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Re: [lammps-users] Question on: ReaxFF + Fix deposit + Molecule
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Re: [lammps-users] Question on: ReaxFF + Fix deposit + Molecule


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 3 Jul 2017 07:41:34 -0400

On Mon, Jul 3, 2017 at 1:26 AM, Cheng Liu <chengliuhappy@...24...> wrote:
> Hello:
>
> I have interest in using ReaxFF potential to simulation oxidation in SiC. Oxygen molecules will be deposited in the vacuum above SiC bulk. Well, I have a problem in using fix deposit molecule command within lammps.
>
> In my simulation, firstly, read_data is used to read in the substrate Si and C atoms coordinates, which included the “1 extra bond per atom” to leave space to add molecules.Then, O2 molecular file is read, which includes atom coordinates, atom types, and bonds information. This is a simplified version from the lammps/example/deposit/molecule, which includes special bond information. Lastly, fix deposit command is used.  Input files have been attached.
>
> However, I continuously get the error messages: ERROR: Molecule topology type exceeds system topology type (../molecule.cpp:1368). I have checked the create_box command instruction. As I used read_data which is an equal command of create_box, and "1 extra bond per atom” is included. I don’t know are there thing wrong with my read_data or O2.txt file.
>
> Could you give me some suggestions on using read_data, reaxff potential and fix_deposit properly?

in reaxff there should be no explicit bonds given anywhere, since
bondorder and its derived interactions are computed dynamically during
the simulation.

axel.

>
> Thanks in advance!
>
> Cheng
>
>
>
>
>
>
>
>
>
>> On May 4, 2017, at 5:39 PM, lammps-users-request@lists.sourceforge.net wrote:
>>
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>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of lammps-users digest..."
>>
>>
>> Today's Topics:
>>
>>   1. Re: reaxFF with kokkos fails to run (Moore, Stan)
>>   2. using lammps as a shared library with c++ (K BHAVANA K BHAVANA)
>>   3. Re: using lammps as a shared library with c++ (Stefan Paquay)
>>   4. Re: [EXTERNAL] Re: Is it possible to combine dipole/chunk
>>      with spatial binning? (Peter Wirnsberger)
>>   5. Re: user-intel optimization (Steve Plimpton)
>>   6. Re: Calling Lammps code from Fortran (Steve Plimpton)
>>   7. Re: Energy discrepancy when using fix box/relax in triclinic
>>      boxes (Steve Plimpton)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 4 May 2017 17:59:55 +0000
>> From: "Moore, Stan" <stamoor@...3...>
>> Subject: Re: [lammps-users] reaxFF with kokkos fails to run
>> To: vaishali a <vaish331@...24...>
>> Cc: "lammps-users@lists.sourceforge.net"
>>       <lammps-users@lists.sourceforge.net>
>> Message-ID:
>>       <4cb8d78273dc45f191ecd0d13b73a43b@...5510...>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Please respond to the mail list, not me.
>>
>> Can you be more specific? Why can?t you run reaxc without Kokkos? Are you getting an error?
>>
>> Stan
>>
>> From: vaishali a [mailto:vaish331@...24...]
>> Sent: Thursday, May 04, 2017 11:55 AM
>> To: Moore, Stan <stamoor@...3...>
>> Subject: [EXTERNAL] Re: [lammps-users] reaxFF with kokkos fails to run
>>
>> I cant run reaxc without kokkos.
>>
>> Vaishali
>>
>> On Thu, May 4, 2017 at 8:38 PM, Moore, Stan <stamoor@...3...<mailto:stamoor@...3...>> wrote:
>> What happens when you turn Kokkos off?
