.2186 456.80456 20.616377 22.773566 + 1000 30 -2572.1111 -2644.2513 458.77119 21.008267 22.861675 + 1100 33 -2571.8664 -2642.2676 460.69037 20.501859 22.947659 + 1200 36 -2571.6698 -2642.4072 462.52036 20.599778 23.029647 + 1300 39 -2571.1188 -2640.8357 464.26327 20.302568 23.107733 + 1400 42 -2570.6841 -2642.0319 465.90618 20.777507 23.181339 + 1500 45 -2570.3755 -2642.5393 467.64779 21.015167 23.259367 + 1600 48 -2570.1086 -2640.3963 469.24937 20.468802 23.331122 + 1700 51 -2569.7084 -2642.3964 470.76324 21.167807 23.398946 + 1800 53 -2569.2903 -2643.213 472.26485 21.527379 23.466222 + 1900 56 -2568.8699 -2641.4957 473.83022 21.149691 23.536354 + 2000 59 -2568.3377 -2641.3608 475.30209 21.265411 23.602297 + 2100 62 -2567.6236 -2639.3792 476.69625 20.896274 23.664759 + 2200 65 -2566.8936 -2642.0946 478.02908 21.899656 23.724472 + 2300 68 -2566.4627 -2640.2742 479.41262 21.494985 23.786458 + 2400 71 -2566.0253 -2638.6268 480.76007 21.142611 23.846827 + 2500 74 -2565.8021 -2639.6421 482.09822 21.503291 23.906779 + 2600 77 -2565.2093 -2642.2012 483.3378 22.421166 23.962315 + 2700 80 -2564.6901 -2639.8567 484.63598 21.889625 24.020477 + 2800 83 -2564.0658 -2636.9481 485.8689 21.22441 24.075714 + 2900 86 -2563.3168 -2639.3155 487.10404 22.131928 24.131051 + 3000 89 -2562.6825 -2635.5318 488.27527 21.214781 24.183525 + 3100 92 -2562.1212 -2635.4426 489.43761 21.352279 24.2356 + 3200 95 -2561.6126 -2636.3019 490.64892 21.750607 24.28987 + 3300 98 -2561.1335 -2639.0741 491.78462 22.697438 24.340752 + 3400 1e+02 -2560.4828 -2638.3251 492.87662 22.66881 24.389676 + 3500 1e+02 -2559.8843 -2635.4238 493.96107 21.998211 24.438262 + 3600 1.1e+02 -2559.2443 -2634.7161 495.09564 21.97848 24.489093 + 3700 1.1e+02 -2558.5654 -2636.1565 496.14063 22.595663 24.535911 + 3800 1.1e+02 -2558.0214 -2636.7671 497.17918 22.931888 24.58244 + 3900 1.2e+02 -2557.9398 -2634.982 498.30063 22.435836 24.632684 + 4000 1.2e+02 -2557.8749 -2635.5655 499.26966 22.624655 24.676098 + 4100 1.2e+02 -2557.8331 -2635.3677 500.27412 22.579214 24.721101 + 4200 1.2e+02 -2557.6329 -2635.9432 501.25564 22.805115 24.765075 + 4300 1.3e+02 -2557.4707 -2636.512 502.24607 23.017987 24.809448 + 4400 1.3e+02 -2557.3019 -2632.8823 503.29942 22.010137 24.856641 + 4500 1.3e+02 -2556.8882 -2633.5726 504.19269 22.331634 24.896661 + 4600 1.4e+02 -2556.5255 -2637.0121 505.14884 23.438878 24.939499 + 4700 1.4e+02 -2556.1965 -2636.3657 506.12562 23.346446 24.983261 + 4800 1.4e+02 -2555.728 -2636.154 507.0392 23.421248 25.024191 + 4900 1.5e+02 -2555.3573 -2634.8572 507.93584 23.151538 25.064363 + 5000 1.5e+02 -2554.8839 -2635.3615 508.86307 23.436248 25.105905 + 5100 1.5e+02 -2554.5001 -2632.2863 509.79029 22.652461 25.147447 + 5200 1.5e+02 -2554.2786 -2635.3015 510.67821 23.595069 25.187227 + 5300 1.6e+02 -2554.1208 -2633.4672 511.56223 23.106822 25.226833 + 5400 1.6e+02 -2553.8571 -2632.9509 512.411 23.033282 25.26486 + 5500 1.6e+02 -2553.4771 -2633.4831 513.27749 23.29891 25.303681 + 5600 1.7e+02 -2552.995 -2634.0399 514.08357 23.601475 25.339795 + 5700 1.7e+02 -2552.6786 -2632.23 514.99251 23.166531 25.380517 + 5800 1.7e+02 -2552.1989 -2634.2926 515.83523 23.906877 25.418273 + 5900 1.8e+02 -2551.9275 -2633.7331 516.69181 23.822967 25.45665 + 6000 1.8e+02 -2551.5879 -2633.4709 517.50304 23.845533 25.492995 + 6100 1.8e+02 -2551.1096 -2633.3576 518.27013 23.951824 25.527362 + 6200 1.8e+02 -2550.6066 -2634.4431 519.07898 24.414427 25.5636 + 6300 1.9e+02 -2550.1427 -2633.9705 519.85788 24.411888 25.598497 + 6400 1.9e+02 -2549.6148 -2630.7643 520.70201 23.631931 25.636316 + 6500 1.9e+02 -2549.2143 -2629.4555 521.48165 23.3674 25.671246 + 6600 2e+02 -2548.823 -2629.4952 522.21153 23.492935 25.703946 + 6700 2e+02 -2548.6124 -2631.6154 523.03499 24.171693 25.740839 + 6800 2e+02 -2548.314 -2627.4378 523.72811 23.041997 25.771892 + 6900 2e+02 -2548.0996 -2632.112 524.53399 24.465645 25.807997 + 7000 2.1e+02 -2547.8468 -2630.457 525.24887 24.057291 25.840026 + 7100 2.1e+02 -2547.5093 -2630.8501 526.01815 24.27005 25.874491 + 7200 2.1e+02 -2547.1919 -2630.0362 526.75581 24.125462 25.90754 + 7300 2.2e+02 -2546.8056 -2631.0682 527.4846 24.538524 25.940191 + 7400 2.2e+02 -2546.541 -2632.4362 528.24198 25.01394 25.974124 + 7500 2.2e+02 -2546.1286 -2629.6863 528.94188 24.33324 26.005481 + 7600 2.3e+02 -2545.959 -2629.3922 529.57701 24.296979 26.033936 + 7700 2.3e+02 -2546.0743 -2629.693 530.30436 24.351001 26.066523 + 7800 2.3e+02 -2546.1431 -2631.6521 530.98889 24.901471 26.097191 + 7900 2.3e+02 -2546.1056 -2629.3749 531.66127 24.249239 26.127315 + 8000 2.4e+02 -2546.0454 -2630.0836 532.37925 24.473159 26.159482 + 8100 2.4e+02 -2545.9725 -2630.5976 533.05102 24.644071 26.18958 + 8200 2.4e+02 -2545.5772 -2629.4844 533.65121 24.435002 26.216469 + 8300 2.5e+02 -2545.5178 -2631.6842 534.43183 25.092927 26.251443 + 8400 2.5e+02 -2545.3432 -2629.5904 535.02156 24.534025 26.277864 + 8500 2.5e+02 -2545.2097 -2631.2853 535.66213 25.06648 26.306563 + 8600 2.6e+02 -2544.9173 -2629.2314 536.3311 24.553498 26.336535 + 8700 2.6e+02 -2544.5414 -2628.3855 536.99695 24.416625 26.366366 + 8800 2.6e+02 -2543.8563 -2629.5985 537.57029 24.969392 26.392053 + 8900 2.6e+02 -2543.2906 -2628.292 538.33031 24.753655 26.426103 + 9000 2.7e+02 -2542.5357 -2627.1708 538.87931 24.64698 26.4507 + 9100 2.7e+02 -2542.1926 -2627.894 539.53269 24.957511 26.479973 + 9200 2.7e+02 -2542.0567 -2627.6595 540.14474 24.928803 26.507394 + 9300 2.8e+02 -2542.1288 -2626.8786 540.80469 24.680402 26.536961 + 9400 2.8e+02 -2541.8301 -2627.2829 541.36001 24.885088 26.561841 + 9500 2.8e+02 -2541.6773 -2628.1451 541.99633 25.180691 26.590349 + 9600 2.9e+02 -2541.3762 -2629.589 542.51985 25.688852 26.613804 + 9700 2.9e+02 -2541.0314 -2625.3135 543.15786 24.544177 26.642389 + 9800 2.9e+02 -2540.6298 -2625.8733 543.76425 24.824163 26.669556 + 9900 2.9e+02 -2540.2376 -2628.1266 544.31076 25.594543 26.694041 + 10000 3e+02 -2540.0111 -2625.9159 544.89126 25.016719 26.720049 +Loop time of 297.023 on 1 procs for 10000 steps with 1440 atoms + +Pair time (%) = 107.376 (36.1506) +Neigh time (%) = 46.5622 (15.6763) +Comm time (%) = 0.924362 (0.311209) +Outpt time (%) = 0.154094 (0.0518793) +Other time (%) = 142.007 (47.81) + +Nlocal: 1440 ave 1440 max 1440 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5320 ave 5320 max 5320 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 419203 