The potential energy change due to this fix is stored as a scalar +
The cummulative energy change due to this fix is stored as a scalar quantity, which can be accessed by various output commands. The scalar value calculated by this fix is "extensive", meaning it scales with the number of atoms in diff -Naur lammps-6May09/doc/fix_nph.txt lammps-12May09/doc/fix_nph.txt --- lammps-6May09/doc/fix_nph.txt 2008-05-13 15:46:42.000000000 -0600 +++ lammps-12May09/doc/fix_nph.txt 2009-05-12 07:33:47.000000000 -0600 @@ -177,7 +177,7 @@ the system's potential energy as part of "thermodynamic output"_thermo_style.html. -The potential energy change due to this fix is stored as a scalar +The cummulative energy change due to this fix is stored as a scalar quantity, which can be accessed by various "output commands"_Section_howto.html#4_15. The scalar value calculated by this fix is "extensive", meaning it scales with the number of atoms in diff -Naur lammps-6May09/doc/fix_npt.html lammps-12May09/doc/fix_npt.html --- lammps-6May09/doc/fix_npt.html 2008-05-13 15:46:42.000000000 -0600 +++ lammps-12May09/doc/fix_npt.html 2009-05-12 07:33:47.000000000 -0600 @@ -224,7 +224,7 @@ barostatting to the system's potential energy as part of thermodynamic output.
-The potential energy change due to this fix is stored as a scalar +
The cummulative energy change due to this fix is stored as a scalar quantity, which can be accessed by various output commands. The scalar value calculated by this fix is "extensive", meaning it scales with the number of atoms in diff -Naur lammps-6May09/doc/fix_npt.txt lammps-12May09/doc/fix_npt.txt --- lammps-6May09/doc/fix_npt.txt 2008-05-13 15:46:42.000000000 -0600 +++ lammps-12May09/doc/fix_npt.txt 2009-05-12 07:33:47.000000000 -0600 @@ -213,7 +213,7 @@ barostatting to the system's potential energy as part of "thermodynamic output"_thermo_style.html. -The potential energy change due to this fix is stored as a scalar +The cummulative energy change due to this fix is stored as a scalar quantity, which can be accessed by various "output commands"_Section_howto.html#4_15. The scalar value calculated by this fix is "extensive", meaning it scales with the number of atoms in diff -Naur lammps-6May09/doc/fix_npt_asphere.html lammps-12May09/doc/fix_npt_asphere.html --- lammps-6May09/doc/fix_npt_asphere.html 2008-05-13 15:46:42.000000000 -0600 +++ lammps-12May09/doc/fix_npt_asphere.html 2009-05-12 07:33:47.000000000 -0600 @@ -198,9 +198,11 @@ barostatting to the system's potential energy as part of thermodynamic output.
-The potential energy change due to this fix is stored as a scalar +
The cummulative energy change due to this fix is stored as a scalar quantity, which can be accessed by various output -commands. +commands. The scalar value calculated by +this fix is "extensive", meaning it scales with the number of atoms in +the simulation.
This fix can ramp its target temperature and pressure over multiple runs, using the start and stop keywords of the run diff -Naur lammps-6May09/doc/fix_npt_asphere.txt lammps-12May09/doc/fix_npt_asphere.txt --- lammps-6May09/doc/fix_npt_asphere.txt 2008-05-13 15:46:42.000000000 -0600 +++ lammps-12May09/doc/fix_npt_asphere.txt 2009-05-12 07:33:47.000000000 -0600 @@ -187,9 +187,11 @@ barostatting to the system's potential energy as part of "thermodynamic output"_thermo_style.html. -The potential energy change due to this fix is stored as a scalar +The cummulative energy change due to this fix is stored as a scalar quantity, which can be accessed by various "output -commands"_Section_howto.html#4_15. +commands"_Section_howto.html#4_15. The scalar value calculated by +this fix is "extensive", meaning it scales with the number of atoms in +the simulation. This fix can ramp its target temperature and pressure over multiple runs, using the {start} and {stop} keywords of the "run"_run.html diff -Naur lammps-6May09/doc/fix_npt_sphere.html lammps-12May09/doc/fix_npt_sphere.html --- lammps-6May09/doc/fix_npt_sphere.html 2008-05-13 15:46:42.000000000 -0600 +++ lammps-12May09/doc/fix_npt_sphere.html 2009-05-12 07:33:47.000000000 -0600 @@ -200,9 +200,11 @@ barostatting to the system's potential energy as part of thermodynamic output.