>>
>> Stan
>>
>> From: vaishali a [mailto:vaish331@...24...<mailto:vaish331@...24...>]
>> Sent: Wednesday, May 03, 2017 11:16 PM
>> To: lammps-users@lists.sourceforge.net<mailto:lammps-users@...430...orge.net>
>> Subject: [EXTERNAL] [lammps-users] reaxFF with kokkos fails to run
>>
>> Hi
>>
>> I had compiled kokkos with omp  using the lammps version 31 March 2017. My system consists of a nanosheet immersed in solvent molecules. I had built four different system on which i had used pair style reaxc and all were running fine with 'fix nvt all'. I then wanted to keep my sheet rigid and hence changed the fix such that it applies only on the solvent molecules. One of my system continued to run without any issues but the other three hangs after 999 steps.I reduced the time step to 0.1fs and the issue still persists; it hangs exactly at the 999th step. Is it a bug ? this is my input script:
>> ===================================================================================================================
>> units           real
>>
>> atom_style      charge
>> read_data       data.R100_water_1024
>>
>> pair_style      reax/c NULL #lmp_control
>> pair_coeff  * * ffield.reax.BNOH B H N O
>>
>> neighbor        2 bin
>> neigh_modify    every 1 delay 0 check yes
>>
>> # compute charge on every type
>> group       type1 type 1
>> compute     charge1 type1 property/atom q
>> compute     q1 type1 reduce ave c_charge1
>> group       type2 type 2
>> compute     charge2 type2 property/atom q
>> compute     q2 type2 reduce ave c_charge2
>> group       type3 type 3
>> compute     charge3 type3 property/atom q
>> compute     q3 type3 reduce ave c_charge3
>> group       type4 type 4
>> compute     charge4 type4 property/atom q
>> compute     q4 type4 reduce ave c_charge4
>>
>>
>> variable    qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3+count(type4)*c_q4
>>
>> thermo_style    custom step etotal pe c_q1 c_q2 c_q3 c_q4 v_qtot lx ly lz pxx pyy pzz press temp
>> thermo      1
>>
>>
>> group BN type 1 3
>> group W type 2 4
>>
>> velocity        W create 300.0 427006 rot yes mom yes dist gaussian
>> fix             1 W nvt temp 300.0 300.0 100 tchain 3
>> fix             2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
>>
>>
>> timestep        0.5
>>
>> dump            num1 all custom 100 dump.100edge_1 id type q x y z
>> dump_modify num1 sort id
>>
>> ===============================================================================================================================
>>
>>
>>
>>
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>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 4 May 2017 22:47:42 +0530
>> From: K BHAVANA K BHAVANA <mfd14i005@...6828...>
>> Subject: [lammps-users] using lammps as a shared library with c++
>> To: lammps-users@lists.sourceforge.net, sjplimp@...24...,
>>       akohlmey@...1086...
>> Message-ID:
>>       <CAPEUWBWYjF=GmK2LFEgHzm-cyRLFvakeCs3qbb+aaepvL6FqFw@...25...>
>> Content-Type: text/plain; charset="utf-8"
>>
>> for a research project i have to simulate particle breaking into given
>> number of sub particles with co ordinates within the Big sphere which
>> breaks and the voids present between it and neighbouring atoms.
>>
>> I went through the lammps site and i used the make mode=shlib ubuntu
>> command .This produces lot of warnings in between.But still it compiles
>> and  produces a 'share library soft link liblammps.so'.
>>
>> However i dont know how to proceed in linking this library as when i put
>>
>> $make install
>> or $sudo make install
>>
>> after make mode command it doesnt work.And when i use the ./configure
>> command
>> in my ubuntu 14.04 it says command doesnt exist.
>>
>> Also i used the $export ADD_LIBRARY_PATH command but nothing works.
>>
>> So how do i link the library to my c++ code.
>>
>> Also can any function directly pack spheres even in voids along with main
>> major space and give info on neighbouring atoms.
>>
>> pS REPLY AS SOON AS POSSIBLE.
>>
>>
>> thank you
>> bhavana
>> mechanical engineering
>> indian institute of information technology,design and manufacturing
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>> ------------------------------
>>
>> Message: 3
>> Date: Thu, 4 May 2017 14:16:50 -0400
>> From: Stefan Paquay <stefanpaquay@...24...>
>> Subject: Re: [lammps-users] using lammps as a shared library with c++
>> To: K BHAVANA K BHAVANA <mfd14i005@...6828...>
>> Cc: Axel Kohlmeyer <akohlmey@...1086...>, Steve Plimpton
>>       <sjplimp@...24...>,    LAMMPS <lammps-users@lists.sourceforge.net>
>> Message-ID:
>>       <CADdYMEiwCCx1nZF+s2p-0TDykGk13rokcsx1k-yVuteAzMoWHQ@...25...>
>> Content-Type: text/plain; charset="utf-8"
>>
>> To link to the library make sure you put it somewhere that is in your
>> LD_LIBRARY_PATH and then link your application to it using the "-llammps"
>> flag during linking.
