thermo keywords = ke, vol, atoms, ... +
thermo keywords = ke, vol, atoms, ... other variables = v_a, v_myvar, ... math functions = div(x,y), mult(x,y), add(x,y), ... group functions = mass(group), xcm(group,x), ... -atom values = x123, y3, vx34, ... -compute values = c_mytemp0, c_thermo_press3, ... - +atom values = x[123], y[3], vx[34], ... +compute values = c_mytemp[0], c_thermo_press[3], ... +
Adding keywords for the thermo_style custom command (which can then be accessed by variables) was discussed here on this page. diff --git a/doc/Section_modify.txt b/doc/Section_modify.txt index ed04384e17..b1e64d1ba0 100644 --- a/doc/Section_modify.txt +++ b/doc/Section_modify.txt @@ -580,8 +580,8 @@ thermo keywords = ke, vol, atoms, ... other variables = v_a, v_myvar, ... math functions = div(x,y), mult(x,y), add(x,y), ... group functions = mass(group), xcm(group,x), ... -atom values = x[123], y[3], vx[34], ... -compute values = c_mytemp[0], c_thermo_press[3], ... +atom values = x\[123\], y\[3\], vx\[34\], ... +compute values = c_mytemp\[0\], c_thermo_press\[3\], ... :pre Adding keywords for the "thermo_style custom"_thermo_style.html command (which can then be accessed by variables) was discussed diff --git a/doc/Section_start.html b/doc/Section_start.html index 0321152035..270f7985a0 100644 --- a/doc/Section_start.html +++ b/doc/Section_start.html @@ -901,11 +901,24 @@ interface and how to extend it for your needs.
By default, LAMMPS runs by reading commands from stdin; e.g. lmp_linux -< in.file. This means you first create an input script (e.g. in.file) -containing the desired commands. This section -describes how input scripts are structured and what commands they -contain. +
By default, LAMMPS runs by reading commands from standard input. Thus +if you run the LAMMPS executable by itself, e.g. +
+lmp_linux ++
it will simply wait, expecting commands from the keyboard. Typically +you should put commands in an input script and use I/O redirection, +e.g. +
+lmp_linux < in.file ++
For parallel environments this should also work. If it does not, use +the '-in' command-line switch, e.g. +
+lmp_linux -in in.file ++
This section describes how input scripts are +structured and what commands they contain.
You can test LAMMPS on any of the sample inputs provided in the examples or bench directory. Input scripts are named in.* and sample @@ -921,8 +934,9 @@ cp lmp_linux ../bench cd ../bench mpirun -np 4 lmp_linux < in.lj -
See this page for timings for this and the other benchmarks -on various platforms. +
See this page for timings for this and the other benchmarks on +various platforms. Note that some of the example scripts require +LAMMPS to be built with one or more of its optional packages.
@@ -951,12 +965,13 @@ with the name of your LAMMPS input script.For the MPI version, which allows you to run LAMMPS under Windows on multiple processors, follow these steps:
-Specify a file to use as an input script. This is an optional switch when running LAMMPS in one-partition mode. If it is not specified, -LAMMPS reads its input script from stdin - e.g. lmp_linux < in.run. -This is a required switch when running LAMMPS in multi-partition mode, -since multiple processors cannot all read from stdin. +LAMMPS reads its script from standard input, typically from a script +via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should +also work in parallel, but if it does not (in the unlikely case that +an MPI implementation does not support it), then use the -in flag. +Note that this is a required switch when running LAMMPS in +multi-partition mode, since multiple processors cannot all read from +stdin.
-help-
Print a list of options compiled into this executable for each LAMMPS -style (atom_style, fix, compute, pair_style, bond_style, etc). This -can help you know if the command you want to use was included via the -appropriate package. LAMMPS will print the info and immediately exit -if this switch is used. +
Print a brief help summary and a list of options compiled into this +executable for each LAMMPS style (atom_style, fix, compute, +pair_style, bond_style, etc). This can tell you if the command you +want to use was included via the appropriate package at compile time. +LAMMPS will print the info and immediately exit if this switch is +used.