-The potential energy change due to this fix is stored as a scalar -quantity, which can be accessed by various output -commands. +
The potential cummulative energy change due to this fix is stored as a +scalar quantity, which can be accessed by various output +commands. The scalar value calculated by +this fix is "extensive", meaning it scales with the number of atoms in +the simulation.
This fix can ramp its target temperature and pressure over multiple runs, using the start and stop keywords of the run diff -Naur lammps-6May09/doc/fix_npt_sphere.txt lammps-12May09/doc/fix_npt_sphere.txt --- lammps-6May09/doc/fix_npt_sphere.txt 2008-05-13 15:46:42.000000000 -0600 +++ lammps-12May09/doc/fix_npt_sphere.txt 2009-05-12 07:33:47.000000000 -0600 @@ -189,9 +189,11 @@ barostatting to the system's potential energy as part of "thermodynamic output"_thermo_style.html. -The potential energy change due to this fix is stored as a scalar -quantity, which can be accessed by various "output -commands"_Section_howto.html#4_15. +The potential cummulative energy change due to this fix is stored as a +scalar quantity, which can be accessed by various "output +commands"_Section_howto.html#4_15. The scalar value calculated by +this fix is "extensive", meaning it scales with the number of atoms in +the simulation. This fix can ramp its target temperature and pressure over multiple runs, using the {start} and {stop} keywords of the "run"_run.html diff -Naur lammps-6May09/doc/fix_nvt.html lammps-12May09/doc/fix_nvt.html --- lammps-6May09/doc/fix_nvt.html 2008-04-04 15:15:50.000000000 -0600 +++ lammps-12May09/doc/fix_nvt.html 2009-05-12 07:33:47.000000000 -0600 @@ -133,7 +133,7 @@ the system's potential energy as part of thermodynamic output.
-The potential energy change due to this fix is stored as a scalar +
The cummulative energy change due to this fix is stored as a scalar quantity, which can be accessed by various output commands. The scalar value calculated by this fix is "extensive", meaning it scales with the number of atoms in diff -Naur lammps-6May09/doc/fix_nvt.txt lammps-12May09/doc/fix_nvt.txt --- lammps-6May09/doc/fix_nvt.txt 2008-04-04 15:15:50.000000000 -0600 +++ lammps-12May09/doc/fix_nvt.txt 2009-05-12 07:33:47.000000000 -0600 @@ -124,7 +124,7 @@ the system's potential energy as part of "thermodynamic output"_thermo_style.html. -The potential energy change due to this fix is stored as a scalar +The cummulative energy change due to this fix is stored as a scalar quantity, which can be accessed by various "output commands"_Section_howto.html#4_15. The scalar value calculated by this fix is "extensive", meaning it scales with the number of atoms in diff -Naur lammps-6May09/doc/fix_nvt_asphere.html lammps-12May09/doc/fix_nvt_asphere.html --- lammps-6May09/doc/fix_nvt_asphere.html 2008-03-19 16:51:12.000000000 -0600 +++ lammps-12May09/doc/fix_nvt_asphere.html 2009-05-12 07:33:47.000000000 -0600 @@ -122,9 +122,11 @@ the system's potential energy as part of thermodynamic output.
-The potential energy change due to this fix is stored as a scalar +
The cummulative energy change due to this fix is stored as a scalar quantity, which can be accessed by various output -commands. +commands. The scalar value calculated by +this fix is "extensive", meaning it scales with the number of atoms in +the simulation.
This fix can ramp its target temperature over multiple runs, using the start and stop keywords of the run command. See the diff -Naur lammps-6May09/doc/fix_nvt_asphere.txt lammps-12May09/doc/fix_nvt_asphere.txt --- lammps-6May09/doc/fix_nvt_asphere.txt 2008-03-19 16:51:12.000000000 -0600 +++ lammps-12May09/doc/fix_nvt_asphere.txt 2009-05-12 07:33:47.000000000 -0600 @@ -113,9 +113,11 @@ the system's potential energy as part of "thermodynamic output"_thermo_style.html. -The potential energy change due to this fix is stored as a scalar +The cummulative energy change due to this fix is stored as a scalar quantity, which can be accessed by various "output -commands"_Section_howto.html#4_15. +commands"_Section_howto.html#4_15. The scalar value calculated by +this fix is "extensive", meaning it scales with the number of atoms in +the simulation. This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff -Naur lammps-6May09/doc/fix_nvt_sllod.html lammps-12May09/doc/fix_nvt_sllod.html --- lammps-6May09/doc/fix_nvt_sllod.html 2008-03-19 16:51:12.000000000 -0600 +++ lammps-12May09/doc/fix_nvt_sllod.html 2009-05-12 07:33:47.000000000 -0600 @@ -141,9 +141,11 @@ the system's potential energy as part of thermodynamic output.