>>
>> On Thu, May 4, 2017 at 1:17 PM, K BHAVANA K BHAVANA <mfd14i005@...6960....>
>> wrote:
>>
>>> for a research project i have to simulate particle breaking into given
>>> number of sub particles with co ordinates within the Big sphere which
>>> breaks and the voids present between it and neighbouring atoms.
>>>
>>> I went through the lammps site and i used the make mode=shlib ubuntu
>>> command .This produces lot of warnings in between.But still it compiles
>>> and  produces a 'share library soft link liblammps.so'.
>>>
>>> However i dont know how to proceed in linking this library as when i put
>>>
>>> $make install
>>> or $sudo make install
>>>
>>> after make mode command it doesnt work.And when i use the ./configure
>>> command
>>> in my ubuntu 14.04 it says command doesnt exist.
>>>
>>> Also i used the $export ADD_LIBRARY_PATH command but nothing works.
>>>
>>> So how do i link the library to my c++ code.
>>>
>>> Also can any function directly pack spheres even in voids along with main
>>> major space and give info on neighbouring atoms.
>>>
>>> pS REPLY AS SOON AS POSSIBLE.
>>>
>>>
>>> thank you
>>> bhavana
>>> mechanical engineering
>>> indian institute of information technology,design and manufacturing
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> lammps-users mailing list
>>> lammps-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>>
>>>
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> Message: 4
>> Date: Thu, 4 May 2017 19:39:57 +0100
>> From: Peter Wirnsberger <peter.wirnsberger@...24...>
>> Subject: Re: [lammps-users] [EXTERNAL] Re: Is it possible to combine
>>       dipole/chunk with spatial binning?
>> To: Steve Plimpton <sjplimp@...3...>
>> Cc: lammps-users@lists.sourceforge.net
>> Message-ID: <9c7912c6-7534-0a9f-477f-94a205cef354@...24...>
>> Content-Type: text/plain; charset=windows-1252
>>
>> Hi Steve,
>>
>>
>> Thank you for thinking about the problem!
>>
>> I think that a compute that assigns per-chunk values to every atom in
>> the chunk would be an extremely useful extension to LAMMPS!
>>
>> It would certainly resolve the problem I was interested in, but I could
>> see this be helpful in other contexts as well.
>>
>>
>> Best wishes,
>>
>> Peter
>>
>>
>>
>> On 05/02/2017 02:49 PM, Steve Plimpton wrote:
>>> Here's another idea.
>>>
>>> What if there was a compute that assigned a per-chunk value to every
>>> atom in the chunk.  We've recently talked about this for use in other
>>> contexts.  E.g. in the case of compute dipole/chunk as an input to the
>>> new compute, it would assign the 3-vector dipole moment for one chunk
>>> (molecule) to each atom in the water (or other) molecule.
>>>
>>> Then the usual fix ave/chunk for spatial bins could
>>> compute an average dipole moment for each spatial bin.
>>>
>>> A water molecule that straddled 2 bins would have 2 copies of the same
>>> dipole momemt summed to one bin, and 1 copy to the other.  In a
>>> weighted manner where the first bin's summed moment was divided by 2
>>> atoms, and the second bin by 1 atom.
>>>
>>> It's a bit different than assigning each molecule's moment to one bin
>>> based on the COM position, but you could argue it's a reasonable
>>> (maybe better) way to spatially average.
>>>
>>> Steve
>>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Thu, 4 May 2017 16:09:06 -0600
>> From: Steve Plimpton <sjplimp@...24...>
>> Subject: Re: [lammps-users] user-intel optimization
>> To: Axel Kohlmeyer <akohlmey@...24...>
>> Cc: Steven Earl Strong <Steven.Strong@...780...>,  LAMMPS Users
>>       Mailing List <lammps-users@lists.sourceforge.net>
>> Message-ID:
>>       <CAENuAmF1V8XA9_4LYUnQbsQC6=SEDNLsahK0XSHB-MxjxndPcA@...25...>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Really that should read set the neighbor binsize to the neighbor cutoff,
>> not half the neighbor cutoff, which is the default.  I'll clarify that on
>> the
>> doc page.