ave 419203 max 419203 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 838406 ave 838406 max 838406 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 838406 +Ave neighs/atom = 582.226 +Neighbor list builds = 1000 +Dangerous builds = 0 diff -Naur lammps-22Sep09/examples/USER/atc/bar1d_thermal/in.bar1d lammps-24Sep09/examples/USER/atc/bar1d_thermal/in.bar1d --- lammps-22Sep09/examples/USER/atc/bar1d_thermal/in.bar1d 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_thermal/in.bar1d 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,100 @@ +#AtC Thermal Coupling +# This benchmark tests heat conducting into and out of the MD region. The +# temperature is intially 20 everywhere and the left boundary BC is fixed at 40. +# The result should show heat diffusing through the FEM to the MD and back out +# to the FEM on the right. Insufficient time is captured to reach the linear +# steady state, but heat crossing both boundaries should be observed. + + +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init +lattice fcc 5.405 origin 0.25 0.25 0.25 +region simRegion block -12 12 -3 3 -3 3 + +# create atoms, NOTE commented out for restart +#region mdRegion block -5 5 -3 3 -3 3 +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 + +# specify interal/ghost atoms +region mdInternal block -4 4 -3 3 -3 3 +group internal region mdInternal +group ghost subtract all internal + +# velocities have Vcm = 0, NOTE next four lines commented out for restart +#velocity internal create 40. 87287 mom yes loop geom + +#pair_style lj/cut 13.5 +##pair_coeff 1 1 0.010323166 3.405 13.5 +#pair_coeff 1 1 .238 3.405 13.5 + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc thermal Ar_thermal.mat + +# ID part keywords nx ny nz region +#fix_modify AtC fem create mesh 12 2 2 simRegion f p p +fix_modify AtC fem create mesh 12 1 1 simRegion f p p + +# specify atom types +#fix_modify AtC transfer internal type internal +fix_modify AtC transfer boundary type ghost + +# fix a temperature +fix_modify AtC transfer fix temperature all 20. + +# turn on thermostat +fix_modify AtC transfer thermal control rescale 10 + +# equilibrate MD field +#dump D1 all atom 100 dump.bar1d +#fix_modify AtC transfer output bar1dfe 100 +timestep 5 +variable xdof equal 3*count(ghost) +compute_modify thermo_temp extra ${xdof} +thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] +thermo_modify format 1 %6i format 2 %7.2g +thermo 100 +run 400 + +# change thermostat to hoover +fix_modify AtC transfer unfix temperature all +fix_modify AtC transfer thermal control hoover +fix_modify AtC transfer filter type exponential +fix_modify AtC transfer filter scale 10000.0 +fix_modify AtC transfer filter on +fix_modify AtC transfer internal_quadrature off + +# add nodesets +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12 +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -12 12 -12 12 +fix_modify AtC transfer fix temperature lbc 40. +fix_modify AtC transfer fix temperature rbc 20. + +# initialize filter +#thermo 1 +run 100 + +# set up output, should be before a "run" +fix_modify AtC transfer output bar1dFE 100 text + +# ouput command +#dump D1 all atom 1000 dump.bar1d +fix_modify AtC transfer atomic_output bar1dMD 100 + +# run with FE +reset_timestep 0 +thermo 100 +run 10000 diff -Naur lammps-22Sep09/examples/USER/atc/bar1d_thermal/in.bar1d_flux lammps-24Sep09/examples/USER/atc/bar1d_thermal/in.bar1d_flux --- lammps-22Sep09/examples/USER/atc/bar1d_thermal/in.bar1d_flux 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_thermal/in.bar1d_flux 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,103 @@ +#AtC Thermal Coupling +# This benchmark tests heat conducting into and out of the MD region. The +# temperature is intially 20 everywhere and the left boundary BC is fixed at +# 40.# The result should show heat diffusing through the FEM to the MD and back +# out # to the FEM on the right. Insufficient time is captured to reach the +# linear # steady state, but heat crossing both boundaries should be observed. +#echo both +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init +lattice fcc 5.405 origin 0.25 0.25 0.25 +region simRegion block -12 12 -3 3 -3 3 + +# create atoms, NOTE commented out for restart +#region mdRegion block -5 5 -3 3 -3 3 +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 + +# specify interal/ghost atoms +region mdInternal block -4 4 -3 3 -3 3 +group internal region mdInternal +group ghost subtract all internal + +# velocities have Vcm = 0, NOTE next four lines commented out for restart +#velocity internal create 40. 87287 mom yes loop geom + +#pair_style lj/cut 13.5 +##pair_coeff 1 1 0.010323166 3.405 13.5 +#pair_coeff 1 1 .238 3.405 13.5 + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +#write_restart tinit.dat + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc thermal Ar_thermal.mat + +# ID part keywords nx ny nz region +#fix_modify AtC fem create mesh 12 2 2 simRegion f p p +fix_modify AtC fem create mesh 12 1 1 simRegion f p p +fix_modify AtC mesh create_faceset ibndy box -4.0 4.0 -12 12 -12 12 in +fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 outward + +# specify atom types +#fix_modify AtC transfer internal type internal +fix_modify AtC transfer boundary type ghost + +# fix a temperature +fix_modify AtC transfer fix temperature all 20. +#fix_modify AtC transfer fix temperature all linear 0 0 0 -0.154 0 0 30. + +# turn on thermostat +fix_modify AtC transfer thermal control rescale 10 + +variable xdof equal 3*count(ghost) +compute_modify thermo_temp extra ${xdof} +thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] +thermo_modify format 1 %6i format 2 %7.2g + +# equilibrate MD field +#fix_modify AtC transfer output bar1dfe_flux_init 100 +timestep 5 +thermo 10 +run 400 + + +# change thermostat to hoover +fix_modify AtC transfer unfix temperature all +fix_modify AtC transfer thermal control flux faceset obndy +fix_modify AtC transfer filter type exponential +fix_modify AtC transfer filter scale 10000.0 +fix_modify AtC transfer filter on + +# add nodesets +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12 +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -12 12 -12 12 +fix_modify AtC transfer fix temperature lbc 40. +fix_modify AtC transfer fix temperature rbc 20. + +# initialize filter +run 100 + +# set up output, should be before a "run" +fix_modify AtC transfer output bar1d_fluxFE 100 text + +# ouput command +#dump D1 all atom 1000 dump.bar1d +fix_modify AtC transfer atomic_output bar1d_fluxMD 100 + +# run with FE +reset_timestep 0 +thermo 100 +run 10000 diff -Naur lammps-22Sep09/examples/USER/atc/bar1d_thermal/in.bar1d_frac_step lammps-24Sep09/examples/USER/atc/bar1d_thermal/in.bar1d_frac_step --- lammps-22Sep09/examples/USER/atc/bar1d_thermal/in.bar1d_frac_step 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_thermal/in.bar1d_frac_step 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,112 @@ +#AtC Thermal Coupling +# This benchmark tests heat conducting into and out of the MD region. The +# temperature is intially 20 everywhere and the left boundary BC is fixed at +# 40.