-The potential energy change due to this fix is stored as a scalar +
The cummulative energy change due to this fix is stored as a scalar quantity, which can be accessed by various output -commands. +commands. The scalar value calculated by +this fix is "extensive", meaning it scales with the number of atoms in +the simulation.
This fix can ramp its target temperature over multiple runs, using the start and stop keywords of the run command. See the diff -Naur lammps-6May09/doc/fix_nvt_sllod.txt lammps-12May09/doc/fix_nvt_sllod.txt --- lammps-6May09/doc/fix_nvt_sllod.txt 2008-03-19 16:51:12.000000000 -0600 +++ lammps-12May09/doc/fix_nvt_sllod.txt 2009-05-12 07:33:47.000000000 -0600 @@ -132,9 +132,11 @@ the system's potential energy as part of "thermodynamic output"_thermo_style.html. -The potential energy change due to this fix is stored as a scalar +The cummulative energy change due to this fix is stored as a scalar quantity, which can be accessed by various "output -commands"_Section_howto.html#4_15. +commands"_Section_howto.html#4_15. The scalar value calculated by +this fix is "extensive", meaning it scales with the number of atoms in +the simulation. This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff -Naur lammps-6May09/doc/fix_nvt_sphere.html lammps-12May09/doc/fix_nvt_sphere.html --- lammps-6May09/doc/fix_nvt_sphere.html 2008-03-19 16:51:12.000000000 -0600 +++ lammps-12May09/doc/fix_nvt_sphere.html 2009-05-12 07:33:47.000000000 -0600 @@ -125,9 +125,11 @@ the system's potential energy as part of thermodynamic output.
-The potential energy change due to this fix is stored as a scalar +
The cummulative energy change due to this fix is stored as a scalar quantity, which can be accessed by various output -commands. +commands. The scalar value calculated by +this fix is "extensive", meaning it scales with the number of atoms in +the simulation.
This fix can ramp its target temperature over multiple runs, using the start and stop keywords of the run command. See the diff -Naur lammps-6May09/doc/fix_nvt_sphere.txt lammps-12May09/doc/fix_nvt_sphere.txt --- lammps-6May09/doc/fix_nvt_sphere.txt 2008-03-19 16:51:12.000000000 -0600 +++ lammps-12May09/doc/fix_nvt_sphere.txt 2009-05-12 07:33:47.000000000 -0600 @@ -116,9 +116,11 @@ the system's potential energy as part of "thermodynamic output"_thermo_style.html. -The potential energy change due to this fix is stored as a scalar +The cummulative energy change due to this fix is stored as a scalar quantity, which can be accessed by various "output -commands"_Section_howto.html#4_15. +commands"_Section_howto.html#4_15. The scalar value calculated by +this fix is "extensive", meaning it scales with the number of atoms in +the simulation. This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff -Naur lammps-6May09/doc/fix_temp_rescale.html lammps-12May09/doc/fix_temp_rescale.html --- lammps-6May09/doc/fix_temp_rescale.html 2008-04-04 15:15:50.000000000 -0600 +++ lammps-12May09/doc/fix_temp_rescale.html 2009-05-12 07:33:47.000000000 -0600 @@ -114,20 +114,14 @@
The fix_modify energy option is supported by this fix to add the energy change implied by a velocity rescaling to the system's potential energy as part of thermodynamic -output. Note that because this fix is invoked -every N steps and thermodynamic info is printed every M steps, that -unless M is a multiple of N, the energy contribution will be zero. +output.
-The potential energy change due to this fix is stored as a scalar +
The cummulative energy change due to this fix is stored as a scalar quantity, which can be accessed by various output commands. The scalar value calculated by this fix is "extensive", meaning it scales with the number of atoms in the simulation.