-log filediff --git a/doc/Section_start.txt b/doc/Section_start.txt index 8f1b624fcd..9ab2f215f9 100644 --- a/doc/Section_start.txt +++ b/doc/Section_start.txt @@ -895,11 +895,24 @@ interface and how to extend it for your needs. 2.6 Running LAMMPS :h4,link(start_6) -By default, LAMMPS runs by reading commands from stdin; e.g. lmp_linux -< in.file. This means you first create an input script (e.g. in.file) -containing the desired commands. "This section"_Section_commands.html -describes how input scripts are structured and what commands they -contain. +By default, LAMMPS runs by reading commands from standard input. Thus +if you run the LAMMPS executable by itself, e.g. + +lmp_linux :pre + +it will simply wait, expecting commands from the keyboard. Typically +you should put commands in an input script and use I/O redirection, +e.g. + +lmp_linux < in.file :pre + +For parallel environments this should also work. If it does not, use +the '-in' command-line switch, e.g. + +lmp_linux -in in.file :pre + +"This section"_Section_commands.html describes how input scripts are +structured and what commands they contain. You can test LAMMPS on any of the sample inputs provided in the examples or bench directory. Input scripts are named in.* and sample @@ -915,8 +928,9 @@ cp lmp_linux ../bench cd ../bench mpirun -np 4 lmp_linux < in.lj :pre -See "this page"_bench for timings for this and the other benchmarks -on various platforms. +See "this page"_bench for timings for this and the other benchmarks on +various platforms. Note that some of the example scripts require +LAMMPS to be built with one or more of its optional packages. :link(bench,http://lammps.sandia.gov/bench.html) @@ -945,12 +959,13 @@ with the name of your LAMMPS input script. :l,ule For the MPI version, which allows you to run LAMMPS under Windows on multiple processors, follow these steps: -Download and install +Download and install "MPICH2"_http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads for Windows. :ulb,l -You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2 package. Put them in -same directory (or path) as the LAMMPS Windows executable. :l +You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2 +package. Put them in same directory (or path) as the LAMMPS Windows +executable. :l Get a command prompt by going to Start->Run... , then typing "cmd". :l @@ -958,15 +973,17 @@ then typing "cmd". :l Move to the directory where you have saved lmp_win_mpi.exe (e.g. by typing: cd "Documents"). :l -Then type something like this: "mpiexec -np 4 -localonly lmp_win_mpi -in in.lj", -replacing in.lj with the name of your LAMMPS input script. :l -Note that you may need to provide smpd with a passphrase --- it doesn't matter what you -type. :l -In this mode, output may not immediately show up on the screen, so -if your input script takes a long time to execute, you may need to be -patient before the output shows up. :l -Alternatively, you can still use this executable to run on a single processor by -typing something like: "lmp_win_mpi -in in.lj". :l,ule +Then type something like this: "mpiexec -localonly 4 lmp_win_mpi -in +in.lj", replacing in.lj with the name of your LAMMPS input script. :l + +Note that you may need to provide smpd with a passphrase (it doesn't +matter what you type). :l + +In this mode, output may not immediately show up on the screen, so if +your input script takes a long time to execute, you may need to be +patient before the output shows up. :l Alternatively, you can still +use this executable to run on a single processor by typing something +like: "lmp_win_mpi -in in.lj". :l,ule :line @@ -1053,17 +1070,22 @@ set by using the "echo"_echo.html command in the input script itself. Specify a file to use as an input script. This is an optional switch when running LAMMPS in one-partition mode. If it is not specified, -LAMMPS reads its input script from stdin - e.g. lmp_linux < in.run. -This is a required switch when running LAMMPS in multi-partition mode, -since multiple processors cannot all read from stdin. +LAMMPS reads its script from standard input, typically from a script +via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should +also work in parallel, but if it does not (in the unlikely case that +an MPI implementation does not support it), then use the -in flag. +Note that this is a required switch when running LAMMPS in +multi-partition mode, since multiple processors cannot all read from +stdin. -help :pre -Print a list of options compiled into this executable for each LAMMPS -style (atom_style, fix, compute, pair_style, bond_style, etc). This -can help you know if the command you want to use was included via the -appropriate package. LAMMPS will print the info and immediately exit -if this switch is used. +Print a brief help summary and a list of options compiled into this +executable for each LAMMPS style (atom_style, fix, compute, +pair_style, bond_style, etc). This can tell you if the command you +want to use was included via the appropriate package at compile time. +LAMMPS will print the info and immediately exit if this switch is +used. -log file :pre diff --git a/doc/Section_tools.html b/doc/Section_tools.html index 5c72e09e76..c6b44e6fb2 100644 --- a/doc/Section_tools.html +++ b/doc/Section_tools.html @@ -47,6 +47,7 @@ own sub-directories with their own Makefiles.
