From 7b264d35fa7eadffafcbe9a22e67977d733c38b8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 15 May 2019 14:53:51 -0400 Subject: [PATCH 01/11] remove dead code --- src/USER-OMP/pair_rebo_omp.cpp | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/USER-OMP/pair_rebo_omp.cpp b/src/USER-OMP/pair_rebo_omp.cpp index bd98c6426c..621de04ebb 100644 --- a/src/USER-OMP/pair_rebo_omp.cpp +++ b/src/USER-OMP/pair_rebo_omp.cpp @@ -41,8 +41,6 @@ void PairREBOOMP::settings(int narg, char ** /* arg */) void PairREBOOMP::spline_init() { PairAIREBO::spline_init(); - int i,j,k; - PCCf[0][2] = 0.007860700254745; PCCf[0][3] = 0.016125364564267; PCCf[1][1] = 0.003026697473481; From 27a2d0cbd4eaef91226d73fb697d24532dc4c039 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 May 2019 08:55:03 -0400 Subject: [PATCH 02/11] add option to restrict coordination number by group --- doc/src/compute_coord_atom.txt | 19 ++++++++++++----- src/compute_coord_atom.cpp | 39 ++++++++++++++++++++++++---------- src/compute_coord_atom.h | 3 +++ 3 files changed, 45 insertions(+), 16 deletions(-) diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt index ddc4cc82d3..893efc6cf6 100644 --- a/doc/src/compute_coord_atom.txt +++ b/doc/src/compute_coord_atom.txt @@ -15,8 +15,9 @@ compute ID group-ID coord/atom cstyle args ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l coord/atom = style name of this compute command :l cstyle = {cutoff} or {orientorder} :l - {cutoff} args = cutoff typeN + {cutoff} args = cutoff \[group group2-ID\] typeN cutoff = distance within which to count coordination neighbors (distance units) + group {group2-ID} = select group-ID to restrict which atoms to cound for coordination number (optional) typeN = atom type for Nth coordination count (see asterisk form below) {orientorder} args = orientorderID threshold orientorderID = ID of an orientorder/atom compute @@ -28,6 +29,7 @@ cstyle = {cutoff} or {orientorder} :l compute 1 all coord/atom cutoff 2.0 compute 1 all coord/atom cutoff 6.0 1 2 compute 1 all coord/atom cutoff 6.0 2*4 5*8 * +compute 1 solute coord/atom cutoff 2.0 group solvent compute 1 all coord/atom orientorder 2 0.5 :pre [Description:] @@ -38,9 +40,14 @@ meaning of the resulting value depend on the {cstyle} keyword used. The {cutoff} cstyle calculates one or more traditional coordination numbers for each atom. A coordination number is defined as the number -of neighbor atoms with specified atom type(s) that are within the -specified cutoff distance from the central atom. Atoms not in the -specified group are included in the coordination number tally. +of neighbor atoms with specified atom type(s), and optionally within +the specified group, that are within the specified cutoff distance from +the central atom. The compute group selects only the central atoms; all +neighboring atoms, unless selected by type, type range, or group option, +are included in the coordinations number tally. + +The optional {group} keyword allows to specify from which group atoms +contribute to the coordination number. Default setting is group 'all'. The {typeN} keywords allow specification of which atom types contribute to each coordination number. One coordination number is @@ -122,7 +129,9 @@ explained above. "compute cluster/atom"_compute_cluster_atom.html "compute orientorder/atom"_compute_orientorder_atom.html -[Default:] none +[Default:] + +group = all :line diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp index 33b318ea17..021d092bc4 100644 --- a/src/compute_coord_atom.cpp +++ b/src/compute_coord_atom.cpp @@ -25,6 +25,7 @@ #include "force.h" #include "pair.h" #include "comm.h" +#include "group.h" #include "memory.h" #include "error.h" @@ -37,10 +38,12 @@ using namespace LAMMPS_NS; ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), typelo(NULL), typehi(NULL), cvec(NULL), carray(NULL), - id_orientorder(NULL), normv(NULL) + group2(NULL), id_orientorder(NULL), normv(NULL) { if (narg < 5) error->all(FLERR,"Illegal compute coord/atom command"); + jgroup = group->find("all"); + jgroupbit = group->bitmask[jgroup]; cstyle = NONE; if (strcmp(arg[3],"cutoff") == 0) { @@ -48,18 +51,29 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) : double cutoff = force->numeric(FLERR,arg[4]); cutsq = cutoff*cutoff; - ncol = narg-5 + 1; + int iarg = 5; + if ((narg > 6) && (strcmp(arg[5],"group") == 0)) { + int len = strlen(arg[6])+1; + group2 = new char[len]; + strcpy(group2,arg[6]); + iarg += 2; + jgroup = group->find(group2); + if (jgroup == -1) + error->all(FLERR,"Compute coord/atom group2 ID does not exist"); + jgroupbit = group->bitmask[jgroup]; + } + + ncol = narg-iarg + 1; int ntypes = atom->ntypes; typelo = new int[ncol]; typehi = new int[ncol]; - if (narg == 5) { + if (narg == iarg) { ncol = 1; typelo[0] = 1; typehi[0] = ntypes; } else { ncol = 0; - int iarg = 5; while (iarg < narg) { force->bounds(FLERR,arg[iarg],ntypes,typelo[ncol],typehi[ncol]); if (typelo[ncol] > typehi[ncol]) @@ -106,6 +120,7 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) : ComputeCoordAtom::~ComputeCoordAtom() { + delete [] group2; delete [] typelo; delete [] typehi; memory->destroy(cvec); @@ -229,13 +244,15 @@ void ComputeCoordAtom::compute_peratom() j = jlist[jj]; j &= NEIGHMASK; - jtype = type[j]; - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - if (rsq < cutsq && jtype >= typelo[0] && jtype <= typehi[0]) - n++; + if (mask[j] & jgroupbit) { + jtype = type[j]; + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq < cutsq && jtype >= typelo[0] && jtype <= typehi[0]) + n++; + } } cvec[i] = n; diff --git a/src/compute_coord_atom.h b/src/compute_coord_atom.h index 2bbc1b6720..0c1cc90f84 100644 --- a/src/compute_coord_atom.h +++ b/src/compute_coord_atom.h @@ -45,6 +45,9 @@ class ComputeCoordAtom : public Compute { double *cvec; double **carray; + char *group2; + int jgroup,jgroupbit; + class ComputeOrientOrderAtom *c_orientorder; char *id_orientorder; double threshold; From fb8d31422d2a41f596489e088b753610d4a8c8b2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 May 2019 09:06:17 -0400 Subject: [PATCH 03/11] fix typo --- doc/src/compute_coord_atom.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt index 893efc6cf6..01901ff77b 100644 --- a/doc/src/compute_coord_atom.txt +++ b/doc/src/compute_coord_atom.txt @@ -44,7 +44,7 @@ of neighbor atoms with specified atom type(s), and optionally within the specified group, that are within the specified cutoff distance from the central atom. The compute group selects only the central atoms; all neighboring atoms, unless selected by type, type range, or group option, -are included in the coordinations number tally. +are included in the coordination number tally. The optional {group} keyword allows to specify from which group atoms contribute to the coordination number. Default setting is group 'all'. From c7eb9a86262b1553a10cddef98982580f9b31b82 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 17 May 2019 15:25:25 -0400 Subject: [PATCH 04/11] there really isn't a problem with calling this compute multiple times --- src/compute_coord_atom.cpp | 6 ------ src/compute_coord_atom.h | 4 ---- 2 files changed, 10 deletions(-) diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp index 021d092bc4..54f4c70c71 100644 --- a/src/compute_coord_atom.cpp +++ b/src/compute_coord_atom.cpp @@ -158,12 +158,6 @@ void ComputeCoordAtom::init() neighbor->requests[irequest]->half = 0; neighbor->requests[irequest]->full = 1; neighbor->requests[irequest]->occasional = 1; - - int count = 0; - for (int i = 0; i < modify->ncompute; i++) - if (strcmp(modify->compute[i]->style,"coord/atom") == 0) count++; - if (count > 1 && comm->me == 0) - error->warning(FLERR,"More than one compute coord/atom"); } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_coord_atom.h b/src/compute_coord_atom.h index 0c1cc90f84..2a54613cc6 100644 --- a/src/compute_coord_atom.h +++ b/src/compute_coord_atom.h @@ -97,8 +97,4 @@ E: Compute coord/atom cutoff is longer than pairwise cutoff Cannot compute coordination at distances longer than the pair cutoff, since those atoms are not in the neighbor list. -W: More than one compute coord/atom - -It is not efficient to use compute coord/atom more than once. - */ From 35bb2ac2a30095e9a3e621cf21fb898ed9742535 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 18 May 2019 09:25:20 -0400 Subject: [PATCH 05/11] fix typo --- doc/src/compute_coord_atom.