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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@907 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2007-09-27 23:25:52 +00:00
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15
doc/Manual.html
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@ -1,4 +1,13 @@
<HTML>
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="Large-scale Atomic/Molecular Massively Parallel Simulator">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
<BODY>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
@ -116,6 +125,8 @@ it gives quick access to documentation for all LAMMPS commands.
4.13 <A HREF = "Section_howto.html#4_13">NEMD simulations</A>
<BR>
4.14 <A HREF = "Section_howto.html#4_14">Aspherical particles</A>
<BR>
4.15 <A HREF = "Section_howto.html#4_15">Output from LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_example.html">Example problems</A>
@ -214,5 +225,9 @@ it gives quick access to documentation for all LAMMPS commands.
</BODY>
</HTML>

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15
doc/Manual.txt
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@ -1,3 +1,12 @@
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="Large-scale Atomic/Molecular Massively Parallel Simulator">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
<BODY>
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
@ -77,7 +86,8 @@ it gives quick access to documentation for all LAMMPS commands.
4.11 "Visualizing LAMMPS snapshots"_4_11 :b
4.12 "Non-orthogonal simulation boxes"_4_12 :b
4.13 "NEMD simulations"_4_13 :b
4.14 "Aspherical particles"_4_14 :ule,b
4.14 "Aspherical particles"_4_14 :b
4.15 "Output from LAMMPS"_4_15 :ule,b
"Example problems"_Section_example.html :l
"Performance & scalability"_Section_perf.html :l
"Additional tools"_Section_tools.html :l
@ -126,6 +136,7 @@ it gives quick access to documentation for all LAMMPS commands.
:link(4_12,Section_howto.html#4_12)
:link(4_13,Section_howto.html#4_13)
:link(4_14,Section_howto.html#4_14)
:link(4_15,Section_howto.html#4_15)
:link(9_1,Section_errors.html#9_1)
:link(9_2,Section_errors.html#9_2)
@ -133,3 +144,5 @@ it gives quick access to documentation for all LAMMPS commands.
:link(10_1,Section_history.html#10_1)
:link(10_2,Section_history.html#10_2)
</BODY>

40
doc/Section_commands.html
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@ -295,7 +295,7 @@ included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "angle_coeff.html">angle_coeff</A></TD><TD ><A HREF = "angle_style.html">angle_style</A></TD><TD ><A HREF = "atom_modify.html">atom_modify</A></TD><TD ><A HREF = "atom_style.html">atom_style</A></TD><TD ><A HREF = "bond_coeff.html">bond_coeff</A></TD><TD ><A HREF = "bond_style.html">bond_style</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "boundary.html">boundary</A></TD><TD ><A HREF = "change_box.html">change_box</A></TD><TD ><A HREF = "clear.html">clear</A></TD><TD ><A HREF = "communicate.html">communicate</A></TD><TD ><A HREF = "compute.html">compute</A></TD><TD ><A HREF = "compute_modify.html">compute_modify</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "create_atoms.html">create_atoms</A></TD><TD ><A HREF = "create_box.html">create_box</A></TD><TD ><A HREF = "delete_atoms.html">delete_atoms</A></TD><TD ><A HREF = "delete_bonds.html">delete_bonds</A></TD><TD ><A HREF = "dielectric.html">dielectric</A></TD><TD ><A HREF = "dihedral_coeff.html">dihedral_coeff</A></TD></TR>
@ -317,14 +317,14 @@ in the command's documentation.
descriptions of each style or click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gran_diag.html">gran/diag</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_dipole.html">nve/dipole</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gran_diag.html">gran/diag</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_dipole.html">nve/dipole</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
</TD></TR></TABLE></DIV>
<HR>
@ -333,11 +333,11 @@ description:
descriptions of each style or click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_ebond_atom.html">ebond/atom</A></TD><TD ><A HREF = "compute_epair_atom.html">epair/atom</A></TD><TD ><A HREF = "compute_etotal_atom.html">etotal/atom</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_dipole.html">temp/dipole</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_variable.html">variable</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_variable_atom.html">variable/atom</A>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_attribute_atom.html">attribute/atom</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_ebond_atom.html">ebond/atom</A></TD><TD ><A HREF = "compute_epair_atom.html">epair/atom</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_sum_atom.html">sum/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_dipole.html">temp/dipole</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_variable.html">variable</A></TD><TD ><A HREF = "compute_variable_atom.html">variable/atom</A>
</TD></TR></TABLE></DIV>
<HR>
@ -346,7 +346,7 @@ description:
for an overview of pair potentials. Click on the style itself for a
full description:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_airebo.html">airebo</A></TD><TD ><A HREF = "pair_buck.html">buck</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/cut</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long</A></TD><TD ><A HREF = "pair_colloid.html">colloid</A></TD><TD ><A HREF = "pair_dipole/cut.html">dipole/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd</A></TD><TD ><A HREF = "pair_eam.html">eam</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD></TR>
@ -366,7 +366,7 @@ full description:
for an overview of bond potentials. Click on the style itself for a
full description:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_none.html">none</A></TD><TD WIDTH="100"><A HREF = "bond_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "bond_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "bond_fene.html">fene</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_fene_expand.html">fene/expand</A></TD><TD WIDTH="100"><A HREF = "bond_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "bond_morse.html">morse</A></TD><TD WIDTH="100"><A HREF = "bond_nonlinear.html">nonlinear</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_quartic.html">quartic</A>
@ -378,7 +378,7 @@ full description:
command for an overview of angle potentials. Click on the style
itself for a full description:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_none.html">none</A></TD><TD WIDTH="100"><A HREF = "angle_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "angle_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "angle_class2.html">class2</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_cosine.html">cosine</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_squared.html">cosine/squared</A></TD><TD WIDTH="100"><A HREF = "angle_harmonic.html">harmonic</A>
</TD></TR></TABLE></DIV>
@ -390,7 +390,7 @@ itself for a full description:
dihedral potentials. Click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_none.html">none</A></TD><TD WIDTH="100"><A HREF = "dihedral_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "dihedral_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "dihedral_class2.html">class2</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "dihedral_helix.html">helix</A></TD><TD WIDTH="100"><A HREF = "dihedral_multi_harmonic.html">multi/harmonic</A></TD><TD WIDTH="100"><A HREF = "dihedral_opls.html">opls</A>
</TD></TR></TABLE></DIV>
@ -402,7 +402,7 @@ description:
improper potentials. Click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_none.html">none</A></TD><TD WIDTH="100"><A HREF = "improper_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "improper_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "improper_cvff.html">cvff</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_harmonic.html">harmonic</A>
</TD></TR></TABLE></DIV>
@ -413,7 +413,7 @@ description:
an overview of Kspace solvers. Click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">ewald</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm/tip4p</A>
</TD></TR></TABLE></DIV>

4
doc/Section_commands.txt
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@ -378,6 +378,7 @@ description:
"addforce"_fix_addforce.html,
"aveforce"_fix_aveforce.html,
"ave/atom"_fix_ave_atom.html,
"ave/spatial"_fix_ave_spatial.html,
"ave/time"_fix_ave_time.html,
"com"_fix_com.html,
@ -436,16 +437,17 @@ Compute commands. See the "compute"_compute.html command for one-line
descriptions of each style or click on the style itself for a full
description:
"attribute/atom"_compute_attribute_atom.html,
"centro/atom"_compute_centro_atom.html,
"coord/atom"_compute_coord_atom.html,
"ebond/atom"_compute_ebond_atom.html,
"epair/atom"_compute_epair_atom.html,
"etotal/atom"_compute_etotal_atom.html,
"ke/atom"_compute_ke_atom.html,
"pressure"_compute_pressure.html,
"rotate/dipole"_compute_rotate_dipole.html,
"rotate/gran"_compute_rotate_gran.html,
"stress/atom"_compute_stress_atom.html,
"sum/atom"_compute_sum_atom.html,
"temp"_compute_temp.html,
"temp/deform"_compute_temp_deform.html,
"temp/asphere"_compute_temp_asphere.html,

2
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@ -30,7 +30,7 @@ Site</A>.
</P>
<P>These are the sample problems in the examples sub-directories:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >colloid</TD><TD > big colloid particles in a small particle solvent, 2d system</TD></TR>
<TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR>
<TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR>