The colvars directory contains a collection of tools for postprocessing +data produced by the colvars collective variable library. +To compile the tools, edit the makefile for your system and run "make". +
+Please report problems and issues the colvars library and its tools +at: https://github.com/colvars/colvars/issues +
+abf_integrate: +
+MC-based integration of multidimensional free energy gradient +Version 20110511 +
+Syntax: ./abf_integrate < filename > [-n < nsteps >] [-t < temp >] [-m [0|1] (metadynamics)] [-h < hill_height >] [-f < variable_hill_factor >] ++
The LAMMPS interface to the colvars collective variable library, as +well as these tools, were created by Axel Kohlmeyer (akohlmey at +gmail.com) at ICTP, Italy. +
+The tools/createatoms directory contains a Fortran program called @@ -156,7 +179,7 @@ suitable for visualizing with the xmovie tool, as if it been output with a dump command from LAMMPS itself. The syntax for running the tool is
-data2xmovie options < infile > outfile +data2xmovie [options] < infile > outfileSee the top of the data2xmovie.c file for a discussion of the options.
@@ -495,7 +518,7 @@ it can find the appropriate X libraries to link against.The syntax for running xmovie is
-xmovie options dump.file1 dump.file2 ... +xmovie [options] dump.file1 dump.file2 ...If you just type "xmovie" you will see a list of options. Note that by default, LAMMPS dump files are in scaled coordinates, so you diff --git a/doc/Section_tools.txt b/doc/Section_tools.txt index c2383a29e8..1d0772b96b 100644 --- a/doc/Section_tools.txt +++ b/doc/Section_tools.txt @@ -43,6 +43,7 @@ own sub-directories with their own Makefiles. "binary2txt"_#binary "ch2lmp"_#charmm "chain"_#chain +"colvars"_#colvars "createatoms"_#create "data2xmovie"_#data "eam database"_#eamdb @@ -132,6 +133,28 @@ system for the "chain benchmark"_Section_perf.html. :line +colvars tools :h4,link(colvars) + +The colvars directory contains a collection of tools for postprocessing +data produced by the colvars collective variable library. +To compile the tools, edit the makefile for your system and run "make". + +Please report problems and issues the colvars library and its tools +at: https://github.com/colvars/colvars/issues + +abf_integrate: + +MC-based integration of multidimensional free energy gradient +Version 20110511 + +Syntax: ./abf_integrate < filename > \[-n < nsteps >\] \[-t < temp >\] \[-m \[0|1\] (metadynamics)\] \[-h < hill_height >\] \[-f < variable_hill_factor >\] :pre + +The LAMMPS interface to the colvars collective variable library, as +well as these tools, were created by Axel Kohlmeyer (akohlmey at +gmail.com) at ICTP, Italy. + +:line + createatoms tool :h4,link(create) The tools/createatoms directory contains a Fortran program called @@ -152,7 +175,7 @@ suitable for visualizing with the "xmovie"_#xmovie tool, as if it had been output with a dump command from LAMMPS itself. The syntax for running the tool is -data2xmovie [options] < infile > outfile :pre +data2xmovie \[options\] < infile > outfile :pre See the top of the