Loading doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="26 Jan 2017 version"> <META NAME="docnumber" CONTENT="13 Feb 2017 version"> <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> Loading @@ -21,7 +21,7 @@ <H1></H1> LAMMPS Documentation :c,h3 26 Jan 2017 version :c,h4 13 Feb 2017 version :c,h4 Version info: :h4 Loading doc/src/Section_commands.txt +1 −1 Original line number Diff line number Diff line Loading @@ -969,7 +969,7 @@ KOKKOS, o = USER-OMP, t = OPT. "lubricateU/poly"_pair_lubricateU.html, "meam"_pair_meam.html, "mie/cut (o)"_pair_mie.html, "morse (got)"_pair_morse.html, "morse (gkot)"_pair_morse.html, "nb3b/harmonic (o)"_pair_nb3b_harmonic.html, "nm/cut (o)"_pair_nm.html, "nm/cut/coul/cut (o)"_pair_nm.html, Loading doc/src/Section_errors.txt +19 −7 Original line number Diff line number Diff line Loading @@ -22,7 +22,7 @@ either conceptually, or as printed out by the program. 12.1 Common problems :link(err_1),h4 If two LAMMPS runs do not produce the same answer on different If two LAMMPS runs do not produce the exact same answer on different machines or different numbers of processors, this is typically not a bug. In theory you should get identical answers on any number of processors and on any machine. In practice, numerical round-off can Loading Loading @@ -80,12 +80,24 @@ order. If you mess this up, LAMMPS will often flag the error, but it may also simply read a bogus argument and assign a value that is valid, but not what you wanted. E.g. trying to read the string "abc" as an integer value of 0. Careful reading of the associated doc page for the command should allow you to fix these problems. Note that some commands allow for variables to be specified in place of numeric constants so that the value can be evaluated and change over the course of a run. This is typically done with the syntax {v_name} for a parameter, where name is the name of the variable. This is only allowed if the command documentation says it is. for the command should allow you to fix these problems. In most cases, where LAMMPS expects to read a number, either integer or floating point, it performs a stringent test on whether the provided input actually is an integer or floating-point number, respectively, and reject the input with an error message (for instance, when an integer is required, but a floating-point number 1.0 is provided): ERROR: Expected integer parameter in input script or data file :pre Some commands allow for using variable references in place of numeric constants so that the value can be evaluated and may change over the course of a run. This is typically done with the syntax {v_name} for a parameter, where name is the name of the variable. On the other hand, immediate variable expansion with the syntax ${name} is performed while reading the input and before parsing commands, NOTE: Using a variable reference (i.e. {v_name}) is only allowed if the documentation of the corresponding command explicitly says it is. Generally, LAMMPS will print a message to the screen and logfile and exit gracefully when it encounters a fatal error. Sometimes it will Loading doc/src/Section_start.txt +4 −5 Original line number Diff line number Diff line Loading @@ -413,7 +413,7 @@ uses (for performing 1d FFTs) when running the particle-particle particle-mesh (PPPM) option for long-range Coulombics via the "kspace_style"_kspace_style.html command. LAMMPS supports various open-source or vendor-supplied FFT libraries LAMMPS supports common open-source or vendor-supplied FFT libraries for this purpose. If you leave these 3 variables blank, LAMMPS will use the open-source "KISS FFT library"_http://kissfft.sf.net, which is included in the LAMMPS distribution. This library is portable to all Loading @@ -423,10 +423,9 @@ package in your build, you can also leave the 3 variables blank. Otherwise, select which kinds of FFTs to use as part of the FFT_INC setting by a switch of the form -DFFT_XXX. Recommended values for XXX are: MKL, SCSL, FFTW2, and FFTW3. Legacy options are: INTEL, SGI, ACML, and T3E. For backward compatability, using -DFFT_FFTW will use the FFTW2 library. Using -DFFT_NONE will use the KISS library described above. are: MKL or FFTW3. FFTW2 and NONE are supported as legacy options. Selecting -DFFT_FFTW will use the FFTW3 library and -DFFT_NONE will use the KISS library described above. You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables, so the compiler and linker can find the needed FFT header and library Loading doc/src/compute_group_group.txt +32 −3 Original line number Diff line number Diff line Loading @@ -16,10 +16,11 @@ ID, group-ID are documented in "compute"_compute.html command :ulb,l group/group = style name of this compute command :l group2-ID = group ID of second (or same) group :l zero or more keyword/value pairs may be appended :l keyword = {pair} or {kspace} or {boundary} :l keyword = {pair} or {kspace} or {boundary} or {molecule} :l {pair} value = {yes} or {no} {kspace} value = {yes} or {no} {boundary} value = {yes} or {no} :pre {boundary} value = {yes} or {no} {molecule} value = {off} or {inter} or {intra} :pre :ule [Examples:] Loading @@ -46,6 +47,13 @@ NOTE: The energies computed by the {pair} keyword do not include tail corrections, even if they are