# The result should show heat diffusing through the FEM to the MD and back +# out # to the FEM on the right. Insufficient time is captured to reach the +# linear # steady state, but heat crossing both boundaries should be observed. + + +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init +lattice fcc 5.405 origin 0.25 0.25 0.25 +region simRegion block -12 12 -3 3 -3 3 + +# create atoms, NOTE commented out for restart +#region mdRegion block -5 5 -3 3 -3 3 +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 + +# specify interal/ghost atoms +region mdInternal block -4 4 -3 3 -3 3 +group internal region mdInternal +group ghost subtract all internal + +# velocities have Vcm = 0, NOTE next four lines commented out for restart +#velocity internal create 40. 87287 mom yes loop geom + +#pair_style lj/cut 13.5 +##pair_coeff 1 1 0.010323166 3.405 13.5 +#pair_coeff 1 1 .238 3.405 13.5 + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc thermal Ar_thermal.mat + +# ID part keywords nx ny nz region +#fix_modify AtC fem create mesh 12 2 2 simRegion f p p +fix_modify AtC fem create mesh 4 1 1 mdInternal f p p +#fix_modify AtC mesh create_faceset ibndy box -4.0 4.0 -12 12 -12 12 in +#fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 outward + +# specify atom types +#fix_modify AtC transfer internal type internal +#fix_modify AtC transfer boundary type ghost + +# fix a temperature +fix_modify AtC transfer fix temperature all 20. + +# turn on thermostat +fix_modify AtC transfer thermal control rescale 10 + +# equilibrate MD field +#dump D1 all atom 100 dump.bar1d +#fix_modify AtC transfer output bar1dfe 100 +timestep 5 +variable xdof equal 3*count(ghost) +compute_modify thermo_temp extra ${xdof} +thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] +thermo_modify format 1 %6i format 2 %7.2g +thermo 100 +run 400 + +# add nodesets +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -4.1 -3.9 -12 12 -12 12 +fix_modify AtC mesh create_nodeset rbc 3.9 4.1 -12 12 -12 12 +fix_modify AtC transfer fix temperature lbc 40. +fix_modify AtC transfer fix temperature rbc 20. + +# initialize filter +#timestep 0.5 +#fix_modify AtC transfer output bar1d_frac_stepFE 1 +#thermo 1 +run 400 + +# change thermostat to hoover +fix_modify AtC transfer pmfc +fix_modify AtC transfer unfix temperature all +fix_modify AtC transfer fix temperature lbc 40. +fix_modify AtC transfer fix temperature rbc 20. +# fix_modify AtC transfer thermal control none +#fix_modify AtC transfer thermal control hoover +fix_modify AtC transfer thermal control flux no_boundary +# #fix_modify AtC transfer thermal control flux interpolate +# #fix_modify AtC transfer thermal control flux faceset obndy +fix_modify AtC transfer filter type exponential +fix_modify AtC transfer filter scale 10000.0 +#fix_modify AtC transfer filter on +fix_modify AtC transfer internal_quadrature off +# #fix_modify AtC transfer localized_lambda on + +# set up output, should be before a "run" +fix_modify AtC transfer output bar1d_frac_stepFE 100 text + +# ouput command +#dump D1 all atom 1000 dump.bar1d +fix_modify AtC transfer atomic_output bar1d_frac_stepMD 100 + +# run with FE +reset_timestep 0 +thermo 100 +run 10000 diff -Naur lammps-22Sep09/examples/USER/atc/bar1d_thermal/temp.init lammps-24Sep09/examples/USER/atc/bar1d_thermal/temp.init --- lammps-22Sep09/examples/USER/atc/bar1d_thermal/temp.init 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_thermal/temp.init 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,2903 @@ +LAMMPS data file from restart file: timestep = 0, procs = 1 + +1440 atoms + +1 atom types + +-27.025 27.025 xlo xhi +-16.215 16.215 ylo yhi +-16.215 16.215 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lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/Ar_ttm.mat lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/Ar_ttm.mat --- lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/Ar_ttm.mat 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/Ar_ttm.mat 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,35 @@ +material Ar +heat_capacity constant +capacity 0.000000063363 +end +electron_heat_capacity constant +capacity 0.000000063363 +end +heat_flux linear +conductivity 0.0000000030111 +end +electron_heat_flux linear +conductivity 0.0000000030111 +end +electron_phonon_exchange linear +coefficient 0.00000000001 +end +end + +material Null +heat_capacity constant +capacity 1.0 +end +electron_heat_capacity constant +capacity 1.0 +end +heat_flux linear +conductivity 0.0 +end +electron_heat_flux linear +conductivity 0.0 +end +electron_phonon_exchange linear +coefficient 0.0 +end +end diff -Naur lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/Cu_ttm.mat lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/Cu_ttm.mat --- lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/Cu_ttm.mat 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/Cu_ttm.mat 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,17 @@ +material Cu +heat_capacity constant +capacity 0.211977459280654 +end +heat_flux linear +conductivity 67.4479848 +end +electron_heat_flux linear +conductivity 441.362750535 +end +electron_heat_capacity constant +capacity 0.005817388689 +end +electron_phonon_exchange linear +coefficient 0.0156575679 +end +end diff -Naur lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/bar1d_ttm.log lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/bar1d_ttm.log --- lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/bar1d_ttm.log 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/bar1d_ttm.log 