data2xmovie.c file for a discussion of the options. @@ -491,7 +514,7 @@ it can find the appropriate X libraries to link against. The syntax for running xmovie is -xmovie [options] dump.file1 dump.file2 ... :pre +xmovie \[options\] dump.file1 dump.file2 ... :pre If you just type "xmovie" you will see a list of options. Note that by default, LAMMPS dump files are in scaled coordinates, so you diff --git a/doc/compute_atom_molecule.html b/doc/compute_atom_molecule.html index cf51daf83b..612812d85c 100644 --- a/doc/compute_atom_molecule.html +++ b/doc/compute_atom_molecule.html @@ -34,7 +34,7 @@
Examples:
compute 1 all atom/molecule c_ke c_pe -compute 1 top atom/molecule v_myFormula c_stress3 +compute 1 top atom/molecule v_myFormula c_stress[3]Description:
diff --git a/doc/compute_atom_molecule.txt b/doc/compute_atom_molecule.txt index af7e72637f..5707becef6 100644 --- a/doc/compute_atom_molecule.txt +++ b/doc/compute_atom_molecule.txt @@ -26,7 +26,7 @@ input = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l [Examples:] compute 1 all atom/molecule c_ke c_pe -compute 1 top atom/molecule v_myFormula c_stress[3] :pre +compute 1 top atom/molecule v_myFormula c_stress\[3\] :pre [Description:] diff --git a/doc/compute_reduce.html b/doc/compute_reduce.html index 6ca3e563d5..6a02a01eea 100644 --- a/doc/compute_reduce.html +++ b/doc/compute_reduce.html @@ -52,8 +52,8 @@compute 1 all reduce sum c_force compute 1 all reduce/region subbox sum c_force -compute 2 all reduce min c_press2 f_ave v_myKE -compute 3 fluid reduce max c_index1 c_index2 c_dist replace 1 3 replace 2 3 +compute 2 all reduce min c_press[2] f_ave v_myKE +compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3Description:
diff --git a/doc/compute_reduce.txt b/doc/compute_reduce.txt index 7034922b30..c4cf88356a 100644 --- a/doc/compute_reduce.txt +++ b/doc/compute_reduce.txt @@ -39,8 +39,8 @@ keyword = {replace} :l compute 1 all reduce sum c_force compute 1 all reduce/region subbox sum c_force -compute 2 all reduce min c_press[2] f_ave v_myKE -compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3 :pre +compute 2 all reduce min c_press\[2\] f_ave v_myKE +compute 3 fluid reduce max c_index\[1\] c_index\[2\] c_dist replace 1 3 replace 2 3 :pre [Description:] diff --git a/doc/fix_property_atom.html b/doc/fix_property_atom.html index 43b9f66c41..133e21322d 100644 --- a/doc/fix_property_atom.html +++ b/doc/fix_property_atom.html @@ -175,7 +175,7 @@ dump file:fix prop all property/atom i_flag1 d_flag2 compute 1 all property/atom i_flag1 d_flag2 -dump 1 all custom 100 tmp.dump id x y z c_11 c_12 +dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2]
diff --git a/doc/fix_property_atom.txt b/doc/fix_property_atom.txt index bdafe9108a..658251cd67 100644 --- a/doc/fix_property_atom.txt +++ b/doc/fix_property_atom.txt @@ -165,7 +165,7 @@ dump file: fix prop all property/atom i_flag1 d_flag2 compute 1 all property/atom i_flag1 d_flag2 -dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2] :pre +dump 1 all custom 100 tmp.dump id x y z c_1\[1\] c_1\[2\] :pre :line