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doc/Section_howto.html
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@ -27,7 +27,8 @@ certain kinds of LAMMPS simulations.
4.11 <A HREF = "#4_11">Visualizing LAMMPS snapshots</A><BR>
4.12 <A HREF = "#4_12">Non-orthogonal simulation boxes</A><BR>
4.13 <A HREF = "#4_13">NEMD simulations</A><BR>
4.14 <A HREF = "#4_14">Aspherical particles</A> <BR>
4.14 <A HREF = "#4_14">Aspherical particles</A><BR>
4.15 <A HREF = "#4_15">Output from LAMMPS</A> <BR>
<P>The example input scripts included in the LAMMPS distribution and
highlighted in <A HREF = "Section_example.html">this section</A> also show how to
@ -793,6 +794,105 @@ lj/cut</A>.
</P>
<HR>
<A NAME = "4_15"></A><H4>4.15 Output from LAMMPS
</H4>
<P>There are two basic kinds of LAMMPS output. The first is
thermodynamic output, which is a list of quantities printed every few
timesteps to the screen and logfile. The second is dump files, which
contain snapshots of atoms and various per-atom values and are written
at a specified frequency. A simulation prints one set of
thermodynamic output; it may generate zero, or one, or multiple dump
files. LAMMPS gives you a variety of ways to determine what
quantities are computed and printed when thermodynamic info or dump
files are output. There are also two fixes which perform time and
spatial averaging of user-defined quantities, fix ave/time and fix
ave/spatial. These produce their own output files and are described
below.
</P>
<P>The frequency and format of thermodynamic output is set by the
<A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_style.html">thermo_style</A>, and
<A HREF = "thermo_modify.html">thermo_modify</A> commands. The
<A HREF = "themo_style.html">thermo_style</A> command also specifies what values are
calculated and written out. Pre-defined keywords can be specified
(e.g. press, etotal, etc) which include time-averaged versions of
temperature, pressure, and a few other variables (tave, pave, etc).
Three addtional kinds of keywords can also be specified (c_ID, f_ID,
v_name), where a <A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or
<A HREF = "variable.html">variable</A> provides the value(s) to be output. Each of
these are described in turn.
</P>
<P>In LAMMPS, a <A HREF = "compute.html">compute</A> comes in two flavors: ones that
compute one or more global values (e.g. temperature, kinetic energy
tensor) and ones that compute one or more per-atom values. Only the
former can be used for thermodynamic output. The user-defined ID of
the compute is used along with an optional subscript as part of the
<A HREF = "thermo_style.html">thermo_style</A> command. E.g. c_myTemp outputs the
single scalar value generated by the compute; c_myTemp[2] would
output the 2nd vector value.
</P>
<P><A HREF = "fix.html">Fixes</A> can also generate values to output with thermodynamic
output, e.g. the energy of an indenter's interaction with the
simulation atoms. These values are accessed via the same format as
compute's values, as f_ID or f_ID[N]. See the doc pages for
individual fix commands to see which ones generate global values that
can be output with thermodynamic info.
</P>
<P>Input script variables of various kinds are defined by the
<A HREF = "variable.html">variable</A> command. All kinds except the atom-style
variable can be used for thermodynamic output. A variable with name
"abc" is referenced in a thermo_style command as v_abc.
</P>
<P>The variable formula defined in the input script can contain math
functions (add, exp, etc), atom values (x[N], fx[N]), groups
quantities (mass(), vcm(), etc), references to thermodynamic
quantities (e.g. temp, volume, etc), or references to other variables
or <A HREF = "compute.html">computes</A>. Thus a variable is the most general way
to define some quantity you want calculated and output with
thermodynamic info.
</P>
<P>Dump file output is specified by the <A HREF = "dump.html">dump</A> and
<A HREF = "dump_modify.html">dump_modify</A> commands. There are several
pre-defined formats (dump atom, dump xtc, etc). There is also a <A HREF = "dump.html">dump
custom</A> format where you specify what values are output with
each atom. Pre-defined keywords can be specified (e.g. tag, type, x,
etc). Two additional kinds of keywords can also be specified (c_ID,
f_ID), where a <A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> provides the
values to be output.
</P>
<P><A HREF = "compute.html">Computes</A> that generate per-atom values can be accessed
by the dump custom command. These are computes that have the word
"atom" in their style name, e.g. ke/atom, stress/atom, etc. The
values are accessed as described above: c_myKE or c_myStress[2].
The <A HREF = "compute_variable_atom.html">compute variable/atom</A> command takes a
user-defined atom-style <A HREF = "variable.html">variable</A> as input and
calculates its value for each atom. Since this compute can be
accessed by the dump custom command, this is a general way to define
some quantity you want calculated and output in a dump file.
</P>
<P><A HREF = "fix.html">Fixes</A> can also generate values to output to dump files.
For example, the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command does
time-averaging of atom quantites, such as velocity or energy or stress
which can then be output in a dump file. These values are accessed as
describe above, as f_ID or f_ID[N].
</P>
<P>Two other fixes are of particular note for output. Neither produces
values for thermodynamic or dump output, rather they output their
results directly to a file.
</P>
<P>The <A HREF = "fix_ave_time.html">fix ave/time</A> command enables time-averaging of
global quantities like temperature or pressure. The global quantities
are calculated by a <A HREF = "compute.html">compute</A>.
</P>
<P>The <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command enables
spatial-averaging of per-atom quantities like per-atom energy or
stress. The per-atom quantities can be atom density (mass or number)
or be calculated by a by a <A HREF = "compute.html">compute</A>. They can also be
quantities calculated by <A HREF = "fix_ave_atom.html">fix ave/atom</A>, which means
you are effectively calculating a time average of a spatial average of
a time-averaged per-atom quantity.
</P>
<HR>
<A NAME = "Cornell"></A>
<P><B>(Cornell)</B> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,

102
doc/Section_howto.txt
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@ -24,7 +24,8 @@ certain kinds of LAMMPS simulations.
4.11 "Visualizing LAMMPS snapshots"_#4_11
4.12 "Non-orthogonal simulation boxes"_#4_12
4.13 "NEMD simulations"_#4_13
4.14 "Aspherical particles"_#4_14 :all(b)
4.14 "Aspherical particles"_#4_14
4.15 "Output from LAMMPS"_#4_15 :all(b)
The example input scripts included in the LAMMPS distribution and
highlighted in "this section"_Section_example.html also show how to
@ -786,6 +787,105 @@ lj/cut"_pair_lj.html.
:line
4.15 Output from LAMMPS :link(4_15),h4
There are two basic kinds of LAMMPS output. The first is
thermodynamic output, which is a list of quantities printed every few
timesteps to the screen and logfile. The second is dump files, which
contain snapshots of atoms and various per-atom values and are written
at a specified frequency. A simulation prints one set of
thermodynamic output; it may generate zero, or one, or multiple dump
files. LAMMPS gives you a variety of ways to determine what
quantities are computed and printed when thermodynamic info or dump
files are output. There are also two fixes which perform time and
spatial averaging of user-defined quantities, fix ave/time and fix
ave/spatial. These produce their own output files and are described
below.
The frequency and format of thermodynamic output is set by the
"thermo"_thermo.html, "thermo_style"_thermo_style.html, and
"thermo_modify"_thermo_modify.html commands. The
"thermo_style"_themo_style.html command also specifies what values are
calculated and written out. Pre-defined keywords can be specified
(e.g. press, etotal, etc) which include time-averaged versions of
temperature, pressure, and a few other variables (tave, pave, etc).
Three addtional kinds of keywords can also be specified (c_ID, f_ID,
v_name), where a "compute"_compute.html or "fix"_fix.html or
"variable"_variable.html provides the value(s) to be output. Each of
these are described in turn.
In LAMMPS, a "compute"_compute.html comes in two flavors: ones that
compute one or more global values (e.g. temperature, kinetic energy
tensor) and ones that compute one or more per-atom values. Only the
former can be used for thermodynamic output. The user-defined ID of
the compute is used along with an optional subscript as part of the
"thermo_style"_thermo_style.html command. E.g. c_myTemp outputs the
single scalar value generated by the compute; c_myTemp\[2\] would
output the 2nd vector value.
"Fixes"_fix.html can also generate values to output with thermodynamic
output, e.g. the energy of an indenter's interaction with the
simulation atoms. These values are accessed via the same format as
compute's values, as f_ID or f_ID\[N\]. See the doc pages for
individual fix commands to see which ones generate global values that
can be output with thermodynamic info.
Input script variables of various kinds are defined by the
"variable"_variable.html command. All kinds except the atom-style
variable can be used for thermodynamic output. A variable with name
"abc" is referenced in a thermo_style command as v_abc.
The variable formula defined in the input script can contain math
functions (add, exp, etc), atom values (x\[N\], fx\[N\]), groups
quantities (mass(), vcm(), etc), references to thermodynamic
quantities (e.g. temp, volume, etc), or references to other variables
or "computes"_compute.html. Thus a variable is the most general way
to define some quantity you want calculated and output with
thermodynamic info.
Dump file output is specified by the "dump"_dump.html and
"dump_modify"_dump_modify.html commands. There are several
pre-defined formats (dump atom, dump xtc, etc). There is also a "dump
custom"_dump.html format where you specify what values are output with
each atom. Pre-defined keywords can be specified (e.g. tag, type, x,
etc). Two additional kinds of keywords can also be specified (c_ID,
f_ID), where a "compute"_compute.html or "fix"_fix.html provides the
values to be output.
"Computes"_compute.html that generate per-atom values can be accessed
by the dump custom command. These are computes that have the word
"atom" in their style name, e.g. ke/atom, stress/atom, etc. The
values are accessed as described above: c_myKE or c_myStress\[2\].
The "compute variable/atom"_compute_variable_atom.html command takes a
user-defined atom-style "variable"_variable.html as input and
calculates its value for each atom. Since this compute can be
accessed by the dump custom command, this is a general way to define
some quantity you want calculated and output in a dump file.
"Fixes"_fix.html can also generate values to output to dump files.
For example, the "fix ave/atom"_fix_ave_atom.html command does
time-averaging of atom quantites, such as velocity or energy or stress
which can then be output in a dump file. These values are accessed as
describe above, as f_ID or f_ID\[N\].
Two other fixes are of particular note for output. Neither produces
values for thermodynamic or dump output, rather they output their
results directly to a file.
The "fix ave/time"_fix_ave_time.html command enables time-averaging of
global quantities like temperature or pressure. The global quantities
are calculated by a "compute"_compute.html.
The "fix ave/spatial"_fix_ave_spatial.html command enables
spatial-averaging of per-atom quantities like per-atom energy or
stress. The per-atom quantities can be atom density (mass or number)
or be calculated by a by a "compute"_compute.html. They can also be
quantities calculated by "fix ave/atom"_fix_ave_atom.html, which means
you are effectively calculating a time average of a spatial average of
a time-averaged per-atom quantity.
:line
:link(Cornell)
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).

8
doc/Section_intro.html
View File

@ -434,11 +434,9 @@ Computing, Minneapolis, MN (March 1997).
</P>
<P>If you use LAMMPS results in your published work, please cite the J
Comp Phys reference and include a pointer to the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>
(http://lammps.sandia.gov). A paper describing the latest version of
LAMMPS is in the works; when it appears in print, you can check the
<A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> for a more current citation.
(http://lammps.sandia.gov).
</P>
<P>If you send me information about your publication, I'll be pleased to
<P>If you send is information about your publication, we'll be pleased to
add it to the Publications page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>. Ditto
for a picture or movie for the Pictures or Movies pages.
</P>
@ -451,7 +449,7 @@ features in LAMMPS:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >Ewald and PPPM solvers</TD><TD > Roy Pollock (LLNL)</TD></TR>
<TR><TD >rRESPA</TD><TD > Mark Stevens & Paul Crozier (Sandia)</TD></TR>
<TR><TD >NVT/NPT integrators</TD><TD > Mark Stevens (Sandia)</TD></TR>

6
doc/Section_intro.txt
View File

@ -420,11 +420,9 @@ Computing, Minneapolis, MN (March 1997).
If you use LAMMPS results in your published work, please cite the J
Comp Phys reference and include a pointer to the "LAMMPS WWW Site"_lws
(http://lammps.sandia.gov). A paper describing the latest version of
LAMMPS is in the works; when it appears in print, you can check the
"LAMMPS WWW Site"_lws for a more current citation.
(http://lammps.sandia.gov).
If you send me information about your publication, I'll be pleased to
If you send is information about your publication, we'll be pleased to
add it to the Publications page of the "LAMMPS WWW Site"_lws. Ditto
for a picture or movie for the Pictures or Movies pages.