enabled via the "pair_modify"_pair_modify.html command. If the {molecule} keyword is set to {inter} or {intra} than an additional check is made based on the molecule IDs of the two atoms in each pair before including their pairwise interaction energy and force. For the {inter} setting, the two atoms must be in different molecules. For the {intra} setting, the two atoms must be in the same molecule. If the {kspace} keyword is set to {yes}, which is not the default, and if a "kspace_style"_kspace_style.html is defined, then the interaction energy will include a Kspace component which is the long-range Loading @@ -66,6 +74,10 @@ affect the force calculation and will be zero if one or both of the groups are charge neutral. This energy correction term is the same as that included in the regular Ewald and PPPM routines. NOTE: The {molecule} setting only affects the group/group contributions calculated by the {pair} keyword. It does not affect the group/group contributions calculated by the {kspace} keyword. This compute does not calculate any bond or angle or dihedral or improper interactions between atoms in the two groups. Loading @@ -78,6 +90,22 @@ work (FFTs, Ewald summation) as computing long-range forces for the entire system. Thus it can be costly to invoke this compute too frequently. NOTE: If you have a bonded system, then the settings of "special_bonds"_special_bonds.html command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This is the default setting for the "special_bonds"_special_bonds.html command, and means those pairwise interactions do not appear in the neighbor list. Because this compute uses a neighbor list, it also means those pairs will not be included in the group/group interaction. This does not apply when using long-range coulomb interactions ({coul/long}, {coul/msm}, {coul/wolf} or similar. One way to get around this would be to set special_bond scaling factors to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the "rerun"_rerun.html command to compute the group/group interactions for snapshots in the dump file. The rerun script can use a "special_bonds"_special_bonds.html command that includes all pairs in the neighbor list. If you desire a breakdown of the interactions into a pairwise and Kspace component, simply invoke the compute twice with the appropriate yes/no settings for the {pair} and {kspace} keywords. This is no more Loading Loading @@ -119,7 +147,8 @@ The {ewald} and {pppm} styles do. [Default:] The option defaults are pair = yes, kspace = no, and boundary = yes. The option defaults are pair = yes, kspace = no, boundary = yes, molecule = off. :line Loading Loading
doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="26 Jan 2017 version"> <META NAME="docnumber" CONTENT="13 Feb 2017 version"> <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> Loading @@ -21,7 +21,7 @@ <H1></H1> LAMMPS Documentation :c,h3 26 Jan 2017 version :c,h4 13 Feb 2017 version :c,h4 Version info: :h4 Loading
doc/src/Section_commands.txt +1 −1 Original line number Diff line number Diff line Loading @@ -969,7 +969,7 @@ KOKKOS, o = USER-OMP, t = OPT. "lubricateU/poly"_pair_lubricateU.html, "meam"_pair_meam.html, "mie/cut (o)"_pair_mie.html, "morse (got)"_pair_morse.html, "morse (gkot)"_pair_morse.html, "nb3b/harmonic (o)"_pair_nb3b_harmonic.html, "nm/cut (o)"_pair_nm.html, "nm/cut/coul/cut (o)"_pair_nm.html, Loading
doc/src/Section_errors.txt +19 −7 Original line number Diff line number Diff line Loading @@ -22,7 +22,7 @@ either conceptually, or as printed out by the program. 12.1 Common problems :link(err_1),h4 If two LAMMPS runs do not produce the same answer on different If two LAMMPS runs do not produce the exact same answer on different machines or different numbers of processors, this is typically not a bug. In theory you should get identical answers on any number of processors and on any machine. In practice, numerical round-off can Loading Loading @@ -80,12 +80,24 @@ order. If you mess this up, LAMMPS will often flag the error, but it may also simply read a bogus argument and assign a value that is valid, but not what you wanted. E.g. trying to read the string "abc" as an integer value of 0. Careful reading of the associated doc page for the command should allow you to fix these problems. Note that some commands allow for variables to be specified in place of numeric constants so that the value can be evaluated and change over the course of a run. This is typically done with the syntax {v_name} for a parameter, where name is the name of the variable. This is only allowed if the command documentation says it is. for the command should allow you to fix these problems. In most cases, where LAMMPS expects to read a number, either integer or floating point, it performs a stringent test on whether the provided input actually is an integer or floating-point number, respectively, and reject the input with an error message (for instance, when an integer is required, but a floating-point number 1.0 is provided): ERROR: Expected integer parameter in input script or data file :pre Some commands allow for using variable references in place of numeric constants so that the value can be evaluated and may change over the course of a run. This is typically done with the syntax {v_name} for a parameter, where name is the name of the variable. On the other hand, immediate variable expansion with the syntax ${name} is performed while reading the input and before parsing commands, NOTE: Using a variable reference (i.e. {v_name}) is only allowed if the documentation of the corresponding command explicitly says it is. Generally, LAMMPS will print a message to the screen and logfile and exit gracefully when it encounters a fatal error. Sometimes it will Loading