>>
>> Thanks,
>> Steve
>>
>> On Tue, May 2, 2017 at 1:06 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>>
>>>
>>>
>>> On Tue, May 2, 2017 at 1:49 PM, Steven Earl Strong <
>>> Steven.Strong@...780...> wrote:
>>>
>>>> Hi-
>>>> I have a question about the documentation
>>>> <http://lammps.sandia.gov/doc/accelerate_intel.html> on the USER-INTEL
>>>> package. It suggests that you use 'neigh_modify binsize 3' Since this is
>>>> setting the bin size in distance units, I don't understand how this setting
>>>> is optimal regardless of the units being used, and the system being
>>>> studied. Any help is appreciated.
>>>>
>>>
>>> ?please note that this suggestion is always given in reference to using
>>> PPPM. this in turn can only be used with certain pair styles for which
>>> either real or metal units are common and both of those use angstroms as
>>> distance unit.
>>>
>>> axel.?
>>>
>>>
>>>
>>>> Thanks, Steve
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> lammps-users mailing list
>>>> lammps-users@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>>>
>>>>
>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> lammps-users mailing list
>>> lammps-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>>
>>>
>> -------------- next part --------------
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>> ------------------------------
>>
>> Message: 6
>> Date: Thu, 4 May 2017 16:10:18 -0600
>> From: Steve Plimpton <sjplimp@...24...>
>> Subject: Re: [lammps-users] Calling Lammps code from Fortran
>> To: Axel Kohlmeyer <akohlmey@...24...>
>> Cc: "Mishkin, Alec S" <amishkin@...1447...>,
>>       "lammps-users@lists.sourceforge.net"
>>       <lammps-users@lists.sourceforge.net>
>> Message-ID:
>>       <CAENuAmHtsMxKPEQ5dzTHWoZM7VaJfBO+sa0mc1LhB=2Hxe7wjA@...25...>
>> Content-Type: text/plain; charset="utf-8"
>>
>> The examples/COUPLE/fortran2 one is the newer of the examples.
>> We'll be adding a fortran3 one soon, which was recently contributed.
>>
>> Steve
>>
>> On Wed, May 3, 2017 at 4:45 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>>
>>>
>>>
>>> On Tue, May 2, 2017 at 11:10 PM, Mishkin,Alec S <amishkin@...1447...> wrote:
>>>
>>>> Hello,
>>>>
>>>> I am using reverse monte carlo code written in Fortran for a simulation
>>>> and would like to use lammps to calculate energy. I would like to do this
>>>> by calling lammps inside my fortran code. To test I wrote a very small
>>>> fortran code that is supposed to start lammps. Unfortunately, whenever I
>>>> try to compile it i get errors. Any assistance would be appreciated.
>>>>
>>> it is not at all surprising that your compiler refused to compile this,
>>> since ?your code is not valid fortran 2003 syntax in several ways and also
>>> not correctly doing the interfacing in places, where the syntax is correct.?
>>> ?
>>> ? ?you need significant help from a fortran expert knowledgeable in using
>>> the ISO_C_BINDINGS module.
>>>
>>> ?
>>> please note, that ?there are ?two examples of fortran wrappers in the
>>> "example/COUPLE/" folder. however, those have not been updated in many
>>> years while there have been some changes to the library interface, so they
>>> are not likely to function completely.
>>>
>>> ?axel.?