20
doc/Section_modify.html
View File

@ -147,7 +147,7 @@ atoms.
<P>Here is a brief description of methods you define in your new derived
class. See atom.h for details.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >grow</TD><TD > re-allocate atom arrays to longer lengths</TD></TR>
<TR><TD >copy</TD><TD > copy info for one atom to another atom's array locations</TD></TR>
<TR><TD >pack_comm</TD><TD > store an atom's info in a buffer communicated every timestep</TD></TR>
@ -187,7 +187,7 @@ commands.
bond class. See bond.h, angle.h, dihedral.h, and improper.h for
details.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >compute</TD><TD > compute the molecular interactions</TD></TR>
<TR><TD >coeff</TD><TD > set coefficients for one bond type</TD></TR>
<TR><TD >equilibrium_distance</TD><TD > length of bond, used by SHAKE</TD></TR>
@ -212,7 +212,7 @@ per-atom kinetic energy.
<P>Here is a brief description of methods you define in your new derived
class. See compute.h for details.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >compute_scalar</TD><TD > compute a scalar quantity</TD></TR>
<TR><TD >compute_vector</TD><TD > compute a vector of quantities</TD></TR>
<TR><TD >compute_peratom</TD><TD > compute one or more quantities per atom</TD></TR>
@ -239,7 +239,7 @@ DumpCustom class contained in the dump_custom.cpp file.
<P>Here is a brief description of methods you define in your new derived
class. See dump.h for details.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >write_header</TD><TD > write the header section of a snapshot of atoms</TD></TR>
<TR><TD >count</TD><TD > count the number of lines a processor will output</TD></TR>
<TR><TD >pack</TD><TD > pack a proc's output data into a buffer</TD></TR>
@ -277,7 +277,7 @@ implement.
<P>Here is a brief description of methods you can define in your new
derived class. See fix.h for details.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >setmask</TD><TD > determines when the fix is called during the timestep</TD></TR>
<TR><TD >init</TD><TD > initialization before a run</TD></TR>
<TR><TD >setup</TD><TD > called immediately before the 1st timestep</TD></TR>
@ -348,7 +348,7 @@ operations it wishes on LAMMPS data structures.
</P>
<P>The single method your new class must define is as follows:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >command</TD><TD > operations performed by the new command
</TD></TR></TABLE></DIV>
@ -368,7 +368,7 @@ styles can be created to add new K-space options to LAMMPS.
<P>Here is a brief description of methods you define in your new derived
class. See kspace.h for details.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >init</TD><TD > initialize the calculation before a run</TD></TR>
<TR><TD >setup</TD><TD > computation before the 1st timestep of a run</TD></TR>
<TR><TD >compute</TD><TD > every-timestep computation</TD></TR>
@ -388,7 +388,7 @@ LAMMPS.
<P>Here is a brief description of methods you define in your new derived
class. See min.h for details.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >init</TD><TD > initialize the minimization before a run</TD></TR>
<TR><TD >run</TD><TD > perform the minimization</TD></TR>
<TR><TD >memory_usage</TD><TD > tally of memory usage
@ -409,7 +409,7 @@ includes some optional methods to enable its use with rRESPA.
</P>
<P>Here is a brief description of the class methods in pair.h:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >compute</TD><TD > workhorse routine that computes pairwise interactions</TD></TR>
<TR><TD >settings</TD><TD > reads the input script line with arguments you define</TD></TR>
<TR><TD >coeff</TD><TD > set coefficients for one i,j type pair</TD></TR>
@ -437,7 +437,7 @@ styles can be created to add new region shapes to LAMMPS.
<P>Here is a brief description of methods you define in your new derived
class. See region.h for details.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >match</TD><TD > determine whether a point is in the region
</TD></TR></TABLE></DIV>

2
doc/Section_perf.html
View File

@ -56,7 +56,7 @@ For example, on a 1.7 GHz Pentium desktop machine (Intel icc compiler
under Red Hat Linux), the CPU run-time in seconds/atom/timestep for
the 5 problems is
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ALIGN ="right">Problem:</TD><TD > LJ</TD><TD > Chain</TD><TD > EAM</TD><TD > Chute</TD><TD > Rhodopsin</TD></TR>
<TR ALIGN="center"><TD ALIGN ="right">CPU/atom/step:</TD><TD > 4.55E-6</TD><TD > 2.18E-6</TD><TD > 9.38E-6</TD><TD > 2.18E-6</TD><TD > 1.11E-4</TD></TR>
<TR ALIGN="center"><TD ALIGN ="right">Ratio to LJ:</TD><TD > 1.0</TD><TD > 0.48</TD><TD > 2.06</TD><TD > 0.48</TD><TD > 24.5

4
doc/Section_start.html
View File

@ -37,7 +37,7 @@ tar xvf lammps*.tar
<P>This will create a LAMMPS directory containing two files and several
sub-directories:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >README</TD><TD > text file</TD></TR>
<TR><TD >LICENSE</TD><TD > the GNU General Public License (GPL)</TD></TR>
<TR><TD >bench</TD><TD > benchmark problems</TD></TR>
@ -273,7 +273,7 @@ fields for molecular systems or granular systems are in packages. You
can see the list of packages by typing "make package". The current
list of packages is as follows:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >asphere </TD><TD > aspherical particles and force fields</TD></TR>
<TR><TD >class2 </TD><TD > class 2 force fields</TD></TR>
<TR><TD >colloid </TD><TD > colloidal particle force fields</TD></TR>

42
doc/compute.html
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@ -30,18 +30,27 @@ compute 3 all ke/atom
</P>
<P>Create a computation that will be performed on a group of atoms.
</P>
<P>In LAMMPS, a "compute" is used in several ways. Computes that
calculate one or more values for the entire group of atoms can output
those values via the <A HREF = "thermo_style.html">thermo_style custom</A> or <A HREF = "fix_ave_time.html">fix
ave/time</A> command. Or the values can be referenced
in a <A HREF = "variable.html">variable equal</A> command. Computes that calculate
a temperature or pressure are used by fixes that do thermostatting or
barostatting and when atom velocities are created. Computes that
calculate one or more values for each atom in the group can output
those values via the <A HREF = "dump.html">dump custom</A> command or the <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> command.
<P>In LAMMPS, a "compute" is used in several ways. There are two kinds
of computes, "global" computes that calculate one or more values for
the entire group of atoms, and "per-atom" computes that calculate one
or more values for each atom in the group. The latter has the word
"atom" in its style name.
</P>
<P>LAMMPS creates its own computes for thermodynamic output. Two
<P>The results of global computes can be output via the <A HREF = "thermo_style.html">thermo_style
custom</A> or <A HREF = "fix_ave_time.html">fix ave/time</A> command.
Or the values can be referenced in a <A HREF = "variable.html">variable equal</A>
command. The results of computes that calculate a global temperature
or pressure can be used by fixes that do thermostatting or
barostatting and when atom velocities are created.
</P>
<P>The results of per-atom computes can be output via the <A HREF = "dump.html">dump
custom</A> command or the <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> command. Or the per-atom values can
be time-averaged via the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command and
then output via the <A HREF = "dump.html">dump custom</A> or <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> commands.
</P>
<P>LAMMPS creates its own global computes for thermodynamic output. Two
computes are always created, named "thermo_temp" and
"thermo_pressure", as if these commands had been invoked:
</P>
@ -57,9 +66,9 @@ documentation for the <A HREF = "dump.html">dump custom</A> and specific
<A HREF = "fix.html">fix</A> commands.
</P>
<P>In all these cases, the default computes can be replaced by computes
defined in the input script, as described by the
<A HREF = "thermo_modify.html">thermo_modify</A> and <A HREF = "fix_modify.html">fix modify</A>
commands.
defined by the user in the input script, as described by the
<A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_modify.html">fix modify</A>, and
<A HREF = "dump.html">dump</A> commands.
</P>
<P>Properties of either a default of user-defined compute can be modified
via the <A HREF = "compute_modify.html">compute_modify</A> command.
@ -74,16 +83,17 @@ calculations accessed in the various ways described above.
and what it does. Here is an alphabetic list of compute styles
defined in LAMMPS:
</P>
<UL><LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
<UL><LI><A HREF = "compute_attribute_atom.html">attribute/atom</A> - attribute (x,v,f,etc) of each atom
<LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
<LI><A HREF = "compute_coord_atom.html">coord/atom</A> - coordination number for each atom
<LI><A HREF = "compute_ebond_atom.html">ebond/atom</A> - bond energy for each atom
<LI><A HREF = "compute_epair_atom.html">epair/atom</A> - pairwise energy for each atom
<LI><A HREF = "compute_etotal_atom.html">etotal/atom</A> - total energy (ke + epair) for each atom
<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor
<LI><A HREF = "compute_rotate_dipole.html">rotate/dipole</A> - rotational energy of dipolar atoms
<LI><A HREF = "compute_rotate_gran.html">rotate/gran</A> - rotational energy of granular atoms
<LI><A HREF = "compute_stress_atom.html">stress/atom</A> - stress tensor for each atom
<LI><A HREF = "compute_sum_atom.html">sum/atom</A> - sum 2 or more quantities for each atom
<LI><A HREF = "compute_temp.html">temp</A> - temperature of group of atoms
<LI><A HREF = "compute_temp_asphere.html">temp/asphere</A> - temperature of aspherical particles
<LI><A HREF = "compute_temp_deform.html">temp/deform</A> - temperature excluding box deformation velocity

40
doc/compute.txt
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@ -27,18 +27,27 @@ compute 3 all ke/atom :pre
Create a computation that will be performed on a group of atoms.
In LAMMPS, a "compute" is used in several ways. Computes that
calculate one or more values for the entire group of atoms can output
those values via the "thermo_style custom"_thermo_style.html or "fix
ave/time"_fix_ave_time.html command. Or the values can be referenced
in a "variable equal"_variable.html command. Computes that calculate
a temperature or pressure are used by fixes that do thermostatting or
barostatting and when atom velocities are created. Computes that
calculate one or more values for each atom in the group can output
those values via the "dump custom"_dump.html command or the "fix
ave/spatial"_fix_ave_spatial.html command.
In LAMMPS, a "compute" is used in several ways. There are two kinds
of computes, "global" computes that calculate one or more values for
the entire group of atoms, and "per-atom" computes that calculate one
or more values for each atom in the group. The latter has the word
"atom" in its style name.
LAMMPS creates its own computes for thermodynamic output. Two
The results of global computes can be output via the "thermo_style
custom"_thermo_style.html or "fix ave/time"_fix_ave_time.html command.
Or the values can be referenced in a "variable equal"_variable.html
command. The results of computes that calculate a global temperature
or pressure can be used by fixes that do thermostatting or
barostatting and when atom velocities are created.
The results of per-atom computes can be output via the "dump
custom"_dump.html command or the "fix
ave/spatial"_fix_ave_spatial.html command. Or the per-atom values can
be time-averaged via the "fix ave/atom"_fix_ave_atom.html command and
then output via the "dump custom"_dump.html or "fix
ave/spatial"_fix_ave_spatial.html commands.
LAMMPS creates its own global computes for thermodynamic output. Two
computes are always created, named "thermo_temp" and
"thermo_pressure", as if these commands had been invoked:
@ -54,9 +63,9 @@ documentation for the "dump custom"_dump.html and specific
"fix"_fix.html commands.
In all these cases, the default computes can be replaced by computes
defined in the input script, as described by the
"thermo_modify"_thermo_modify.html and "fix modify"_fix_modify.html
commands.
defined by the user in the input script, as described by the
"thermo_modify"_thermo_modify.html, "fix modify"_fix_modify.html, and
"dump"_dump.html commands.
Properties of either a default of user-defined compute can be modified
via the "compute_modify"_compute_modify.html command.
@ -71,16 +80,17 @@ Each compute style has its own doc page which describes its arguments
and what it does. Here is an alphabetic list of compute styles
defined in LAMMPS:
"attribute/atom"_compute_attribute_atom.html - attribute (x,v,f,etc) of each atom
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
"coord/atom"_compute_coord_atom.html - coordination number for each atom
"ebond/atom"_compute_ebond_atom.html - bond energy for each atom
"epair/atom"_compute_epair_atom.html - pairwise energy for each atom
"etotal/atom"_compute_etotal_atom.html - total energy (ke + epair) for each atom
"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
"pressure"_compute_pressure.html - total pressure and pressure tensor
"rotate/dipole"_compute_rotate_dipole.html - rotational energy of dipolar atoms
"rotate/gran"_compute_rotate_gran.html - rotational energy of granular atoms
"stress/atom"_compute_stress_atom.html - stress tensor for each atom
"sum/atom"_compute_sum_atom.html - sum 2 or more quantities for each atom
"temp"_compute_temp.html - temperature of group of atoms
"temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
"temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity

3
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View File

@ -25,8 +25,7 @@
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the centro-symmetry parameter for
each atom in a group. This can be output via the <A HREF = "dump.html">dump
custom</A> command. In solid state systems the centro-symmetry
each atom in a group. In solid-state systems the centro-symmetry
parameter is a useful measure of the local lattice disorder around an
atom and can be used to characterize whether the atom is part of a
perfect lattice, a local defect (e.g. a dislocation or stacking

3
doc/compute_centro_atom.txt
View File

@ -22,8 +22,7 @@ compute 1 all centro/atom :pre
[Description:]
Define a computation that calculates the centro-symmetry parameter for
each atom in a group. This can be output via the "dump
custom"_dump.html command. In solid state systems the centro-symmetry
each atom in a group. In solid-state systems the centro-symmetry
parameter is a useful measure of the local lattice disorder around an
atom and can be used to characterize whether the atom is part of a
perfect lattice, a local defect (e.g. a dislocation or stacking

3
doc/compute_coord_atom.html
View File

@ -26,8 +26,7 @@
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the coordination number for each
atom in a group. This can be output via the <A HREF = "dump.html">dump custom</A>
command.
atom in a group.
</P>
<P>The coordination number is defined as the number of neighbor atoms
within the specified cutoff distance from the central atom. Atoms not

3
doc/compute_coord_atom.txt
View File

@ -23,8 +23,7 @@ compute 1 all coord/atom 2.0 :pre
[Description:]
Define a computation that calculates the coordination number for each
atom in a group. This can be output via the "dump custom"_dump.html
command.
atom in a group.
The coordination number is defined as the number of neighbor atoms
within the specified cutoff distance from the central atom. Atoms not

3
doc/compute_ebond_atom.html
View File

@ -25,8 +25,7 @@
<P><B>Description:</B>
</P>
<P>Define a computation that computes the per-atom bond energy for each
atom in a group. This can be output via the <A HREF = "dump.html">dump custom</A>
command.
atom in a group.
</P>
<P>The bond energy for each atom is computed by looping over the atoms it
is bonded to and computing the bond energy associated with the defined

3
doc/compute_ebond_atom.txt
View File

@ -22,8 +22,7 @@ compute 1 all ebond/atom :pre
[Description:]
Define a computation that computes the per-atom bond energy for each
atom in a group. This can be output via the "dump custom"_dump.html
command.
atom in a group.
The bond energy for each atom is computed by looping over the atoms it
is bonded to and computing the bond energy associated with the defined

3
doc/compute_epair_atom.html
View File

@ -25,8 +25,7 @@
<P><B>Description:</B>
</P>
<P>Define a computation that computes the per-atom pairwise energy for
each atom in a group. This can be output via the <A HREF = "dump.html">dump
custom</A> command.
each atom in a group.
</P>
<P>The pairwise energy for each atom is computed by looping over its
neighbors and computing the energy associated with the defined

3
doc/compute_epair_atom.txt
View File

@ -22,8 +22,7 @@ compute 1 all epair/atom :pre
[Description:]
Define a computation that computes the per-atom pairwise energy for
each atom in a group. This can be output via the "dump
custom"_dump.html command.
each atom in a group.
The pairwise energy for each atom is computed by looping over its
neighbors and computing the energy associated with the defined

60
doc/compute_etotal_atom.html
View File

@ -1,60 +0,0 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute etotal/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID etotal/atom compute-ID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>etotal/atom = style name of this compute command
<LI>compute-ID = ID of compute that calculates per-atom pairwise energy
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all etotal/atom atomEng
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that computes the total energy (kinetic +
pairwise) for each atom in a group. This can be output via the <A HREF = "dump.html">dump
custom</A> command.
</P>
<P>IMPORTANT NOTE: The per-atom total energy does NOT include
contributions due to bonds, angles, dihedrals, impropers that the atom
is part of, or a long-range Coulombic contribution. The bond
contribution can be computed separately via the <A HREF = "compute_ebond_atom.html">compute
ebond/atom</A> command. Currently, there is no
way in LAMMPS to calculate per-atom energy from angles, dihedrals,
improper, or long-range interactions.
</P>
<P>The kinetic energy for each atom is computed the same way as in the
<A HREF = "compute_ke_atom.html">compute ke/atom</A> command, namely as 1/2 m v^2.
</P>
<P>The pairwise energy for each atom is computed the same way as in the
<A HREF = "compute_epair_atom.html">compute epair/atom</A> command. In fact, the
last argument to this command is the ID of the epair/atom compute that
performs this calculation.
</P>
<P><B>Restrictions:</B>
</P>
<P>Some pair potentials do not allow the calculation of per-atom energy
and via the auxiliary <A HREF = "compute_epair_atom.html">compute epair/atom</A>
compute that is an argument to this command.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_epair_atom.html">compute epair/atom</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

55
doc/compute_etotal_atom.txt
View File

@ -1,55 +0,0 @@
"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
compute etotal/atom command :h3
[Syntax:]
compute ID group-ID etotal/atom compute-ID :pre
ID, group-ID are documented in "compute"_compute.html command
etotal/atom = style name of this compute command
compute-ID = ID of compute that calculates per-atom pairwise energy :ul
[Examples:]
compute 1 all etotal/atom atomEng :pre
[Description:]
Define a computation that computes the total energy (kinetic +
pairwise) for each atom in a group. This can be output via the "dump
custom"_dump.html command.
IMPORTANT NOTE: The per-atom total energy does NOT include
contributions due to bonds, angles, dihedrals, impropers that the atom
is part of, or a long-range Coulombic contribution. The bond
contribution can be computed separately via the "compute
ebond/atom"_compute_ebond_atom.html command. Currently, there is no
way in LAMMPS to calculate per-atom energy from angles, dihedrals,
improper, or long-range interactions.
The kinetic energy for each atom is computed the same way as in the
"compute ke/atom"_compute_ke_atom.html command, namely as 1/2 m v^2.
The pairwise energy for each atom is computed the same way as in the
"compute epair/atom"_compute_epair_atom.html command. In fact, the
last argument to this command is the ID of the epair/atom compute that
performs this calculation.
[Restrictions:]
Some pair potentials do not allow the calculation of per-atom energy
and via the auxiliary "compute epair/atom"_compute_epair_atom.html
compute that is an argument to this command.
[Related commands:]
"compute epair/atom"_compute_epair_atom.html
[Default:] none

3
doc/compute_ke_atom.html
View File

@ -25,8 +25,7 @@
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the per-atom kinetic energy for
each atom in a group. This can be output via the <A HREF = "dump.html">dump
custom</A> command.
each atom in a group.
</P>
<P>The kinetic energy is simply 1/2 m v^2, where m is the mass and v is
the velocity of each atom.

3
doc/compute_ke_atom.txt
View File

@ -22,8 +22,7 @@ compute 1 all ke/atom :pre
[Description:]
Define a computation that calculates the per-atom kinetic energy for
each atom in a group. This can be output via the "dump
custom"_dump.html command.
each atom in a group.
The kinetic energy is simply 1/2 m v^2, where m is the mass and v is
the velocity of each atom.

7
doc/compute_stress_atom.html
View File

@ -41,8 +41,11 @@
<P><B>Description:</B>
</P>
<P>Define a computation that computes the per-atom stress tensor for each
atom in a group. The 6 components can be output via the <A HREF = "dump.html">dump
custom</A> command.
atom in a group. The tensor for each atom has 6 components: xx, yy,
zz, xy, xz, yz. The resulting values can be accessed by indices 1-6
by any command that uses per-atom computes, e.g. the <A HREF = "dump.html">dump
custom</A> command or <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>
command or <A HREF = "fix_ave_atom.html">fix ave/atom</A> command.
</P>
<P>The stress tensor for each atom is the sum of 3 terms in the following
formula. Any of the terms can be excluded by setting the <I>ke</I>,

7
doc/compute_stress_atom.txt
View File

@ -32,8 +32,11 @@ compute 1 all stress/atom ke no :pre
[Description:]
Define a computation that computes the per-atom stress tensor for each
atom in a group. The 6 components can be output via the "dump
custom"_dump.html command.
atom in a group. The tensor for each atom has 6 components: xx, yy,
zz, xy, xz, yz. The resulting values can be accessed by indices 1-6
by any command that uses per-atom computes, e.g. the "dump
custom"_dump.html command or "fix ave/spatial"_fix_ave_spatial.html
command or "fix ave/atom"_fix_ave_atom.html command.
The stress tensor for each atom is the sum of 3 terms in the following
formula. Any of the terms can be excluded by setting the {ke},

7
doc/compute_variable_atom.html
View File

@ -26,9 +26,10 @@
<P><B>Description:</B>
</P>
<P>Define a computation that calculates a formula for each atom in the
group. The per-atom quantities can be output via the <A HREF = "dump.html">dump
custom</A> command or spatially averaged via the <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> command.
group. The resulting values can be accessed by any command that uses
per-atom computes, e.g. the <A HREF = "dump.html">dump custom</A> command or <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> command or <A HREF = "fix_ave_atom.html">fix
ave/atom</A> command.
</P>
<P>The formula is defined by the <A HREF = "variable.html">variable atom</A> command.
A variable of style <I>atom</I> can access properties of the system, such

7
doc/compute_variable_atom.txt
View File

@ -23,9 +23,10 @@ compute 1 flow variable/atom myVar :pre
[Description:]
Define a computation that calculates a formula for each atom in the
group. The per-atom quantities can be output via the "dump
custom"_dump.html command or spatially averaged via the "fix
ave/spatial"_fix_ave_spatial.html command.
group. The resulting values can be accessed by any command that uses
per-atom computes, e.g. the "dump custom"_dump.html command or "fix
ave/spatial"_fix_ave_spatial.html command or "fix
ave/atom"_fix_ave_atom.html command.
The formula is defined by the "variable atom"_variable.html command.
A variable of style {atom} can access properties of the system, such