doc/src/Section_start.txt +4 −5 Original line number Diff line number Diff line Loading @@ -413,7 +413,7 @@ uses (for performing 1d FFTs) when running the particle-particle particle-mesh (PPPM) option for long-range Coulombics via the "kspace_style"_kspace_style.html command. LAMMPS supports various open-source or vendor-supplied FFT libraries LAMMPS supports common open-source or vendor-supplied FFT libraries for this purpose. If you leave these 3 variables blank, LAMMPS will use the open-source "KISS FFT library"_http://kissfft.sf.net, which is included in the LAMMPS distribution. This library is portable to all Loading @@ -423,10 +423,9 @@ package in your build, you can also leave the 3 variables blank. Otherwise, select which kinds of FFTs to use as part of the FFT_INC setting by a switch of the form -DFFT_XXX. Recommended values for XXX are: MKL, SCSL, FFTW2, and FFTW3. Legacy options are: INTEL, SGI, ACML, and T3E. For backward compatability, using -DFFT_FFTW will use the FFTW2 library. Using -DFFT_NONE will use the KISS library described above. are: MKL or FFTW3. FFTW2 and NONE are supported as legacy options. Selecting -DFFT_FFTW will use the FFTW3 library and -DFFT_NONE will use the KISS library described above. You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables, so the compiler and linker can find the needed FFT header and library Loading
doc/src/compute_group_group.txt +32 −3 Original line number Diff line number Diff line Loading @@ -16,10 +16,11 @@ ID, group-ID are documented in "compute"_compute.html command :ulb,l group/group = style name of this compute command :l group2-ID = group ID of second (or same) group :l zero or more keyword/value pairs may be appended :l keyword = {pair} or {kspace} or {boundary} :l keyword = {pair} or {kspace} or {boundary} or {molecule} :l {pair} value = {yes} or {no} {kspace} value = {yes} or {no} {boundary} value = {yes} or {no} :pre {boundary} value = {yes} or {no} {molecule} value = {off} or {inter} or {intra} :pre :ule [Examples:] Loading @@ -46,6 +47,13 @@ NOTE: The energies computed by the {pair} keyword do not include tail corrections, even if they are enabled via the "pair_modify"_pair_modify.html command. If the {molecule} keyword is set to {inter} or {intra} than an additional check is made based on the molecule IDs of the two atoms in each pair before including their pairwise interaction energy and force. For the {inter} setting, the two atoms must be in different molecules. For the {intra} setting, the two atoms must be in the same molecule. If the {kspace} keyword is set to {yes}, which is not the default, and if a "kspace_style"_kspace_style.html is defined, then the interaction energy will include a Kspace component which is the long-range Loading @@ -66,6 +74,10 @@ affect the force calculation and will be zero if one or both of the groups are charge neutral. This energy correction term is the same as that included in the regular Ewald and PPPM routines. NOTE: The {molecule} setting only affects the group/group contributions calculated by the {pair} keyword. It does not affect the group/group contributions calculated by the {kspace} keyword. This compute does not calculate any bond or angle or dihedral or improper interactions between atoms in the two groups. Loading @@ -78,6 +90,22 @@ work (FFTs, Ewald summation) as computing long-range forces for the entire system. Thus it can be costly to invoke this compute too frequently. NOTE: If you have a bonded system, then the settings of "special_bonds"_special_bonds.html command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This is the default setting for the "special_bonds"_special_bonds.html command, and means those pairwise interactions do not appear in the neighbor list. Because this compute uses a neighbor list, it also means those pairs will not be included in the group/group interaction. This does not apply when using long-range coulomb interactions ({coul/long}, {coul/msm}, {coul/wolf} or similar. One way to get around this would be to set special_bond scaling factors to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the "rerun"_rerun.html command to compute the group/group interactions for snapshots in the dump file. The rerun script can use a "special_bonds"_special_bonds.html command that includes all pairs in the neighbor list. If you desire a breakdown of the interactions into a pairwise and Kspace component, simply invoke the compute twice with the appropriate yes/no settings for the {pair} and {kspace} keywords. This is no more Loading Loading @@ -119,7 +147,8 @@ The {ewald} and {pppm} styles do. [Default:] The option defaults are pair = yes, kspace = no, and boundary = yes. The option defaults are pair = yes, kspace = no, boundary = yes, molecule = off. :line Loading