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt index 01901ff77b..af0be4be56 100644 --- a/doc/src/compute_coord_atom.txt +++ b/doc/src/compute_coord_atom.txt @@ -17,7 +17,7 @@ coord/atom = style name of this compute command :l cstyle = {cutoff} or {orientorder} :l {cutoff} args = cutoff \[group group2-ID\] typeN cutoff = distance within which to count coordination neighbors (distance units) - group {group2-ID} = select group-ID to restrict which atoms to cound for coordination number (optional) + group {group2-ID} = select group-ID to restrict which atoms to consider for coordination number (optional) typeN = atom type for Nth coordination count (see asterisk form below) {orientorder} args = orientorderID threshold orientorderID = ID of an orientorder/atom compute From e3823a521c6b5d260399b4fd1e93478a9b96190f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 18 May 2019 15:36:13 -0400 Subject: [PATCH 06/11] remove leftover references to removed MEAM package --- doc/src/Build_extras.txt | 44 --------------------------------------- doc/src/Build_package.txt | 1 - 2 files changed, 45 deletions(-) diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index 3b9da2db39..3fc23c5618 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -30,7 +30,6 @@ This is the list of packages that may require additional steps. "KIM"_#kim, "KOKKOS"_#kokkos, "LATTE"_#latte, -"MEAM"_#meam, "MESSAGE"_#message, "MSCG"_#mscg, "OPT"_#opt, @@ -351,49 +350,6 @@ the compiler you use on your system to build LATTE. :line -MEAM package :h4,link(meam) - -NOTE: the use of the MEAM package is discouraged, as it has been -superseded by the USER-MEAMC package, which is a direct translation of -the Fortran code in the MEAM library to C++. The code in USER-MEAMC -should be functionally equivalent to the MEAM package, fully supports -use of "pair_style hybrid"_pair_hybrid.html (the MEAM package does -not), and has optimizations that make it significantly faster than the -MEAM package. - -[CMake build]: - -No additional settings are needed besides "-D PKG_MEAM=yes". - -[Traditional make]: - -Before building LAMMPS, you must build the MEAM library in lib/meam. -You can build the MEAM library manually if you prefer; follow the -instructions in lib/meam/README. You can also do it in one step from -the lammps/src dir, using a command like these, which simply invoke -the lib/meam/Install.py script with the specified args: - -make lib-meam # print help message -make lib-meam args="-m mpi" # build with default Fortran compiler compatible with your MPI library -make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran) -make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre - -NOTE: You should test building the MEAM library with both the Intel -and GNU compilers to see if a simulation runs faster with one versus -the other on your system. - -The build should produce two files: lib/meam/libmeam.a and -lib/meam/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with -Fortran (MEAM library). Typically the two compilers used for LAMMPS -and the MEAM library need to be consistent (e.g. both Intel or both -GNU compilers). If necessary, you can edit/create a new -lib/meam/Makefile.machine file for your system, which should define an -EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine -file. - -:line - MESSAGE package :h4,link(message) This package can optionally include support for messaging via sockets, diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt index 401f53f638..869175e160 100644 --- a/doc/src/Build_package.txt +++ b/doc/src/Build_package.txt @@ -41,7 +41,6 @@ packages: "KIM"_Build_extras.html#kim, "KOKKOS"_Build_extras.html#kokkos, "LATTE"_Build_extras.html#latte, -"MEAM"_Build_extras.html#meam, "MESSAGE"_Build_extras.html#message, "MSCG"_Build_extras.html#mscg, "OPT"_Build_extras.html#opt, From 50082c287d181b6b34165a9a9542ef80e8a90471 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 18 May 2019 15:41:38 -0400 Subject: [PATCH 07/11] sphinxcontrib-spelling has been updated for Sphinx 2.x. remove enforcing to use old version --- doc/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/Makefile b/doc/Makefile index fa60aa3698..5c679440b8 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -211,7 +211,7 @@ $(VENV): @( \ $(VIRTUALENV) -p $(PYTHON) $(VENV); \ . $(VENV)/bin/activate; \ - pip install Sphinx==1.7.6; \ + pip install Sphinx; \ deactivate;\ ) From 10419345682dfdf224c3cf8833a2ae3a346b7f9f Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Mon, 20 May 2019 10:01:40 -0600 Subject: [PATCH 08/11] Fix bug in pair_eam_alloy_kokkos and pair_eam_fs_kokkos --- src/KOKKOS/pair_eam_alloy_kokkos.cpp | 4 ++-- src/KOKKOS/pair_eam_fs_kokkos.cpp | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index b580f00ed0..b5442c0d29 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -569,13 +569,13 @@ void PairEAMAlloyKokkos::operator()(TagPairEAMAlloyKernelA::operator()(TagPairEAMFSKernelA Date: Mon, 20 May 2019 14:15:04 -0400 Subject: [PATCH 09/11] avoid segfault and print more meaningful error message with empty lines in coeff sections --- doc/src/Errors_messages.txt | 20 ++++++++++---------- src/read_data.cpp | 20 ++++++++++++++------ src/read_data.h | 20 ++++++++++---------- 3 files changed, 34 insertions(+), 26 deletions(-) diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt index fb5003e602..4f3bbe8c24 100644 --- a/doc/src/Errors_messages.txt +++ b/doc/src/Errors_messages.txt @@ -9990,25 +9990,25 @@ quote. :dd Self-explanatory. :dd -{Unexpected end of AngleCoeffs section} :dt +{Unexpected empty line in AngleCoeffs section} :dt -Read a blank line. :dd +Read a blank line where there should be coefficient data. :dd -{Unexpected end of BondCoeffs section} :dt +{Unexpected empty line in BondCoeffs section} :dt -Read a blank line. :dd +Read a blank line where there should be coefficient data. :dd -{Unexpected end of DihedralCoeffs section} :dt +{Unexpected empty line in DihedralCoeffs section} :dt -Read a blank line. :dd +Read a blank line where there should be coefficient data. :dd -{Unexpected end of ImproperCoeffs section} :dt +{Unexpected empty line in ImproperCoeffs section} :dt -Read a blank line. :dd +Read a blank line where there should be coefficient data. :dd -{Unexpected end of PairCoeffs section} :dt +{Unexpected empty line in PairCoeffs section} :dt -Read a blank line. :dd +Read a blank line where there should be coefficient data. :dd {Unexpected end of custom file} :dt diff --git a/src/read_data.cpp b/src/read_data.cpp index e2efbaaefa..e70a526c38 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -1768,7 +1768,8 @@ void ReadData::paircoeffs() next = strchr(buf,'\n'); *next = '\0'; parse_coeffs(buf,NULL,1,2,toffset); - if (narg == 0) error->all(FLERR,"Unexpected end of PairCoeffs section"); + if (narg == 0) + error->all(FLERR,"Unexpected empty line in PairCoeffs section"); force->pair->coeff(narg,arg); buf = next + 1; } @@ -1794,7 +1795,8 @@ void ReadData::pairIJcoeffs() next = strchr(buf,'\n'); *next = '\0'; parse_coeffs(buf,NULL,0,2,toffset); - if (narg == 0) error->all(FLERR,"Unexpected end of PairCoeffs section"); + if (narg == 0) + error->all(FLERR,"Unexpected empty line in PairCoeffs section"); force->pair->coeff(narg,arg); buf = next + 1; } @@ -1818,7 +1820,8 @@ void ReadData::bondcoeffs() next = strchr(buf,'\n'); *next = '\0'; parse_coeffs(buf,NULL,0,1,boffset); - if (narg == 0) error->all(FLERR,"Unexpected end of BondCoeffs section"); + if (narg == 0) + error->all(FLERR,"Unexpected empty line in BondCoeffs section"); force->bond->coeff(narg,arg); buf = next + 1; } @@ -1844,7 +1847,7 @@ void ReadData::anglecoeffs(int which) if (which == 0) parse_coeffs(buf,NULL,0,1,aoffset); else if (which == 1) parse_coeffs(buf,"bb",0,1,aoffset); else if (which == 2) parse_coeffs(buf,"ba",0,1,aoffset); - if (narg == 0) error->all(FLERR,"Unexpected end of AngleCoeffs section"); + if (narg == 0) error->all(FLERR,"Unexpected empty line in AngleCoeffs section"); force->angle->coeff(narg,arg); buf = next + 1; } @@ -1873,7 +1876,8 @@ void ReadData::dihedralcoeffs(int which) else if (which == 3) parse_coeffs(buf,"at",0,1,doffset); else if (which == 4) parse_coeffs(buf,"aat",0,1,doffset); else if (which == 5) parse_coeffs(buf,"bb13",0,1,doffset); - if (narg == 0) error->all(FLERR,"Unexpected end of DihedralCoeffs section"); + if (narg == 0) + error->all(FLERR,"Unexpected empty line in DihedralCoeffs section"); force->dihedral->coeff(narg,arg); buf = next + 1; } @@ -1898,7 +1902,7 @@ void ReadData::impropercoeffs(int which) *next = '\0'; if (which == 0) parse_coeffs(buf,NULL,0,1,ioffset); else if (which == 1) parse_coeffs(buf,"aa",0,1,ioffset); - if (narg == 0) error->all(FLERR,"Unexpected end of ImproperCoeffs section"); + if (narg == 0) error->all(FLERR,"Unexpected empty line in ImproperCoeffs section"); force->improper->coeff(narg,arg); buf = next + 1; } @@ -2092,6 +2096,10 @@ void ReadData::parse_coeffs(char *line, const char *addstr, word = strtok(NULL," \t\n\r\f"); } + // to avoid segfaults on empty lines + + if (narg == 0) return; + if (noffset) { int value = force->inumeric(FLERR,arg[0]); sprintf(argoffset1,"%d",value+offset); diff --git a/src/read_data.h b/src/read_data.h index 7d011c710a..26ab6ff381 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -533,25 +533,25 @@ E: Too many lines in one body in data file - boost MAXBODY MAXBODY is a setting at the top of the src/read_data.cpp file. Set it larger and re-compile the code. -E: Unexpected end of PairCoeffs section +E: Unexpected empty line in PairCoeffs section -Read a blank line. +Read a blank line where there should be coefficient data. -E: Unexpected end of BondCoeffs section +E: Unexpected empty line in BondCoeffs section -Read a blank line. +Read a blank line where there should be coefficient data. -E: Unexpected end of AngleCoeffs section +E: Unexpected empty line in AngleCoeffs section -Read a blank line. +Read a blank line where there should be coefficient data. -E: Unexpected end of DihedralCoeffs section +E: Unexpected empty line in DihedralCoeffs section -Read a blank line. +Read a blank line where there should be coefficient data. -E: Unexpected end of ImproperCoeffs section +E: Unexpected empty line in ImproperCoeffs section -Read a blank line. +Read a blank line where there should be coefficient data. E: Cannot open gzipped file From 0349e9fee9edb4a3261c0153b5855dda31637ba9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 20 May 2019 15:08:33 -0400 Subject: [PATCH 10/11] update/correct list of example folders --- doc/src/Examples.txt | 10 +++++++++- examples/HEAT/README | 2 +- examples/README | 27 +++++++++++++-------------- 3 files changed, 23 insertions(+), 16 deletions(-) diff --git a/doc/src/Examples.txt b/doc/src/Examples.txt index daf9966155..fcf01de383 100644 --- a/doc/src/Examples.txt +++ b/doc/src/Examples.txt @@ -52,13 +52,14 @@ Lowercase directories :h4 accelerate: run with various acceleration options (OpenMP, GPU, Phi) airebo: polyethylene with AIREBO potential +atm: Axilrod-Teller-Muto potential example balance: dynamic load balancing, 2d system body: body particles, 2d system cmap: CMAP 5-body contributions to CHARMM force field colloid: big colloid particles in a small particle solvent, 2d system comb: models using the COMB potential -coreshell: core/shell model using CORESHELL package controller: use of fix controller as a thermostat +coreshell: core/shell model using CORESHELL package crack: crack propagation in a 2d solid deposit: deposit atoms and molecules on a surface dipole: point dipolar particles, 2d system @@ -70,10 +71,13 @@ friction: frictional contact of spherical asperities between 2d surfaces gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command granregion: use of fix wall/region/gran as boundary on granular particles hugoniostat: Hugoniostat shock dynamics +hyper: global and local hyperdynamics of diffusion on Pt surface indent: spherical indenter into a 2d solid kim: use of potentials in Knowledge Base for Interatomic Models (KIM) +latte: examples for using fix latte for DFTB via the LATTE library meam: MEAM test for SiC and shear (same as shear examples) melt: rapid melt of 3d LJ system +message: demos for LAMMPS client/server coupling with the MESSAGE package micelle: self-assembly of small lipid-like molecules into 2d bilayers min: energy minimization of 2d LJ melt mscg: parameterize a multi-scale coarse-graining (MSCG) model @@ -88,6 +92,7 @@ pour: pouring of granular particles into a 3d box, then chute flow prd: parallel replica dynamics of vacancy diffusion in bulk Si python: using embedded Python in a LAMMPS input script qeq: use of the QEQ package for charge equilibration +rdf-adf: computing radial and angle