112
doc/dump.html
View File

@ -39,9 +39,7 @@
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
epair, ebond, ke, etotal, centro,
sxx, syy, szz, sxy, sxz, syz,
c_ID, c_ID[N]
c_ID, c_ID[N], f_ID, f_ID[N]
tag = atom ID
mol = molecule ID
type = atom type
@ -55,14 +53,10 @@
mux,muy,muz = orientation of dipolar atom
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on aspherical particles
epair = per-atom pairwise energy
ebond = per-atom bond energy
ke = per-atom kinetic energy
etotal = per-atom total energy (ke + epair, not ebond)
centro = per-atom centro-symmetry parameter
sxx, syy, szz, sxy, sxz, syz = per-atom stress tensor components
c_ID = scalar per-atom quantity calculated by a compute identified by its ID
c_ID[N] = Nth per-atom vector quantity calculated by a compute identified by its ID
c_ID[N] = Nth per-atom vector quantity calculated by a compute identified by its ID
f_ID = scalar per-atom quantity calculated by a fix identified by its ID
f_ID[N] = Nth per-atom vector quantity calculated by a fix identified by its ID
</PRE>
</UL>
@ -71,7 +65,7 @@
<PRE>dump myDump all atom 100 dump.atom
dump 2 subgroup atom 50 dump.run.bin
dump 4a all custom 100 dump.myforce.* tag type x y vx fx
dump 4b flow custom 100 dump.%.myforce tag type epair sxx syy szz c_myF[3]
dump 4b flow custom 100 dump.%.myforce tag type c_myF[3]
dump 1 all xtc 1000 file.xtc 100.0
</PRE>
<P><B>Description:</B>
@ -136,8 +130,8 @@ to specify a quantity that is not defined for a particular simulation
- such as <I>q</I> for atom style <I>bond</I>, since that atom style doesn't
assign charges. Dumps occur at the very end of a timestep, so atom
attributes will include effects due to fixes that are applied during
the timestep. An explanation of some of the dump custom quantities is
given below.
the timestep. An explanation of the dump custom quantities is given
below.
</P>
<P>The <I>dcd</I> style writes DCD files, a standard atomic trajectory format
used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
@ -218,16 +212,16 @@ part of the <I>custom</I> style.
<I>fz</I>, <I>q</I> keywords are self-explanatory. <I>Tag</I> is the atom ID. <I>Mol</I>
is the molecule ID, included in the data file for molecular systems.
The <I>x</I>, <I>y</I>, <I>z</I> keywords write atom coordinates "unscaled", in the
appropriate distance units (Angstroms, sigma, etc). Use <I>xs</I>, <I>ys</I>,
<I>zs</I> if you want the coordinates "scaled" to the box size, so that
each value is 0.0 to 1.0. Use <I>xu</I>, <I>yu</I>, <I>zu</I> if you want the
coordinates "unwrapped" by the image flags for each atom. Unwrapped
means that if the atom has passed thru a periodic boundary one or more
times, the value is printed for what the coordinate would be if it had
not been wrapped back into the periodic box. Note that using <I>xu</I>,
<I>yu</I>, <I>zu</I> means that the coordinate values may be far outside the box
size printed with the snapshot. The image flags can be printed
directly using the <I>ix</I>, <I>iy</I>, <I>iz</I> keywords. The
appropriate distance <A HREF = "units.html">units</A> (Angstroms, sigma, etc). Use
<I>xs</I>, <I>ys</I>, <I>zs</I> if you want the coordinates "scaled" to the box size,
so that each value is 0.0 to 1.0. Use <I>xu</I>, <I>yu</I>, <I>zu</I> if you want
the coordinates "unwrapped" by the image flags for each atom.
Unwrapped means that if the atom has passed thru a periodic boundary
one or more times, the value is printed for what the coordinate would
be if it had not been wrapped back into the periodic box. Note that
using <I>xu</I>, <I>yu</I>, <I>zu</I> means that the coordinate values may be far
outside the box size printed with the snapshot. The image flags can
be printed directly using the <I>ix</I>, <I>iy</I>, <I>iz</I> keywords. The
<A HREF = "dump_modify.html">dump_modify</A> command describes in more detail what
is meant by scaled vs unscaled coordinates and the image flags.
</P>
@ -241,57 +235,45 @@ are specific to aspherical particles defined with an atom style of
define the orientiation of the particle. The final 3 give the
rotational torque on the particle.
</P>
<P>The <I>epair</I>, <I>ebond</I>, <I>ke</I>, <I>etotal</I>, <I>centro</I>, and <I>sxx</I>, etc
keywords print the pairwise energy, bond energy, kinetic energy, total
energy (pairwise + kinetic), centro-symmetry parameter, and components
of the per-atom stress tensor for each atom. These quantities are
calculated by computes that the dump defines, as if these commands had
been issued:
</P>
<PRE>compute dump-ID_epair/atom group-ID <A HREF = "compute_epair_atom.html">epair/atom</A>
compute dump-ID_ebond/atom group-ID <A HREF = "compute_ebond_atom.html">ebond/atom</A>
compute dump-ID_ke/atom group-ID <A HREF = "compute_ke_atom.html">ke/atom</A>
compute dump-ID_etotal/atom group-ID <A HREF = "compute_etotal_atom.html">etotal/atom</A> dump-ID_epair/atom
compute dump-ID_centro/atom group-ID <A HREF = "compute_centro_atom.html">centro/atom</A>
compute dump-ID_stress/atom group-ID <A HREF = "compute_stress_atom.html">stress/atom</A>
</PRE>
<P>See the corresponding <A HREF = "compute.html">compute</A> style commands for
details on what is computed for each atom. Note that the ID of each
new compute is the dump-ID with the compute style appended (with an
underscore). The group for each new compute is the same as the dump
group. Note that for <I>etotal</I>, an auxiliary compute for calculating
the pairwise energy is created, since the <A HREF = "compute_etotal_atom.html">compute
etotal/atom</A> command requires it as an extra
argument.
</P>
<P>IMPORTANT NOTE: The <I>etotal</I> keyword does NOT include contributions
due to bonds, angles, etc that the atom is part of. The bond
contribution can be computed separately via the <I>ebond</I> keyword.
Currently, there is no way in LAMMPS to dump per-atom energy for
angles, dihedrals, improper, or long-range interactions.
</P>
<P>The <I>sxx</I>, <I>syy</I>, <I>szz</I>, <I>sxy</I>, <I>sxz</I>, <I>syz</I> keywords access the 6
components of the stress tensor calculated for each atom by the
<A HREF = "compute_stress_atom.html">compute stress/atom</A> style.
</P>
<P>The <I>c_ID</I> and <I>c_ID[N]</I> keywords allow scalar or vector per-atom
quantities calculated by a compute to be output. The ID in the
keyword should be replaced by the actual ID of the compute that has
been defined elsewhere in the input script. See the
<A HREF = "compute.html">compute</A> command for details. Note that scalar and
vector quantities that are not calculated on a per-atom basis
(e.g. global temperature or pressure) cannot be output in a dump.
Rather, these quantities are output by the <A HREF = "thermo_style.html">thermo_style
custom</A> command.
been defined previously in the input script. See the
<A HREF = "compute.html">compute</A> command for details. There are pre-defined
computes for calculating the energy, stress, centro-symmetry
parameter, and coordination number of individual atoms. The "compute
variable/atom" command will evaluate a per-atom formula you define via
the <A HREF = "variable.html">variable atom</A> command, for each atom, which can
then be dumped.
</P>
<P>Note that scalar and vector quantities that are not calculated on a
per-atom basis by a compute (e.g. global temperature or pressure)
cannot be output in a dump. Rather, these quantities can be output by
the <A HREF = "thermo_style.html">thermo_style custom</A> command.
</P>
<P>If <I>c_ID</I> is used as a keyword, then the scalar per-atom quantity
calculated by the compute is printed. If <I>c_ID[N]</I> is used, then N
in the range from 1-M will print the Nth component of the M-length
per-atom vector calculated by the compute.
</P>
<P>See <A HREF = "Section_modify.html">this section</A> for information on how to add
new compute styles to LAMMPS that calculate per-atom quantities which
could then be output with these keywords.
<P>The <I>f_ID</I> and <I>f_ID[N]</I> keywords allow scalar or vector per-atom
quantities calculated by a fix to be output. The ID in the keyword
should be replaced by the actual ID of the fix that has been defined
previously in the input script. Currently the <A HREF = "fix_ave_atom.html">fix
ave/atom</A> command is the only fix that calculates
per-atom quantities. Since it takes a per-atom <A HREF = "compute.html">compute</A>
as an argument it effectively time-averages any of the previously
described compute quantities so the time-averaged result can be
written to a dump file.
</P>
<P>If <I>f_ID</I> is used as a keyword, then the scalar per-atom quantity
calculated by the fix is printed. If <I>f_ID[N]</I> is used, then N
in the range from 1-M will print the Nth component of the M-length
per-atom vector calculated by the fix.
</P>
<P>See <A HREF = "Section_modify.html">this section</A> of the manual for information
on how to add new compute and fix styles to LAMMPS that calculate
per-atom quantities which could then be output with these keywords.
</P>
<HR>