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,537 @@ +LAMMPS (7 Jul 2009) +# in this example the electron temperature on the left is ramped up in time +# and held fixed on the right. the phonon temperature is free on the left +# and fixed and consistent with the electron temperature on the right. +# this mimics some simplified pumped system +# also a volume source is added to mimic Joule heating + +#echo both + +# units +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, +# where N = 4 for fcc, +# s = 3.405 A (Wagner) +# a = 5.25 A (Ashcroft & Mermin, p. 70) +#if {restart} +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init + orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215) + 1 by 1 by 1 processor grid + 3456 atoms + 3456 velocities +#endif + +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region feRegion block -14 14 -3 3 -3 3 +region mdRegion block -12 12 -3 3 -3 3 +region mdInternal block -10 10 -3 3 -3 3 + +# NOTE: don't define ghosts if they are outside the feRegion +group internal region mdInternal +2880 atoms in group internal +group ghost subtract all internal +576 atoms in group ghost + +# create atoms +#if !{restart} +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 +#pair_style lj/cut 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +#velocity internal create 40 87287 mom yes loop geom +#endif + +# timestep & neighboring +timestep 5.0 +thermo 10 +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc two_temperature Ar_ttm.mat + +# ID part keywords nx ny nz region +fix_modify AtC fem create mesh 14 1 1 feRegion f p p + +# specify atom types for the atc fix +#fix_modify AtC transfer internal type internal +fix_modify AtC transfer boundary type ghost + +# fix initial temperatures +#if !{restart} +#velocity internal create 40 87287 mom yes loop geom +#endif +fix_modify AtC transfer initial temperature all 20 +fix_modify AtC transfer fix temperature all 20 +fix_modify AtC transfer initial electron_temperature all 20 +fix_modify AtC transfer fix electron_temperature all 20 + +# equilibrate MD field with rescale +fix_modify AtC extrinsic exchange off +fix_modify AtC transfer thermal control rescale 10 +#if !{restart} +#run 1000 +#endif + +# change thermostat +fix_modify AtC extrinsic exchange on +fix_modify AtC transfer unfix temperature all +fix_modify AtC transfer unfix electron_temperature all +# note does not handle "inf"s +#fix_modify AtC mesh create_faceset bndy -8 8 inf inf inf inf +fix_modify AtC mesh create_faceset bndy box -10 10 -10 10 -10 10 +fix_modify AtC transfer thermal control flux faceset bndy +# .. this controls the time filtering .... +#fix_modify AtC transfer filter scale 500.0 + +# add nodesets & boundary temperature controls +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +# NOTE create_nodeset doesn't handle "inf" +fix_modify AtC mesh create_nodeset lbc -14.1 -13.9 -6 6 -6 6 +fix_modify AtC mesh create_nodeset rbc 13.9 14.1 -6 6 -6 6 +fix_modify AtC transfer fix electron_temperature lbc 40. +fix_modify AtC transfer fix electron_temperature rbc 20. +fix_modify AtC transfer fix temperature rbc 20. +#fix_modify AtC transfer source electron_temperature all 0.0015 +fix_modify AtC transfer source electron_temperature all 9.50445e-11 + + +# output filename frequency [text output] +fix_modify AtC transfer output bar1d_ttmFE 100 text + +# run transient to steady state +thermo 10 +reset_timestep 0 +run 4000 +Memory usage per processor = 20.4457 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 16.671491 -6505.7593 0 -6334.0647 -1236.2423 + 10 16.651705 -6505.5537 0 -6334.0628 -1236.063 + 20 16.530158 -6504.2726 0 -6334.0335 -1232.9374 + 30 16.484745 -6503.7602 0 -6333.9888 -1231.0691 + 40 16.543953 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-925.86436 + 3740 26.46159 -6407.1775 0 -6134.6575 -922.39462 + 3750 26.396595 -6405.9681 0 -6134.1175 -918.45094 + 3760 26.440196 -6405.8064 0 -6133.5068 -917.56053 + 3770 26.743112 -6408.2451 0 -6132.8259 -923.15375 + 3780 27.038748 -6410.6332 0 -6132.1693 -928.92314 + 3790 27.002397 -6409.6317 0 -6131.5421 -927.11925 + 3800 26.812667 -6407.1061 0 -6130.9705 -921.57646 + 3810 26.751391 -6405.9331 0 -6130.4286 -918.81768 + 3820 26.79566 -6405.8688 0 -6129.9083 -918.41904 + 3830 26.818814 -6405.6095 0 -6129.4106 -917.33046 + 3840 26.779516 -6404.6176 0 -6128.8234 -914.63692 + 3850 26.811121 -6404.3106 0 -6128.1909 -913.56294 + 3860 26.8958 -6404.519 0 -6127.5273 -913.78855 + 3870 26.921326 -6404.1181 0 -6126.8635 -912.87443 + 3880 27.099964 -6405.3939 0 -6126.2995 -915.28328 + 3890 27.27787 -6406.7453 0 -6125.8188 -917.59696 + 3900 27.219648 -6405.6017 0 -6125.2748 -914.50763 + 3910 27.105833 -6403.8204 0 -6124.6656 -910.07587 + 3920 27.116709 -6403.2885 0 -6124.0216 -908.42333 + 3930 27.081527 -6402.2517 0 -6123.3472 -905.89446 + 3940 26.932756 -6400.0687 0 -6122.6964 -901.1286 + 3950 26.930705 -6399.4167 0 -6122.0655 -899.88995 + 3960 27.236836 -6401.9835 0 -6121.4795 -905.52465 + 3970 27.502217 -6404.206 0 -6120.969 -910.18191 + 3980 27.430879 -6402.9045 0 -6120.4021 -907.21813 + 3990 27.280358 -6400.7263 0 -6119.7741 -902.29762 + 4000 27.27069 -6399.9508 0 -6119.0981 -900.12014 +Loop time of 344.483 on 1 procs for 4000 steps with 3456 atoms + +Pair time (%) = 115.899 (33.6442) +Neigh time (%) = 49.9152 (14.4899) +Comm time (%) = 1.06949 (0.310462) +Outpt time (%) = 0.0676758 (0.0196456) +Other time (%) = 177.532 (51.5358) + +Nlocal: 3456 ave 3456 max 3456 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 12768 ave 12768 max 12768 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1.0891e+06 ave 1.0891e+06 max 1.0891e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 2.1782e+06 ave 2.1782e+06 max 2.1782e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2178196 +Ave neighs/atom = 630.265 +Neighbor list builds = 400 +Dangerous builds = 0 diff -Naur lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/gaussianIC_ttm.log lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/gaussianIC_ttm.log --- lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/gaussianIC_ttm.log 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/gaussianIC_ttm.log 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,168 @@ +LAMMPS (7 Jul 2009) +#AtC Two temperature Coupling +# DESCRIPTION: +# full overlap of MD and FE regions w/ free ends & lateral periodic bcs +# initial gaussian electron temperature profile and uniform phonon temperature +# results in fast exchange followed by slower diffusion and finally relaxation +# to equilibrium +# +echo both +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, +# where N = 4 for fcc, +# s = 3.405 A (Wagner) +# a = 5.25 A (Ashcroft & Mermin, p. 70) +# to create restart : +# write_restart temp.bin +# then : restart2data temp.bin temp.init +#if {restart} +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init + orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215) + 1 by 1 by 1 processor grid + 3456 atoms + 3456 velocities +#endif + +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region feRegion block -10 10 -3 3 -3 3 +region mdRegion block -12 12 -3 3 -3 3 +region mdInternal block -10 10 -3 3 -3 3 + + +# create atoms, NOTE commented out for restart +#if !