>>>
>>>>
>>>> The code I am trying to compile is:
>>>>
>>>>
>>>> Program adder
>>>> IMPLICIT NONE
>>>>
>>>> !void lammps_open_no_mpi(int argc, char **argv, void **ptr)
>>>> !int sally[2][3]  = {{2,3,4},{5,6,7}};
>>>> !char start_ups[][] = [['-l'], ['log' ]] ;
>>>> !character(1) , dimension (2) ::  argv
>>>> INTERFACE
>>>>        SUBROUTINE lammps_open_no_mpi(argc, argv, ptr) BIND(C)
>>>>                USE, INTRINSIC :: ISO_C_BINDING, only : C_char, C_ptr,
>>>> C_int
>>>>                INTEGER (C_INT) :: argc
>>>>                CHARACTER (C_CHAR ) :: argv
>>>>                POINTER (C_ptr) :: ptr
>>>>         END SUBROUTINE lammps_open_no_mpi
>>>> END INTERFACE
>>>>        integer a,b
>>>>
>>>>        a = 1
>>>>        b = 2
>>>>        call lammps_open_no_mpi(1 ,'lmp -log log.simple' , &void)
>>>>
>>>>
>>>>        PRINT *, 'Hello World'
>>>> end Program
>>>>
>>>> The error message I am getting is
>>>>
>>>> adder.f90(13): error #5082: Syntax error, found ')' when expecting one
>>>> of: ,
>>>>                POINTER (C_ptr) :: ptr
>>>> ------------------------------^
>>>> adder.f90(20): error #5082: Syntax error, found IDENTIFIER 'VOID' when
>>>> expecting one of: <POUND_VAL> <INTEGER_KIND_CON> <POUND_BASE>
>>>> <INTEGER_CONSTANT>
>>>>        call lammps_open_no_mpi(1 ,'lmp -log log.simple' , &void)
>>>>
>>>> I am using mpif90 adder.f90 to compile it.
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> lammps-users mailing list
>>>> lammps-users@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>>>
>>>>
>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> lammps-users mailing list
>>> lammps-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>>
>>>
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>> ------------------------------
>>
>> Message: 7
>> Date: Thu, 4 May 2017 16:39:14 -0600
>> From: Steve Plimpton <sjplimp@...24...>
>> Subject: Re: [lammps-users] Energy discrepancy when using fix
>>       box/relax in triclinic boxes
>> To: Axel Kohlmeyer <akohlmey@...24...>
>> Cc: LAMMPS Users Mailing List <lammps-users@lists.sourceforge.net>
>> Message-ID:
>>       <CAENuAmGcm95X1=s5fOKj7L0qU63HTPQLC7EtmbUKY=TBgf=SDg@...462....>
>> Content-Type: text/plain; charset="utf-8"
>>
>> I'll add that the examples/min/in.min.box shows how
>> to setup your thermo output so that you see the
>> pe (for atoms), the delta added by fix box/relax, and
>> the pe (for atoms + box equation) that is used by the minimizer.
>>
>> The last quantity should agree with what the minimizer
>> stats print out at the end.
>>
>> Steve
>>
>> On Wed, May 3, 2017 at 1:32 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>>
>>>
>>>
>>> On Wed, May 3, 2017 at 11:08 AM, Martinez Saez, Enrique <enriquem@...1745...5...
>>>> wrote:
>>>
>>>> Hi Axel,
>>>>
>>>> It is indeed explained in the documentation. Maybe issuing a warning when
>>>> using box/relax will help the users.
>>>>
>>>
>>> the LAMMPS philosophy in general is to provide explanations and
>>> (conceptual) warnings in the documentation rather than in the code.
>>> however, the case of fix box/relax is somewhat different from how fix
>>> energies are handled in LAMMPS, so i think printing a warning may be
>>> justified here. it is conceptually not different from the warning about
>>> resetting neighbor list parameters during minimization.
>>>
>>> although, the _consistent_ solution, would be to have fix box/relax
>>> respond to fix_modify energy yes and then make fix box/relax print a
>>> warning, when it is called without this proper fix_modify setting. however,
>>> since this breaks backward compatibility for a lot of cases, i am hesitant
>>> to implement such a change without a detailed discussion with other LAMMPS
>>> developers (cc: steve & aidan).
>>>
>>> i am attaching a patch that implements an informational warning as
>>> suggested, that can be included without changing LAMMPS' behavior.
>>>
>>> ?this will change the output to something like this:
>>>
>>> minimize 0.0 1e-4 10000 100000
>>> WARNING: Resetting reneighboring criteria during minimization
>>> (../min.cpp:168)
>>> Setting up cg style minimization ...