112
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@ -30,9 +30,7 @@ args = list of arguments for a particular style :l
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
epair, ebond, ke, etotal, centro,
sxx, syy, szz, sxy, sxz, syz,
c_ID, c_ID\[N\]
c_ID, c_ID\[N\], f_ID, f_ID\[N\]
tag = atom ID
mol = molecule ID
type = atom type
@ -46,14 +44,10 @@ args = list of arguments for a particular style :l
mux,muy,muz = orientation of dipolar atom
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on aspherical particles
epair = per-atom pairwise energy
ebond = per-atom bond energy
ke = per-atom kinetic energy
etotal = per-atom total energy (ke + epair, not ebond)
centro = per-atom centro-symmetry parameter
sxx, syy, szz, sxy, sxz, syz = per-atom stress tensor components
c_ID = scalar per-atom quantity calculated by a compute identified by its ID
c_ID\[N\] = Nth per-atom vector quantity calculated by a compute identified by its ID :pre
c_ID\[N\] = Nth per-atom vector quantity calculated by a compute identified by its ID
f_ID = scalar per-atom quantity calculated by a fix identified by its ID
f_ID\[N\] = Nth per-atom vector quantity calculated by a fix identified by its ID :pre
:ule
[Examples:]
@ -61,7 +55,7 @@ args = list of arguments for a particular style :l
dump myDump all atom 100 dump.atom
dump 2 subgroup atom 50 dump.run.bin
dump 4a all custom 100 dump.myforce.* tag type x y vx fx
dump 4b flow custom 100 dump.%.myforce tag type epair sxx syy szz c_myF\[3\]
dump 4b flow custom 100 dump.%.myforce tag type c_myF\[3\]
dump 1 all xtc 1000 file.xtc 100.0 :pre
[Description:]
@ -126,8 +120,8 @@ to specify a quantity that is not defined for a particular simulation
- such as {q} for atom style {bond}, since that atom style doesn't
assign charges. Dumps occur at the very end of a timestep, so atom
attributes will include effects due to fixes that are applied during
the timestep. An explanation of some of the dump custom quantities is
given below.
the timestep. An explanation of the dump custom quantities is given
below.
The {dcd} style writes DCD files, a standard atomic trajectory format
used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
@ -208,16 +202,16 @@ The {tag}, {mol}, {type}, {x}, {y}, {z}, {vx}, {vy}, {vz}, {fx}, {fy},
{fz}, {q} keywords are self-explanatory. {Tag} is the atom ID. {Mol}
is the molecule ID, included in the data file for molecular systems.
The {x}, {y}, {z} keywords write atom coordinates "unscaled", in the
appropriate distance units (Angstroms, sigma, etc). Use {xs}, {ys},
{zs} if you want the coordinates "scaled" to the box size, so that
each value is 0.0 to 1.0. Use {xu}, {yu}, {zu} if you want the
coordinates "unwrapped" by the image flags for each atom. Unwrapped
means that if the atom has passed thru a periodic boundary one or more
times, the value is printed for what the coordinate would be if it had
not been wrapped back into the periodic box. Note that using {xu},
{yu}, {zu} means that the coordinate values may be far outside the box
size printed with the snapshot. The image flags can be printed
directly using the {ix}, {iy}, {iz} keywords. The
appropriate distance "units"_units.html (Angstroms, sigma, etc). Use
{xs}, {ys}, {zs} if you want the coordinates "scaled" to the box size,
so that each value is 0.0 to 1.0. Use {xu}, {yu}, {zu} if you want
the coordinates "unwrapped" by the image flags for each atom.
Unwrapped means that if the atom has passed thru a periodic boundary
one or more times, the value is printed for what the coordinate would
be if it had not been wrapped back into the periodic box. Note that
using {xu}, {yu}, {zu} means that the coordinate values may be far
outside the box size printed with the snapshot. The image flags can
be printed directly using the {ix}, {iy}, {iz} keywords. The
"dump_modify"_dump_modify.html command describes in more detail what
is meant by scaled vs unscaled coordinates and the image flags.
@ -231,57 +225,45 @@ are specific to aspherical particles defined with an atom style of
define the orientiation of the particle. The final 3 give the
rotational torque on the particle.
The {epair}, {ebond}, {ke}, {etotal}, {centro}, and {sxx}, etc
keywords print the pairwise energy, bond energy, kinetic energy, total
energy (pairwise + kinetic), centro-symmetry parameter, and components
of the per-atom stress tensor for each atom. These quantities are
calculated by computes that the dump defines, as if these commands had
been issued:
compute dump-ID_epair/atom group-ID "epair/atom"_compute_epair_atom.html
compute dump-ID_ebond/atom group-ID "ebond/atom"_compute_ebond_atom.html
compute dump-ID_ke/atom group-ID "ke/atom"_compute_ke_atom.html
compute dump-ID_etotal/atom group-ID "etotal/atom"_compute_etotal_atom.html dump-ID_epair/atom
compute dump-ID_centro/atom group-ID "centro/atom"_compute_centro_atom.html
compute dump-ID_stress/atom group-ID "stress/atom"_compute_stress_atom.html :pre
See the corresponding "compute"_compute.html style commands for
details on what is computed for each atom. Note that the ID of each
new compute is the dump-ID with the compute style appended (with an
underscore). The group for each new compute is the same as the dump
group. Note that for {etotal}, an auxiliary compute for calculating
the pairwise energy is created, since the "compute
etotal/atom"_compute_etotal_atom.html command requires it as an extra
argument.
IMPORTANT NOTE: The {etotal} keyword does NOT include contributions
due to bonds, angles, etc that the atom is part of. The bond
contribution can be computed separately via the {ebond} keyword.
Currently, there is no way in LAMMPS to dump per-atom energy for
angles, dihedrals, improper, or long-range interactions.
The {sxx}, {syy}, {szz}, {sxy}, {sxz}, {syz} keywords access the 6
components of the stress tensor calculated for each atom by the
"compute stress/atom"_compute_stress_atom.html style.
The {c_ID} and {c_ID\[N\]} keywords allow scalar or vector per-atom
quantities calculated by a compute to be output. The ID in the
keyword should be replaced by the actual ID of the compute that has
been defined elsewhere in the input script. See the
"compute"_compute.html command for details. Note that scalar and
vector quantities that are not calculated on a per-atom basis
(e.g. global temperature or pressure) cannot be output in a dump.
Rather, these quantities are output by the "thermo_style
custom"_thermo_style.html command.
been defined previously in the input script. See the
"compute"_compute.html command for details. There are pre-defined
computes for calculating the energy, stress, centro-symmetry
parameter, and coordination number of individual atoms. The "compute
variable/atom" command will evaluate a per-atom formula you define via
the "variable atom"_variable.html command, for each atom, which can
then be dumped.
Note that scalar and vector quantities that are not calculated on a
per-atom basis by a compute (e.g. global temperature or pressure)
cannot be output in a dump. Rather, these quantities can be output by
the "thermo_style custom"_thermo_style.html command.
If {c_ID} is used as a keyword, then the scalar per-atom quantity
calculated by the compute is printed. If {c_ID\[N\]} is used, then N
in the range from 1-M will print the Nth component of the M-length
per-atom vector calculated by the compute.
See "this section"_Section_modify.html for information on how to add
new compute styles to LAMMPS that calculate per-atom quantities which
could then be output with these keywords.
The {f_ID} and {f_ID\[N\]} keywords allow scalar or vector per-atom
quantities calculated by a fix to be output. The ID in the keyword
should be replaced by the actual ID of the fix that has been defined
previously in the input script. Currently the "fix
ave/atom"_fix_ave_atom.html command is the only fix that calculates
per-atom quantities. Since it takes a per-atom "compute"_compute.html
as an argument it effectively time-averages any of the previously
described compute quantities so the time-averaged result can be
written to a dump file.
If {f_ID} is used as a keyword, then the scalar per-atom quantity
calculated by the fix is printed. If {f_ID\[N\]} is used, then N
in the range from 1-M will print the Nth component of the M-length
per-atom vector calculated by the fix.
See "this section"_Section_modify.html of the manual for information
on how to add new compute and fix styles to LAMMPS that calculate
per-atom quantities which could then be output with these keywords.
:line

1
doc/fix.html
View File

@ -75,6 +75,7 @@ for individual fixes for info on which ones can be restarted.
</P>
<UL><LI><A HREF = "fix_addforce.html">fix addforce</A> - add a force to each atom
<LI><A HREF = "fix_aveforce.html">fix aveforce</A> - add an averaged force to each atom
<LI><A HREF = "fix_ave_atom.html">fix ave/atom</A> - compute per-atom time-averaged quantities
<LI><A HREF = "fix_ave_spatial.html">fix ave/spatial</A> - output per-atom quantities by layer
<LI><A HREF = "fix_ave_time.html">fix ave/time</A> - output time-averaged compute quantities
<LI><A HREF = "fix_com.html">fix com</A> - compute a center-of-mass

1
doc/fix.txt
View File

@ -72,6 +72,7 @@ Here is an alphabetic list of fix styles available in LAMMPS:
"fix addforce"_fix_addforce.html - add a force to each atom
"fix aveforce"_fix_aveforce.html - add an averaged force to each atom
"fix ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities
"fix ave/spatial"_fix_ave_spatial.html - output per-atom quantities by layer
"fix ave/time"_fix_ave_time.html - output time-averaged compute quantities
"fix com"_fix_com.html - compute a center-of-mass