{restart} +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 +#pair_style lj/cut 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +#velocity internal create 40 87287 mom yes loop geom +#endif + +# specify interal/ghost atoms +group internal region mdInternal +2880 atoms in group internal +# do not define ghosts if outside fe region +#group ghost subtract all internal + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc two_temperature Ar_ttm.mat + +# ID part keywords nx ny nz region +fix_modify AtC fem create mesh 10 1 1 feRegion f p p + +# specify atom types +#fix_modify AtC transfer internal type internal + +# fix a temperature +fix_modify AtC transfer fix temperature all 20.0 +fix_modify AtC transfer initial temperature all 20.0 +fix_modify AtC transfer initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 +fix_modify AtC transfer fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 + + +# turn on thermostat +fix_modify AtC extrinsic exchange off +fix_modify AtC transfer thermal control rescale 10 + +# equilibrate MD field +timestep 5.0 +#timestep 0.1 +thermo 10 +#if !{restart} +#run 1000 +#endif + +# write restart file (for atoms) +#if !{restart} +#write_restart gaussianT0.dat +#endif + +#output +fix_modify AtC transfer output gaussianIC_ttmFE 10 text + +# change thermostat +fix_modify AtC transfer unfix temperature all +fix_modify AtC transfer unfix electron_temperature all +fix_modify AtC transfer thermal control flux +fix_modify AtC extrinsic exchange on +fix_modify AtC extrinsic electron_integration explicit 10 + +# run with FE +thermo_style custom step temp pe f_AtC[2] f_AtC[4] +reset_timestep 0 +run 400 +Memory usage per processor = 20.4457 Mbytes +Step Temp PotEng AtC[2] AtC[4] + 0 16.671491 -6505.7593 20 21.852118 + 10 16.677475 -6505.5427 20.002541 21.837728 + 20 16.576352 -6504.1927 19.867309 21.822847 + 30 16.543006 -6503.5347 19.829679 21.807329 + 40 16.606315 -6503.9098 19.948237 21.79227 + 50 16.657241 -6504.1495 20.063768 21.77819 + 60 16.632334 -6503.6282 20.043346 21.764516 + 70 16.575817 -6502.7756 19.922594 21.750359 + 80 16.582959 -6502.556 19.854482 21.735666 + 90 16.619481 -6502.6709 19.843443 21.720989 + 100 16.61416 -6502.3553 19.823604 21.706411 + 110 16.63 -6502.2515 19.868881 21.692096 + 120 16.693117 -6502.6546 19.982758 21.67865 + 130 16.690721 -6502.395 19.998489 21.665851 + 140 16.614049 -6501.3546 19.912824 21.652674 + 150 16.61038 -6501.0505 19.922441 21.639146 + 160 16.722799 -6501.9758 20.079964 21.626427 + 170 16.770602 -6502.2509 20.17121 21.614856 + 180 16.650892 -6500.7765 20.054544 21.603105 + 190 16.541447 -6499.381 19.906876 21.590204 + 200 16.645228 -6500.2039 19.964842 21.577132 + 210 16.869527 -6502.3001 20.162483 21.565509 + 220 16.964383 -6503.0601 20.257183 21.55523 + 230 16.911611 -6502.3326 20.238311 21.545157 + 240 16.817036 -6501.1565 20.182711 21.534754 + 250 16.768709 -6500.4545 20.137714 21.524032 + 260 16.815288 -6500.7352 20.15617 21.51338 + 270 16.910049 -6501.5019 20.224357 21.50326 + 280 16.977499 -6502.0383 20.29341 21.493767 + 290 16.956659 -6501.6276 20.291231 21.484565 + 300 16.835262 -6500.213 20.164202 21.474772 + 310 16.71985 -6498.8264 20.004642 21.463806 + 320 16.69098 -6498.3213 19.932827 21.452076 + 330 16.761703 -6498.8528 20.012407 21.440668 + 340 16.868998 -6499.7478 20.16924 21.430476 + 350 16.984511 -6500.7709 20.340112 21.421697 + 360 17.123542 -6502.0546 20.527447 21.414404 + 370 17.196695 -6502.6994 20.623027 21.408269 + 380 17.078535 -6501.3567 20.479029 21.401788 + 390 16.82808 -6498.6218 20.180491 21.393274 + 400 16.644633 -6496.5257 19.969187 21.382648 +Loop time of 38.0403 on 1 procs for 400 steps with 3456 atoms + +Pair time (%) = 11.5723 (30.4211) +Neigh time (%) = 4.98386 (13.1015) +Comm time (%) = 0.111562 (0.293273) +Outpt time (%) = 0.00291038 (0.00765077) +Other time (%) = 21.3697 (56.1764) + +Nlocal: 3456 ave 3456 max 3456 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 12768 ave 12768 max 12768 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1.09177e+06 ave 1.09177e+06 max 1.09177e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 2.18354e+06 ave 2.18354e+06 max 2.18354e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2183544 +Ave neighs/atom = 631.812 +Neighbor list builds = 40 +Dangerous builds = 0 diff -Naur lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/in.bar1d_ttm lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/in.bar1d_ttm --- lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/in.bar1d_ttm 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/in.bar1d_ttm 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,105 @@ +# in this example the electron temperature on the left is ramped up in time +# and held fixed on the right. the phonon temperature is free on the left +# and fixed and consistent with the electron temperature on the right. +# this mimics some simplified pumped system +# also a volume source is added to mimic Joule heating + +#echo both + +# units +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, +# where N = 4 for fcc, +# s = 3.405 A (Wagner) +# a = 5.25 A (Ashcroft & Mermin, p. 70) +#if {restart} +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init +#endif + +lattice fcc 5.405 origin 0.25 0.25 0.25 +region feRegion block -14 14 -3 3 -3 3 +region mdRegion block -12 12 -3 3 -3 3 +region mdInternal block -10 10 -3 3 -3 3 + +# NOTE: don't define ghosts if they are outside the feRegion +group internal region mdInternal +group ghost subtract all internal + +# create atoms +#if !