-The energy change can be printed as part of thermodynamic output via -the keyword f_ID, where ID is the fix-ID of this fix. See the -thermo_style custom command for details. -
This fix can ramp its target temperature over multiple runs, using the start and stop keywords of the run command. See the run command for details of how to do this. diff -Naur lammps-6May09/doc/fix_temp_rescale.txt lammps-12May09/doc/fix_temp_rescale.txt --- lammps-6May09/doc/fix_temp_rescale.txt 2008-04-04 15:15:50.000000000 -0600 +++ lammps-12May09/doc/fix_temp_rescale.txt 2009-05-12 07:33:47.000000000 -0600 @@ -111,20 +111,14 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this fix to add the energy change implied by a velocity rescaling to the system's potential energy as part of "thermodynamic -output"_thermo_style.html. Note that because this fix is invoked -every N steps and thermodynamic info is printed every M steps, that -unless M is a multiple of N, the energy contribution will be zero. +output"_thermo_style.html. -The potential energy change due to this fix is stored as a scalar +The cummulative energy change due to this fix is stored as a scalar quantity, which can be accessed by various "output commands"_Section_howto.html#4_15. The scalar value calculated by this fix is "extensive", meaning it scales with the number of atoms in the simulation. -The energy change can be printed as part of thermodynamic output via -the keyword f_ID, where ID is the fix-ID of this fix. See the -"thermo_style custom"_thermo_style.html command for details. - This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the "run"_run.html command for details of how to do this. diff -Naur lammps-6May09/doc/pair_gran.html lammps-12May09/doc/pair_gran.html --- lammps-6May09/doc/pair_gran.html 2009-01-08 16:18:29.000000000 -0700 +++ lammps-12May09/doc/pair_gran.html 2009-05-12 07:34:00.000000000 -0600 @@ -50,10 +50,11 @@
Description:
The gran styles use the following formulas for the frictional force -between two granular particles, as described in (Silbert) -and in (Zhang), when the distance r between two particles of -radii Ri and Rj is less than their contact distance d = Ri + Rj. -There is no force between the particles when r > d. +between two granular particles, as described in +(Brilliantov), (Silbert), and +(Zhang), when the distance r between two particles of radii +Ri and Rj is less than their contact distance d = Ri + Rj. There is +no force between the particles when r > d.
The two Hookean styles use this formula:
@@ -196,6 +197,11 @@(Brilliantov) Brilliantov, Spahn, Hertzsch, Poschel, Phys Rev E, 53, +p 5382-5392 (1996). +
(Silbert) Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev diff -Naur lammps-6May09/doc/pair_gran.txt lammps-12May09/doc/pair_gran.txt --- lammps-6May09/doc/pair_gran.txt 2009-01-08 16:18:29.000000000 -0700 +++ lammps-12May09/doc/pair_gran.txt 2009-05-12 07:34:00.000000000 -0600 @@ -39,10 +39,11 @@ [Description:] The {gran} styles use the following formulas for the frictional force -between two granular particles, as described in "(Silbert)"_#Silbert -and in "(Zhang)"_#Zhang, when the distance r between two particles of -radii Ri and Rj is less than their contact distance d = Ri + Rj. -There is no force between the particles when r > d. +between two granular particles, as described in +"(Brilliantov)"_#Brilliantov, "(Silbert)"_#Silbert, and +"(Zhang)"_#Zhang, when the distance r between two particles of radii +Ri and Rj is less than their contact distance d = Ri + Rj. There is +no force between the particles when r > d. The two Hookean styles use this formula: @@ -186,6 +187,10 @@ :line +:link(Brilliantov) +[(Brilliantov)] Brilliantov, Spahn, Hertzsch, Poschel, Phys Rev E, 53, +p 5382-5392 (1996). + :link(Silbert) [(Silbert)] Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev E, 64, p 051302 (2001). diff -Naur lammps-6May09/src/fix_temp_rescale.cpp lammps-12May09/src/fix_temp_rescale.cpp --- lammps-6May09/src/fix_temp_rescale.cpp 2008-07-28 08:14:31.000000000 -0600 +++ lammps-12May09/src/fix_temp_rescale.cpp 2009-05-12 07:24:20.000000000 -0600 @@ -101,7 +101,6 @@ temperature->init(); // not yet called by Modify::init() efactor = (0.5 * force->boltz * temperature->dof); - energy = 0.0; } /* ---------------------------------------------------------------------- */ @@ -149,7 +148,7 @@ } } - } else energy = 0.0; + } } /* ---------------------------------------------------------------------- */