101
doc/fix_ave_spatial.html
View File

@ -13,7 +13,7 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID ave/spatial Nevery Nfreq dim origin delta file style args keyword value ...
<PRE>fix ID group-ID ave/spatial Nevery Nrepeat Nfreq dim origin delta file style args keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
@ -21,7 +21,9 @@
<LI>Nevery = calculate property every this many timesteps
<LI>Nfreq = write average property to file every this many steps
<LI>Nrepeat = # of times to repeat the Nevery calculation before averaging
<LI>Nfreq = timestep frequency at which the average value is written to file
<LI>dim = <I>x</I> or <I>y</I> or <I>z</I>
@ -31,13 +33,15 @@
<LI>file = filename to write results to
<LI>style = <I>density</I> or <I>atom</I> or <I>compute</I>
<LI>style = <I>density</I> or <I>compute</I> or <I>fix</I>
<PRE> <I>density</I> arg = <I>mass</I> or <I>number</I>
<I>mass</I> = compute mass density
<I>number</I> = compute number density
<I>atom</I> arg = <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>fx</I> or <I>fy</I> or <I>fz</I>
<I>compute</I> arg = compute-ID that calculates per-atom quantities
<I>compute</I> arg = compute-ID that stores or calculates per-atom quantities
<I>fix</I> arg = fix-ID that stores or calculates per-atom quantities
</PRE>
<PRE>
</PRE>
<LI>zero or more keyword/value pairs may be appended
@ -49,36 +53,49 @@
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all ave/spatial 10000 10000 z lower 2.0 centro.profile compute myCentro
fix 1 flow ave/spatial 100 1000 y 0.0 1.0 vel.profile atom vx norm sample
fix 1 flow ave/spatial 100 1000 y 0.0 2.5 dens.profile density mass
<PRE>fix 1 all ave/spatial 10000 1 10000 z lower 2.0 centro.profile compute myCentro
fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vel.profile compute Vx norm sample
fix 1 flow ave/spatial 100 5 1000 y 0.0 2.5 dens.profile density mass
</PRE>
<P><B>Description:</B>
</P>
<P>Calculate one or more instantaneous per-atom quantities every few
timesteps, average them by layer in a chosen dimension and over a
longer timescale, and print the results to a file. This can be used
to spatially average per-atom properties such as velocity or energy or
a quantity calculated by an equation you define; see the <A HREF = "variable.html">variable
atom</A> command.
to spatially average per-atom properties (velocity, force) or per-atom
quantities calculated by a <A HREF = "compute.html">compute</A> (energy, stress) or
by another fix (see the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command) or
by a variable via an equation you define (see the <A HREF = "compute_variable_atom.html">compute
variable/atom</A> command).
</P>
<P>The <I>density</I> styles means to simply count the number of atoms in each
layer, either by mass or number. The <I>atom</I> style allows an atom
property such as x-velocity to be specified. The <I>compute</I> style
allows specification of a <A HREF = "compute.html">compute</A> which will be invoked
to calculate the desired property. The compute can be previously
defined in the input script. Note that the "compute variable/atom"
style allows you to calculate any quantity for an atom that can be
specified by a <A HREF = "variable.html">variable atom</A> equation. Users can also
write code for their own compute styles and <A HREF = "Section_modify.html">add them to
LAMMPS</A>. Note that the <A HREF = "dump.html">dump custom</A>
command can also be used to output per-atom quantities calculated by a
compute.
layer, either by mass or number. The <I>compute</I> style allows
specification of a <A HREF = "compute.html">compute</A> which will be invoked to
calculate the desired property. The compute can be previously defined
in the input script or it can be a compute defined by a <A HREF = "dump.html">dump
custom</A> command.
</P>
<P>For the <I>compute</I> style, the fix ave/spatial style uses the per-atom
scalar or vector calculated by the compute. See the <A HREF = "fix_ave_time.html">fix
ave/time</A> command if you wish to time-average a
global quantity, e.g. via a compute that temperature or pressure.
<P>For the <I>compute</I> style, the fix ave/spatial command accesses the
per-atom scalar or vector values stored by the compute. Thus it must
be a "per-atom" compute with the word "atom" in its style name, rather
than a "global" compute. See the <A HREF = "fix_ave_time.html">fix ave/time</A>
command if you wish to time-average a global quantity calculated by a
compute without the word atom in its style name, e.g. a compute that
calculates a temperature or pressure.
</P>
<P>See the <A HREF = "compute.html">compute</A> command for a list of pre-defined
per-atom computes. Two special computes are as follows. The <A HREF = "compute_attribute_atom.html">compute
attribute/atom</A> command selects one or
more atom attributes like vx or fz. The "compute variable/atom" style
can calculate a value for an atom that can be specified by a <A HREF = "variable.html">variable
atom</A> equation. Users can also write code for their own
per-atom compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
Note that the <A HREF = "dump.html">dump custom</A> command can also be used to
directly output per-atom quantities calculated by a per-atom compute.
</P>
<P>For the <I>fix</I> style, the fix ave/spatial command accesses the per-atom
scalar or vector values stored by another fix. The <A HREF = "fix_ave_atom.html">fix
ave/atom</A> command is an example of such a fix.
</P>
<P>In all cases, the calculated property is averaged over atoms in each
layer, where the layers are in a particular <I>dim</I> and have a thickness
@ -130,12 +147,14 @@ the lower "b" cross "c" plane of the simulation box and an <I>origin</I> of
A <I>delta</I> value of 0.1 means there will be 10 layers from 0.0 to 1.0,
regardless of the current size or shape of the simulation box.
</P>
<P>The <I>Nevery</I> and <I>Nfreq</I> arguments specify how the property calculated
for each layer is time-averaged. The property is calculated once each
Nevery timesteps. It is averaged and output every Nfreq timesteps.
Nfreq must be a multiple of Nevery. In the 2nd example above, the
property is calculated every 100 steps. After 10 calculations, the
average result is written to the file, once every 1000 steps.
<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify how the
property will be time-averaged. The final averaged value(s) are
computed every <I>Nfreq</I> timesteps. The average is over <I>Nrepeat</I>
values, computed in the preceeding portion of the simulation every
<I>Nevery</I> timesteps. Thus if Nevery=2, Nrepeat=6, and Nfreq=100, then
values on timesteps 90,92,94,96,98,100 will be used to compute the
final average written to the file on timestep 100. Similary for
timesteps 190,192,194,196,198,200 on timestep 200, etc.
</P>
<P>The <I>norm</I> keyword also affects how time-averaging is done. For an
<I>all</I> setting, a layer quantity is summed over all atoms in all
@ -159,16 +178,16 @@ is <I>box</I> or <I>lattice</I>, the "coord" is printed in box units. If the
value of the <I>units</I> keyword is <I>reduced</I>, the "coord" is printed in
reduced units (0-1).
</P>
<P>If the <I>density</I> or <I>atom</I> keyword is used, or the <I>compute</I> keyword
with a compute that calculates a single quantity per atom, then a
single value will be printed for each layer. If the <I>compute</I> keyword
is used with a compute that calculates N quantities per atom, then N
values per line will be written, each of them averaged independently.
<P>If the <I>density</I> keyword is used, or the <I>compute</I> or <I>fix</I> keyword
with a compute/fix that calculates a single quantity per atom, then a
single value will be printed for each layer. If the <I>compute</I> or
<I>fix</I> keyword is used with a compute/fix that calculates N quantities
per atom, then N values per line will be written, each of them
averaged independently.
</P>
<P>For the <I>compute</I> keyword, the calculation performed by the compute in
on the group defined by the compute. However, only atoms in the fix
group are included in the layer averaging. LAMMPS prints a warning if
the fix group and compute group do not match.
<P>For the <I>compute</I> and <I>fix</I> keywords, the calculation performed by the
compute or fix is on the group defined by the that command. However,
only atoms in the fix group are included in the layer averaging.
</P>
<P>Note that some computes perform costly calculations, involving use of
or creation of neighbor lists. If the compute is invoked too often by

100
doc/fix_ave_spatial.txt
View File

@ -10,22 +10,25 @@ fix ave/spatial command :h3
[Syntax:]
fix ID group-ID ave/spatial Nevery Nfreq dim origin delta file style args keyword value ... :pre
fix ID group-ID ave/spatial Nevery Nrepeat Nfreq dim origin delta file style args keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
ave/spatial = style name of this fix command :l
Nevery = calculate property every this many timesteps :l
Nfreq = write average property to file every this many steps :l
Nrepeat = # of times to repeat the Nevery calculation before averaging :l
Nfreq = timestep frequency at which the average value is written to file :l
dim = {x} or {y} or {z} :l
origin = {lower} or {center} or {upper} or coordinate value (distance units) :l
delta = thickness of spatial layers in dim (distance units) :l
file = filename to write results to :l
style = {density} or {atom} or {compute} :l
style = {density} or {compute} or {fix} :l
{density} arg = {mass} or {number}
{mass} = compute mass density
{number} = compute number density
{atom} arg = {vx} or {vy} or {vz} or {fx} or {fy} or {fz}
{compute} arg = compute-ID that calculates per-atom quantities :pre
{compute} arg = compute-ID that stores or calculates per-atom quantities
{fix} arg = fix-ID that stores or calculates per-atom quantities :pre
:pre
zero or more keyword/value pairs may be appended :l
keyword = {norm} or {units}
@ -36,36 +39,49 @@ keyword = {norm} or {units}
[Examples:]
fix 1 all ave/spatial 10000 10000 z lower 2.0 centro.profile compute myCentro
fix 1 flow ave/spatial 100 1000 y 0.0 1.0 vel.profile atom vx norm sample
fix 1 flow ave/spatial 100 1000 y 0.0 2.5 dens.profile density mass :pre
fix 1 all ave/spatial 10000 1 10000 z lower 2.0 centro.profile compute myCentro
fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vel.profile compute Vx norm sample
fix 1 flow ave/spatial 100 5 1000 y 0.0 2.5 dens.profile density mass :pre
[Description:]
Calculate one or more instantaneous per-atom quantities every few
timesteps, average them by layer in a chosen dimension and over a
longer timescale, and print the results to a file. This can be used
to spatially average per-atom properties such as velocity or energy or
a quantity calculated by an equation you define; see the "variable
atom"_variable.html command.
to spatially average per-atom properties (velocity, force) or per-atom
quantities calculated by a "compute"_compute.html (energy, stress) or
by another fix (see the "fix ave/atom"_fix_ave_atom.html command) or
by a variable via an equation you define (see the "compute
variable/atom"_compute_variable_atom.html command).
The {density} styles means to simply count the number of atoms in each
layer, either by mass or number. The {atom} style allows an atom
property such as x-velocity to be specified. The {compute} style
allows specification of a "compute"_compute.html which will be invoked
to calculate the desired property. The compute can be previously
defined in the input script. Note that the "compute variable/atom"
style allows you to calculate any quantity for an atom that can be
specified by a "variable atom"_variable.html equation. Users can also
write code for their own compute styles and "add them to
LAMMPS"_Section_modify.html. Note that the "dump custom"_dump.html
command can also be used to output per-atom quantities calculated by a
compute.
layer, either by mass or number. The {compute} style allows
specification of a "compute"_compute.html which will be invoked to
calculate the desired property. The compute can be previously defined
in the input script or it can be a compute defined by a "dump
custom"_dump.html command.
For the {compute} style, the fix ave/spatial style uses the per-atom
scalar or vector calculated by the compute. See the "fix
ave/time"_fix_ave_time.html command if you wish to time-average a
global quantity, e.g. via a compute that temperature or pressure.
For the {compute} style, the fix ave/spatial command accesses the
per-atom scalar or vector values stored by the compute. Thus it must
be a "per-atom" compute with the word "atom" in its style name, rather
than a "global" compute. See the "fix ave/time"_fix_ave_time.html
command if you wish to time-average a global quantity calculated by a
compute without the word atom in its style name, e.g. a compute that
calculates a temperature or pressure.
See the "compute"_compute.html command for a list of pre-defined
per-atom computes. Two special computes are as follows. The "compute
attribute/atom"_compute_attribute_atom.html command selects one or
more atom attributes like vx or fz. The "compute variable/atom" style
can calculate a value for an atom that can be specified by a "variable
atom"_variable.html equation. Users can also write code for their own
per-atom compute styles and "add them to LAMMPS"_Section_modify.html.
Note that the "dump custom"_dump.html command can also be used to
directly output per-atom quantities calculated by a per-atom compute.
For the {fix} style, the fix ave/spatial command accesses the per-atom
scalar or vector values stored by another fix. The "fix
ave/atom"_fix_ave_atom.html command is an example of such a fix.
In all cases, the calculated property is averaged over atoms in each
layer, where the layers are in a particular {dim} and have a thickness
@ -117,12 +133,14 @@ the lower "b" cross "c" plane of the simulation box and an {origin} of
A {delta} value of 0.1 means there will be 10 layers from 0.0 to 1.0,
regardless of the current size or shape of the simulation box.
The {Nevery} and {Nfreq} arguments specify how the property calculated
for each layer is time-averaged. The property is calculated once each
Nevery timesteps. It is averaged and output every Nfreq timesteps.
Nfreq must be a multiple of Nevery. In the 2nd example above, the
property is calculated every 100 steps. After 10 calculations, the
average result is written to the file, once every 1000 steps.
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify how the
property will be time-averaged. The final averaged value(s) are
computed every {Nfreq} timesteps. The average is over {Nrepeat}
values, computed in the preceeding portion of the simulation every
{Nevery} timesteps. Thus if Nevery=2, Nrepeat=6, and Nfreq=100, then
values on timesteps 90,92,94,96,98,100 will be used to compute the
final average written to the file on timestep 100. Similary for
timesteps 190,192,194,196,198,200 on timestep 200, etc.
The {norm} keyword also affects how time-averaging is done. For an
{all} setting, a layer quantity is summed over all atoms in all
@ -146,16 +164,16 @@ is {box} or {lattice}, the "coord" is printed in box units. If the
value of the {units} keyword is {reduced}, the "coord" is printed in
reduced units (0-1).
If the {density} or {atom} keyword is used, or the {compute} keyword
with a compute that calculates a single quantity per atom, then a
single value will be printed for each layer. If the {compute} keyword
is used with a compute that calculates N quantities per atom, then N
values per line will be written, each of them averaged independently.
If the {density} keyword is used, or the {compute} or {fix} keyword
with a compute/fix that calculates a single quantity per atom, then a
single value will be printed for each layer. If the {compute} or
{fix} keyword is used with a compute/fix that calculates N quantities
per atom, then N values per line will be written, each of them
averaged independently.
For the {compute} keyword, the calculation performed by the compute in
on the group defined by the compute. However, only atoms in the fix
group are included in the layer averaging. LAMMPS prints a warning if
the fix group and compute group do not match.
For the {compute} and {fix} keywords, the calculation performed by the
compute or fix is on the group defined by the that command. However,
only atoms in the fix group are included in the layer averaging.
Note that some computes perform costly calculations, involving use of
or creation of neighbor lists. If the compute is invoked too often by