>>>  Unit style    : metal
>>>  Current step  : 919
>>> WARNING: Energy due to 6 extra global DOFs will be included in minimizer
>>> energies
>>> Per MPI rank memory allocation (min/avg/max) = 7.512 | 7.516 | 7.52 Mbytes
>>> Step Temp E_pair E_mol TotEng Press Volume
>>>     919            0   -11604.619            0   -11604.619  -0.91658651
>>>   175219.93
>>>     920            0   -11604.619            0   -11604.619  -0.91658651
>>>   175219.93
>>> Loop time of 0.1029 on 8 procs for 1 steps with 7656 atoms
>>>
>>> ?please note, that you can access the energy contributed by the fix
>>> through a global scalar property. e.g. via:
>>>
>>> variable etot equal etotal+f_relax
>>>
>>> axel.?
>>>
>>>
>>>>
>>>> Thanks,
>>>> Enrique
>>>> ----------------------------------------
>>>> Enrique Martinez Saez
>>>> MST-8, MS G755
>>>> Los Alamos National Laboratory
>>>> Los Alamos, NM, 87544
>>>> Ph: 505 606 2149 <(505)%20606-2149>
>>>> Fax: 505 667 8021 <(505)%20667-8021>
>>>> enriquem@...795...
>>>> http://enriquemasa.snack.ws
>>>>
>>>>
>>>>
>>>>
>>>> On May 2, 2017, at 12:54 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>>>>
>>>>
>>>>
>>>> On Tue, May 2, 2017 at 1:18 PM, Martinez Saez, Enrique <enriquem@...1745...5...
>>>>> wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>> I am having a disturbing discrepancy between energies at the end of a
>>>>> minimization when using fix box/relax in triclinic boxes. Here is an
>>>>> example:
>>>>>
>>>>> Total # of neighbors = 570502
>>>>> Ave neighs/atom = 74.517
>>>>> Neighbor list builds = 0
>>>>> Dangerous builds = 0
>>>>> WARNING: Resetting reneighboring criteria during minimization
>>>>> (../min.cpp:168)
>>>>> Setting up cg style minimization ...
>>>>>  Unit style    : metal
>>>>> Memory usage per processor = 7.24358 Mbytes
>>>>> Step Temp E_pair E_mol TotEng Press Volume
>>>>>     919            0   -11604.619            0   -11604.619
>>>>> -0.91658651    175219.93
>>>>>     920            0   -11604.619            0   -11604.619
>>>>> -0.91658651    175219.93
>>>>> Loop time of 0.0569309 on 32 procs for 1 steps with 7656 atoms
>>>>>
>>>>> 78.9% CPU use with 32 MPI tasks x no OpenMP threads
>>>>>
>>>>> Minimization stats:
>>>>>  Stopping criterion = linesearch alpha is zero
>>>>>  Energy initial, next-to-last, final =
>>>>>        -11701.1483369     -11701.1483369     -11701.1483369
>>>>>  Force two-norm initial, final = 6.88862 6.88862
>>>>>  Force max component initial, final = 1.27913 1.27913
>>>>>  Final line search alpha, max atom move = 1.49113e-10 1.90735e-10
>>>>>  Iterations, force evaluations = 1 20
>>>>>
>>>>> The numbers highlighted in red are the source of the discrepancy. After
>>>>> minimizing I do run 0 and the energy that I get is the same as in the last
>>>>> step of the minimization (-11604.619 in this case). The problem is that as
>>>>> you see the difference might be pretty large and might change the results
>>>>> qualitatively. Which energy should I take?
>>>>>
>>>>
>>>> ?the difference is due to your use of fix box/relax. in the fix box/relax
>>>> documentation, it is mentioned, that the energy for the minimizer is
>>>> augmented by the fix. there is more information about what is happening. i
>>>> suggest you check the docs again and the referenced equations and paper?
>>>> and explanations and then make an educated decision.
>>>>
>>>> ?axel?
>>>>
>>>>
>>>>
>>>>>
>>>>> I am attaching an input file, data file and output for you to check.
>>>>>
>>>>> Thanks a lot,
>>>>> Best,
>>>>> Enrique
>>>>>
>>>>> ------------------------------------------------------------
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>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
>>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>
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-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.