{restart} +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 +#pair_style lj/cut 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +#velocity internal create 40 87287 mom yes loop geom +#endif + +# timestep & neighboring +timestep 5.0 +thermo 10 +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc two_temperature Ar_ttm.mat + +# ID part keywords nx ny nz region +fix_modify AtC fem create mesh 14 1 1 feRegion f p p + +# specify atom types for the atc fix +#fix_modify AtC transfer internal type internal +fix_modify AtC transfer boundary type ghost + +# fix initial temperatures +#if !{restart} +#velocity internal create 40 87287 mom yes loop geom +#endif +fix_modify AtC transfer initial temperature all 20 +fix_modify AtC transfer fix temperature all 20 +fix_modify AtC transfer initial electron_temperature all 20 +fix_modify AtC transfer fix electron_temperature all 20 + +# equilibrate MD field with rescale +fix_modify AtC extrinsic exchange off +fix_modify AtC transfer thermal control rescale 10 +#if !{restart} +#run 1000 +#endif + +# change thermostat +fix_modify AtC extrinsic exchange on +fix_modify AtC transfer unfix temperature all +fix_modify AtC transfer unfix electron_temperature all +# note does not handle "inf"s +#fix_modify AtC mesh create_faceset bndy -8 8 inf inf inf inf +fix_modify AtC mesh create_faceset bndy box -10 10 -10 10 -10 10 +fix_modify AtC transfer thermal control flux faceset bndy +# .. this controls the time filtering .... +#fix_modify AtC transfer filter scale 500.0 + +# add nodesets & boundary temperature controls +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +# NOTE create_nodeset doesn't handle "inf" +fix_modify AtC mesh create_nodeset lbc -14.1 -13.9 -6 6 -6 6 +fix_modify AtC mesh create_nodeset rbc 13.9 14.1 -6 6 -6 6 +fix_modify AtC transfer fix electron_temperature lbc 40. +fix_modify AtC transfer fix electron_temperature rbc 20. +fix_modify AtC transfer fix temperature rbc 20. +#fix_modify AtC transfer source electron_temperature all 0.0015 +fix_modify AtC transfer source electron_temperature all 9.50445e-11 + + +# output filename frequency [text output] +fix_modify AtC transfer output bar1d_ttmFE 100 text + +# run transient to steady state +thermo 10 +reset_timestep 0 +run 4000 diff -Naur lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/in.gaussianIC_ttm lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/in.gaussianIC_ttm --- lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/in.gaussianIC_ttm 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/in.gaussianIC_ttm 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,97 @@ +#AtC Two temperature Coupling +# DESCRIPTION: +# full overlap of MD and FE regions w/ free ends & lateral periodic bcs +# initial gaussian electron temperature profile and uniform phonon temperature +# results in fast exchange followed by slower diffusion and finally relaxation +# to equilibrium +# +echo both +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, +# where N = 4 for fcc, +# s = 3.405 A (Wagner) +# a = 5.25 A (Ashcroft & Mermin, p. 70) +# to create restart : +# write_restart temp.bin +# then : restart2data temp.bin temp.init +#if {restart} +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init +#endif + +lattice fcc 5.405 origin 0.25 0.25 0.25 +region feRegion block -10 10 -3 3 -3 3 +region mdRegion block -12 12 -3 3 -3 3 +region mdInternal block -10 10 -3 3 -3 3 + + +# create atoms, NOTE commented out for restart +#if !{restart} +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 +#pair_style lj/cut 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +#velocity internal create 40 87287 mom yes loop geom +#endif + +# specify interal/ghost atoms +group internal region mdInternal +# do not define ghosts if outside fe region +#group ghost subtract all internal + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc two_temperature Ar_ttm.mat + +# ID part keywords nx ny nz region +fix_modify AtC fem create mesh 10 1 1 feRegion f p p + +# specify atom types +#fix_modify AtC transfer internal type internal + +# fix a temperature +fix_modify AtC transfer fix temperature all 20.0 +fix_modify AtC transfer initial temperature all 20.0 +fix_modify AtC transfer initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 +fix_modify AtC transfer fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 + + +# turn on thermostat +fix_modify AtC extrinsic exchange off +fix_modify AtC transfer thermal control rescale 10 + +# equilibrate MD field +timestep 5.0 +#timestep 0.1 +thermo 10 +#if !{restart} +#run 1000 +#endif + +# write restart file (for atoms) +#if !{restart} +#write_restart gaussianT0.dat +#endif + +#output +fix_modify AtC transfer output gaussianIC_ttmFE 10 text + +# change thermostat +fix_modify AtC transfer unfix temperature all +fix_modify AtC transfer unfix electron_temperature all +fix_modify AtC transfer thermal control flux +fix_modify AtC extrinsic exchange on +fix_modify AtC extrinsic electron_integration explicit 10 + +# run with FE +thermo_style custom step temp pe f_AtC[2] f_AtC[4] +reset_timestep 0 +run 400 diff -Naur lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/in.no_atoms lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/in.no_atoms --- lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/in.no_atoms 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/in.no_atoms 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,57 @@ +#AtC Two temperature Coupling +# DESCRIPTION: +# no atoms and FE regions with periodic boundary conditions. +# heating and then relaxation + +echo both +#units real +units metal + +atom_style atomic + +lattice fcc 5.405 origin 0.25 0.25 0.25 +region simRegion block -14 14 -3 3 -3 3 +region feRegion block -12 12 -3 3 -3 3 + +# create atoms +region mdRegion block -12 12 -3 3 -3 3 +boundary f p p +create_box 1 mdRegion +mass 1 39.95 # need to keep this + +# ID group atc PhysicsType ParameterFile +fix AtC all atc two_temperature Cu_ttm.mat +timestep 0.002 +thermo 20 + +# ID part keywords nx ny nz region +fix_modify AtC fem create mesh 12 1 1 feRegion f p p + +# fix a temperature +fix_modify AtC transfer initial temperature all 20.0 +#fix_modify AtC transfer initial electron_temperature all 30.0 +fix_modify AtC transfer initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 + +# relaxation +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] +fix_modify AtC transfer output no_atomsFE 10 text +#fix_modify AtC extrinsic electron_integration subcycle 100 +fix_modify AtC extrinsic electron_integration implicit +run 400 + +# heating +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12 +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -12 12 -12 12 +fix_modify AtC transfer fix electron_temperature lbc 20. +fix_modify AtC transfer fix electron_temperature rbc 20. +#fix_modify AtC extrinsic exchange off +#fix_modify AtC transfer fix temperature lbc 20. +#fix_modify AtC transfer fix temperature rbc 20. +#fix_modify AtC extrinsic electron_integration lockstep +#fix_modify AtC transfer source electron_temperature all 1000.0 +fix_modify AtC transfer source electron_temperature all 0.521981 +run 400 + +# relaxation +fix_modify AtC transfer remove_source electron_temperature all +run 400 diff -Naur lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/in.uniform_exchange lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/in.uniform_exchange --- lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/in.uniform_exchange 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/in.uniform_exchange 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,67 @@ +#AtC Two temperature Coupling +# DESCRIPTION: +# full overlap of MD and FE regions with full periodic boundary conditions. +# initial electron and phonon temperatures are different and then allowed to +# relax. +# + +units real +atom_style atomic +boundary p p p + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, +# where N = 4 for fcc, +# s = 3.405 A (Wagner) +# a = 5.25 A (Ashcroft & Mermin, p. 70) +lattice fcc 5.405 origin 0.25 0.25 0.25 + +pair_style lj/cut 13.5 + +read_data uniform_exchange_init.data + +region simRegion block -12 12 -3 3 -3 3 +region feRegion block -12 12 -3 3 -3 3 + +# create atoms +region mdRegion block -12 12 -3 3 -3 3 + +# specify interal/ghost atoms +region mdInternal block -12 12 -3 3 -3 3 +group internal region mdInternal + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc two_temperature Ar_ttm.mat + +# ID part keywords nx ny nz region +fix_modify AtC fem create mesh 4 1 1 feRegion p p p + +# fix a temperature +fix_modify AtC transfer fix temperature all 20.0 +fix_modify AtC transfer fix electron_temperature all 30.0 + +timestep 5.0 + +# output +thermo_style custom step pe temp f_AtC[2] f_AtC[4] +thermo 10 + +# equilibrate MD field +fix_modify AtC transfer thermal control rescale 13 +run 500 + +# relax +fix_modify AtC transfer output uniform_exchangeFE 100 text +fix_modify AtC transfer atomic_output uniform_exchangeMD 10000 +fix_modify AtC transfer filter type exponential +fix_modify AtC transfer filter scale 5.0e2 +fix_modify AtC transfer filter on +fix_modify AtC transfer unfix temperature all +fix_modify AtC transfer unfix electron_temperature all +fix_modify AtC transfer thermal control flux + +# run with FE +run 5000 diff -Naur lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/in.uniform_heating lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/in.uniform_heating --- lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/in.uniform_heating 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/in.uniform_heating 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,74 @@ +#AtC Thermal Coupling + +echo both +units real +atom_style atomic +boundary f p p + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) + +pair_style lj/cut 13.5 + +read_data uniform_heating_init.data +lattice fcc 5.405 origin 0.25 0.25 0.25 + +region mdRegion block -8 8 -3 3 -3 3 +region mdInternal block -6 6 -3 3 -3 3 + +group internal region mdInternal + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc two_temperature Ar_ttm.mat + +# ID part keywords nx ny nz region +fix_modify AtC fem create mesh 6 1 1 mdInternal f p p + +# specify atom types +#fix_modify AtC transfer internal type internal + +# fix a temperature +fix_modify AtC transfer initial temperature all 20. +fix_modify AtC transfer fix temperature all 20. +fix_modify AtC transfer initial electron_temperature all 20. +fix_modify AtC transfer fix electron_temperature all 20. + +# turn on thermostat +fix_modify AtC transfer thermal control rescale 10 + +# output +thermo_style custom step cpu pe etotal temp f_AtC[1] f_AtC[2] +thermo 100 +log uniform_heating.log + +# make thermo output the correct temperature by removing ghost dof +# variable xdof equal 3*count(ghost) +# compute_modify thermo_temp extra ${xdof} + +# equilibrate MD field +timestep 5 +run 400 + +# change thermostat +fix_modify AtC transfer output uniform_heatingFE 100 text +fix_modify AtC transfer unfix temperature all +fix_modify AtC transfer thermal control flux + +# fix boundary +fix_modify AtC mesh create_nodeset lbc -6.1 -5.9 -12 12 -12 12 +fix_modify AtC transfer fix temperature lbc 20. +fix_modify AtC mesh create_nodeset rbc 5.9 6.1 -12 12 -12 12 +fix_modify AtC transfer fix temperature rbc 20. + + +# add source +fix_modify AtC transfer internal_quadrature on +#fix_modify AtC transfer source temperature all 0.01 +fix_modify AtC transfer source temperature all 6.3363e-10 + +# run with FE +reset_timestep 0 +run 1000 diff -Naur lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/no_atoms.log lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/no_atoms.log --- lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/no_atoms.log 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/no_atoms.log 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,190 @@ +LAMMPS (7 Jul 2009) +#AtC Two temperature Coupling +# DESCRIPTION: +# no atoms and FE regions with periodic boundary conditions. +# heating and then relaxation + +echo both +#units real +units metal + +atom_style atomic + +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region simRegion block -14 14 -3 3 -3 3 +region feRegion block -12 12 -3 3 -3 3 + +# create atoms +region mdRegion block -12 12 -3 3 -3 3 +boundary f p p +create_box 1 mdRegion +Created orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215) + 1 by 1 by 1 processor grid +mass 1 39.95 # need to keep this + +# ID group atc PhysicsType ParameterFile +fix AtC all atc two_temperature Cu_ttm.mat +timestep 0.002 +thermo 20 + +# ID part keywords nx ny nz region +fix_modify AtC fem create mesh 12 1 1 feRegion f p p + +# fix a temperature +fix_modify AtC transfer initial temperature all 20.0 +#fix_modify AtC transfer initial electron_temperature all 30.0 +fix_modify AtC transfer initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 + +# relaxation +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] +fix_modify AtC transfer output no_atomsFE 10 text +#fix_modify AtC extrinsic electron_integration subcycle 100 +fix_modify AtC extrinsic electron_integration implicit +run 400 +Memory usage per processor = 0.412468 Mbytes +Step CPU AtC[1] AtC[2] AtC[3] AtC[4] + 0 0 59.94586 20 1.7847722 21.567177 + 20 0.46597385 59.95972 20.00454 1.770575 21.52456 + 40 0.93160486 59.97247 20.008795 1.7578608 21.370605 + 60 1.368351 59.983888 20.012606 1.7464745 21.232182 + 80 1.8008358 59.994113 20.016019 1.7362775 21.108216 + 100 2.2340729 60.00327 20.019076 1.7271457 20.997198 + 120 2.667372 60.01147 20.021814 1.7189676 20.897776 + 140 3.101615 60.018815 20.024266 1.7116438 20.808739 + 160 3.5347569 60.025391 20.026462 1.7050849 20.729002 + 180 3.9713268 60.031281 20.028429 1.6992111 20.657594 + 200 4.4060199 60.036556 20.030191 1.6939509 20.593644 + 220 4.8383729 60.04128 20.031768 1.6892401 20.536374 + 240 5.2700989 60.045511 20.033181 1.6850213 20.485086 + 260 5.702713 60.049299 20.034447 1.6812432 20.439154 + 280 6.1313 60.052692 20.035581 1.6778597 20.398021 + 300 6.552902 60.05573 20.036596 1.6748297 20.361184 + 320 6.978493 60.058451 20.037506 1.6721161 20.328194 + 340 7.3976619 60.060888 20.03832 1.6696859 20.298651 + 360 7.817637 60.063071 20.03905 1.6675096 20.272193 + 380 8.227901 60.065025 20.039703 1.6655606 20.248499 + 400 8.6359458 60.066775 20.040289 1.6638152 20.227279 +Loop time of 8.63894 on 1 procs for 400 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000214577 (0.00248383) +Outpt time (%) = 0.0595214 (0.68899) +Other time (%) = 8.5792 (99.3085) + +Nlocal: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +# heating +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12 +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -12 12 -12 12 +fix_modify AtC transfer fix electron_temperature lbc 20. +fix_modify AtC transfer fix electron_temperature rbc 20. +#fix_modify AtC extrinsic exchange off +#fix_modify AtC transfer fix temperature lbc 20. +#fix_modify AtC transfer fix temperature rbc 20. +#fix_modify AtC extrinsic electron_integration lockstep +#fix_modify AtC transfer source electron_temperature all 1000.0 +fix_modify AtC transfer source electron_temperature all 0.521981 +run 400 +Memory usage per processor = 0.412468 Mbytes +Step CPU AtC[1] AtC[2] AtC[3] AtC[4] + 400 0 60.066775 20.040289 1.6638152 20.227279 + 420 0.46465707 60.074057 20.042563 1.7526734 21.206964 + 440 0.93380594 60.08642 20.046435 1.7697616 21.398727 + 460 1.4028659 60.099602 20.050578 1.7726213 21.43082 + 480 1.872489 60.112889 20.054768 1.7731138 21.436346 + 500 2.341527 60.126162 20.058968 1.7732124 21.437452 + 520 2.8146279 60.139402 20.063168 1.7732452 21.437821 + 540 3.2863479 60.152606 20.067367 1.773267 21.438066 + 560 3.7559209 60.165773 20.071564 1.7732869 21.438289 + 580 4.2253721 60.178904 20.075757 1.7733063 21.438507 + 600 4.696142 60.191997 20.079946 1.7733256 21.438723 + 620 5.164628 60.205055 20.084131 1.7733447 21.438937 + 640 5.633961 60.218075 20.08831 1.7733637 21.43915 + 660 6.1026099 60.23106 20.092484 1.7733825 21.439362 + 680 6.5716951 60.244008 20.096653 1.7734013 21.439572 + 700 7.0413561 60.256919 20.100815 1.7734199 21.439781 + 720 7.5101869 60.269795 20.10497 1.7734384 21.439989 + 740 7.9797149 60.282635 20.109119 1.7734568 21.440195 + 760 8.4487319 60.295439 20.11326 1.7734751 21.4404 + 780 8.9184639 60.308207 20.117395 1.7734932 21.440604 + 800 9.3883049 60.320939 20.121522 1.7735113 21.440807 +Loop time of 9.39129 on 1 procs for 400 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000202179 (0.00215284) +Outpt time (%) = 0.0597332 (0.636049) +Other time (%) = 9.33135 (99.3618) + +Nlocal: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +# relaxation +fix_modify AtC transfer remove_source electron_temperature all +run 400 +Memory usage per processor = 0.412468 Mbytes +Step CPU AtC[1] AtC[2] AtC[3] AtC[4] + 800 0 60.320939 20.121522 1.7735113 21.440807 + 820 0.46552801 60.326208 20.123317 1.6666305 20.24139 + 840 0.93443298 60.326191 20.123452 1.6491438 20.045155 + 860 1.4037609 60.325301 20.123302 1.6462322 20.012481 + 880 1.87309 60.324267 20.123096 1.6457454 20.007018 + 900 2.341542 60.323212 20.122873 1.6456621 20.006083 + 920 2.810395 60.322156 20.122641 1.6456459 20.005902 + 940 3.279598 60.321102 20.122402 1.645641 20.005846 + 960 3.7478158 60.320051 20.122158 1.645638 20.005813 + 980 4.21626 60.319003 20.121908 1.6456354 20.005783 + 1000 4.6847739 60.317957 20.121654 1.6456328 20.005754 + 1020 5.1538019 60.316914 20.121396 1.6456303 20.005726 + 1040 5.622643 60.315874 20.121135 1.6456279 20.005699 + 1060 6.0918579 60.314837 20.120871 1.6456255 20.005672 + 1080 6.561069 60.313803 20.120603 1.6456231 20.005645 + 1100 7.0291269 60.312771 20.120334 1.6456208 20.005619 + 1120 7.497472 60.311742 20.120061 1.6456185 20.005593 + 1140 7.9661739 60.310716 20.119787 1.6456162 20.005568 + 1160 8.4346058 60.309693 20.119511 1.645614 20.005543 + 1180 8.9034901 60.308673 20.119234 1.6456118 20.005519 + 1200 9.373548 60.307655 20.118954 1.6456097 20.005495 +Loop time of 9.37655 on 1 procs for 400 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000205755 (0.00219436) +Outpt time (%) = 0.0598149 (0.637921) +Other time (%) = 9.31653 (99.3599) + +Nlocal: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 diff -Naur lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/temp.init lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/temp.init --- lammps-22Sep09/examples/USER/atc/bar1d_two_temperature/temp.init 1969-12-31 17:00:00.000000000 -0700 +++ lammps-24Sep09/examples/USER/atc/bar1d_two_temperature/temp.init 2009-09-24 10:32:26.000000000 -0600 @@ -0,0 +1,6935 @@ +LAMMPS data file from restart file: timestep = 1000, procs = 1 + +3456 atoms + +1 atom types + +-64.86 64.86 xlo xhi +-16.215 16.215 ylo yhi +-16.215 16.215 zlo zhi + +Masses + +1 39.95 + +Pair Coeffs + +1 0.238 3.405 + +Atoms + +1 1 -63.50875 -14.86375 -14.86375 0 0 0 +2 1 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