38
doc/fix_ave_time.html
View File

@ -13,46 +13,52 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID ave/time Nevery Nfreq compute-ID flag file
<PRE>fix ID group-ID ave/time Nevery Nrepeat Nfreq compute-ID flag file
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>ave/time = style name of this fix command
<LI>Nevery = calculate property every this many timesteps
<LI>Nfreq = write average property to file every this many steps
<LI>Nrepeat = # of times to repeat the Nevery calculation before averaging
<LI>Nfreq = timestep frequency at which the average value is written to file
<LI>compute-ID = ID of compute that performs the calculation
<LI>flag = 0 for scalar quantity, 1 for vector quantity, 2 for both
<LI>file = filename to write results to
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all ave/time 100 1000 myTemp 0 temp.stats
<PRE>fix 1 all ave/time 100 5 1000 myTemp 0 temp.stats
</PRE>
<P><B>Description:</B>
</P>
<P>Calculate one or more instantaneous quantities every few timesteps,
average them over a longer timescale, and print the results to a file.
This can be used to time-average any "compute" entity in LAMMPS such
as a temperature or pressure.
This can be used to time-average any "compute" entity in LAMMPS which
calculates a global quantity such as a temperature or pressure.
Per-atom computes cannot be used with this fix.
</P>
<P>The <I>compute-ID</I> specifies a <A HREF = "compute.html">compute</A> which calculates
the desired property. The compute can be previously defined in the
input script. Or it can be a compute defined by <A HREF = "thermo_style.html">thermodynamic
the desired property. The compute must be a "global" compute that
calculates one or more global properties rather than a "per-atom"
compute. The compute can be previously defined in the input script.
Or it can be a compute defined by <A HREF = "thermo_style.html">thermodynamic
output</A> or other fixes such as <A HREF = "fix_nvt.html">fix
nvt</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>. Users
can also write code for their own compute styles and <A HREF = "Section_modify.html">add them to
LAMMPS</A>.
</P>
<P>In all these cases, the fix ave/time style uses the global scalar or
<P>In all these cases, the fix ave/time command uses the global scalar or
vector calculated by the compute. See the <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> command if you wish to average
spatially, e.g. via a compute that calculates per-atom quantities.
</P>
<P>The <I>Nevery</I> and <I>Nfreq</I> arguments specify how the property will be
averaged. The property is calculated once each Nevery timesteps. It
is averaged and output every Nfreq timesteps. Nfreq must be a
multiple of Nevery. In the example above, the property is calculated
every 100 steps. After 10 calculations, the average result is written
to the file, once every 1000 steps.
<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify how the
property will be time-averaged. The final averaged value(s) are
computed every <I>Nfreq</I> timesteps. The average is over <I>Nrepeat</I>
values, computed in the preceeding portion of the simulation every
<I>Nevery</I> timesteps. Thus if Nevery=2, Nrepeat=6, and Nfreq=100, then
values on timesteps 90,92,94,96,98,100 will be used to compute the
final average written to the file on timestep 100. Similary for
timesteps 190,192,194,196,198,200 on timestep 200, etc.
</P>
<P>The <I>flag</I> argument chooses whether the scalar and/or vector
calculation of the compute is invoked. The former computes a single
@ -62,9 +68,7 @@ case, each of the N values is averaged independently and N values are
written to the file at each output.
</P>
<P>Since the calculation is performed by the compute which stores its own
"group" definition, the group specified for the fix is ignored.
LAMMPS prints a warning if the fix group and compute group do not
match.
"group" definition, the group specified for this fix is ignored.
</P>
<P>If the compute calculates pressure, it will cause the force
computations performed by LAMMPS (pair, bond, angle, etc) to calculate

38
doc/fix_ave_time.txt
View File

@ -10,46 +10,52 @@ fix ave/time command :h3
[Syntax:]
fix ID group-ID ave/time Nevery Nfreq compute-ID flag file :pre
fix ID group-ID ave/time Nevery Nrepeat Nfreq compute-ID flag file :pre
ID, group-ID are documented in "fix"_fix.html command
ave/time = style name of this fix command
Nevery = calculate property every this many timesteps
Nfreq = write average property to file every this many steps
Nrepeat = # of times to repeat the Nevery calculation before averaging
Nfreq = timestep frequency at which the average value is written to file
compute-ID = ID of compute that performs the calculation
flag = 0 for scalar quantity, 1 for vector quantity, 2 for both
file = filename to write results to :ul
[Examples:]
fix 1 all ave/time 100 1000 myTemp 0 temp.stats :pre
fix 1 all ave/time 100 5 1000 myTemp 0 temp.stats :pre
[Description:]
Calculate one or more instantaneous quantities every few timesteps,
average them over a longer timescale, and print the results to a file.
This can be used to time-average any "compute" entity in LAMMPS such
as a temperature or pressure.
This can be used to time-average any "compute" entity in LAMMPS which
calculates a global quantity such as a temperature or pressure.
Per-atom computes cannot be used with this fix.
The {compute-ID} specifies a "compute"_compute.html which calculates
the desired property. The compute can be previously defined in the
input script. Or it can be a compute defined by "thermodynamic
the desired property. The compute must be a "global" compute that
calculates one or more global properties rather than a "per-atom"
compute. The compute can be previously defined in the input script.
Or it can be a compute defined by "thermodynamic
output"_thermo_style.html or other fixes such as "fix
nvt"_fix_nvt.html or "fix temp/rescale"_fix_temp_rescale.html. Users
can also write code for their own compute styles and "add them to
LAMMPS"_Section_modify.html.
In all these cases, the fix ave/time style uses the global scalar or
In all these cases, the fix ave/time command uses the global scalar or
vector calculated by the compute. See the "fix
ave/spatial"_fix_ave_spatial.html command if you wish to average
spatially, e.g. via a compute that calculates per-atom quantities.
The {Nevery} and {Nfreq} arguments specify how the property will be
averaged. The property is calculated once each Nevery timesteps. It
is averaged and output every Nfreq timesteps. Nfreq must be a
multiple of Nevery. In the example above, the property is calculated
every 100 steps. After 10 calculations, the average result is written
to the file, once every 1000 steps.
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify how the
property will be time-averaged. The final averaged value(s) are
computed every {Nfreq} timesteps. The average is over {Nrepeat}
values, computed in the preceeding portion of the simulation every
{Nevery} timesteps. Thus if Nevery=2, Nrepeat=6, and Nfreq=100, then
values on timesteps 90,92,94,96,98,100 will be used to compute the
final average written to the file on timestep 100. Similary for
timesteps 190,192,194,196,198,200 on timestep 200, etc.
The {flag} argument chooses whether the scalar and/or vector
calculation of the compute is invoked. The former computes a single
@ -59,9 +65,7 @@ case, each of the N values is averaged independently and N values are
written to the file at each output.
Since the calculation is performed by the compute which stores its own
"group" definition, the group specified for the fix is ignored.
LAMMPS prints a warning if the fix group and compute group do not
match.
"group" definition, the group specified for this fix is ignored.
If the compute calculates pressure, it will cause the force
computations performed by LAMMPS (pair, bond, angle, etc) to calculate

13
doc/fix_recenter.html
View File

@ -82,6 +82,19 @@ the input script, since the adjustments it makes to atom coordinates
should come after the changes made by time integration. LAMMPS will
warn you if your fixes are not ordered this way.
</P>
<P>IMPORTANT NOTE: If you use this fix on a small group of atoms (e.g. a
molecule in solvent) without using the <I>shift</I> keyword to adjust the
positions of all atoms in the system, then the results can be
unpredictable. For example, if the molecule is pushed in one
direction by the solvent, its velocity will increase. But its
coordinates will be recentered, meaning it is pushed back towards the
force. Thus over time, the velocity and temperature of the molecule
could become very large (though it won't appear to be moving due to
the recentering). If you are thermostatting the entire system, then
the solvent would be cooled to compensate. A better solution for this
simulation scenario is to use the <A HREF = "fix_spring.html">fix spring</A> command
to tether the molecule in place.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart

13
doc/fix_recenter.txt
View File

@ -74,6 +74,19 @@ the input script, since the adjustments it makes to atom coordinates
should come after the changes made by time integration. LAMMPS will
warn you if your fixes are not ordered this way.
IMPORTANT NOTE: If you use this fix on a small group of atoms (e.g. a
molecule in solvent) without using the {shift} keyword to adjust the
positions of all atoms in the system, then the results can be
unpredictable. For example, if the molecule is pushed in one
direction by the solvent, its velocity will increase. But its
coordinates will be recentered, meaning it is pushed back towards the
force. Thus over time, the velocity and temperature of the molecule
could become very large (though it won't appear to be moving due to
the recentering). If you are thermostatting the entire system, then
the solvent would be cooled to compensate. A better solution for this
simulation scenario is to use the "fix spring"_fix_spring.html command
to tether the molecule in place.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart

4
doc/read_data.html
View File

@ -250,7 +250,7 @@ integers (1, not 1.0).
header section. The atoms can be listed in any order. These are the
line formats for each <A HREF = "atom_style.html">atom style</A> in LAMMPS:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >angle</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
<TR><TD >atomic</TD><TD > atom-ID atom-type x y z</TD></TR>
<TR><TD >bond</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
@ -642,7 +642,7 @@ style dipole or ellipsoid.
<UL><LI>one line per atom
<LI>line syntax: depends on atom style
</UL>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >all styles except those listed</TD><TD > atom-ID vx vy vz</TD></TR>
<TR><TD >dipole</TD><TD > atom-ID vx vy vz wx wy wz</TD></TR>
<TR><TD >ellipsoid</TD><TD > atom-ID vx vy vz lx ly lz</TD></TR>

2
doc/variable.html
View File

@ -203,7 +203,7 @@ functions, group functions, atom vectors, compute references, and
other variables. There is one difference between <I>equal</I> and <I>atom</I>
variables; the syntax of Atom vector references is different.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >Number</TD><TD > 0.2, 1.0e20, -15.4, etc</TD></TR>
<TR><TD >Thermo keywords</TD><TD > vol, pe, ebond, etc</TD></TR>
<TR><TD >Math functions</TD><TD > add(x,y), sub(x,y), mult(x,y), div(x,y), neg(x), pow(x,y), exp(x), ln(x), sqrt(x)</TD></TR>