distribution functions for water reax: RDX and TATB models using the ReaxFF rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void @@ -95,6 +100,7 @@ snap: NVE dynamics for BCC tantalum crystal using SNAP potential srd: stochastic rotation dynamics (SRD) particles as solvent streitz: use of Streitz/Mintmire potential with charge equilibration tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si +threebody: regression test input for a variety of manybody potentials vashishta: use of the Vashishta potential voronoi: Voronoi tesselation via compute voronoi/atom command :tb(s=:) @@ -131,8 +137,10 @@ COUPLE: examples of how to use LAMMPS as a library DIFFUSE: compute diffusion coefficients via several methods ELASTIC: compute elastic constants at zero temperature ELASTIC_T: compute elastic constants at finite temperature +HEAT: compute thermal conductivity for LJ and water via fix ehex KAPPA: compute thermal conductivity via several methods MC: using LAMMPS in a Monte Carlo mode to relax the energy of a system +SPIN: examples for features of the SPIN package USER: examples for USER packages and USER-contributed commands VISCOSITY: compute viscosity via several methods :tb(s=:) diff --git a/examples/HEAT/README b/examples/HEAT/README index b827838091..89ad04398f 100644 --- a/examples/HEAT/README +++ b/examples/HEAT/README @@ -1,6 +1,6 @@ This directory contains 4 input scripts for carrying out NEMD simulations of thermal gradients for a Lennard-Jones fluid and SPC/E -water using the HEX/a (fix heat) and eHEX/a (fix ehex) algorithms. +water using the HEX/a (fix ehex w/ hex option) and eHEX/a (fix ehex) algorithms. All input scripts are part of the supplementary (open access) material supporting the publication of Wirnsberger et al. [J. Chem. Phys. 143, diff --git a/examples/README b/examples/README index e03dacec82..dbfdb3363b 100644 --- a/examples/README +++ b/examples/README @@ -64,37 +64,37 @@ balance: dynamic load balancing, 2d system body: body particles, 2d system cmap: CMAP 5-body contributions to CHARMM force field colloid: big colloid particles in a small particle solvent, 2d system -comb: models using the COMB potential +comb: models using the COMB potential coreshell: adiabatic core/shell model controller: use of fix controller as a thermostat -crack: crack propagation in a 2d solid +crack: crack propagation in a 2d solid deposit: deposition of atoms and molecules onto a 3d substrate dipole: point dipolar particles, 2d system dreiding: methanol via Dreiding FF eim: NaCl using the EIM potential ellipse: ellipsoidal particles in spherical solvent, 2d system -flow: Couette and Poiseuille flow in a 2d channel +flow: Couette and Poiseuille flow in a 2d channel friction: frictional contact of spherical asperities between 2d surfaces gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command granregion: use of fix wall/region/gran as boundary on granular particles hugoniostat: Hugoniostat shock dynamics hyper: global and local hyperdynamics of diffusion on Pt surface -indent: spherical indenter into a 2d solid +indent: spherical indenter into a 2d solid kim: use of potentials in Knowledge Base for Interatomic Models (KIM) latte: use of LATTE density-functional tight-binding quantum code -meam: MEAM test for SiC and shear (same as shear examples) -melt: rapid melt of 3d LJ system +meam: MEAM test for SiC and shear (same as shear examples) +melt: rapid melt of 3d LJ system message: client/server coupling of 2 codes micelle: self-assembly of small lipid-like molecules into 2d bilayers -min: energy minimization of 2d LJ melt +min: energy minimization of 2d LJ melt mscg: parameterize a multi-scale coarse-graining (MSCG) model -msst: MSST shock dynamics +msst: MSST shock dynamics nb3b: use of nonbonded 3-body harmonic pair style -neb: nudged elastic band (NEB) calculation for barrier finding -nemd: non-equilibrium MD of 2d sheared system +neb: nudged elastic band (NEB) calculation for barrier finding +nemd: non-equilibrium MD of 2d sheared system obstacle: flow around two voids in a 2d channel peptide: dynamics of a small solvated peptide chain (5-mer) -peri: Peridynamic model of cylinder impacted by indenter +peri: Peridynamic model of cylinder impacted by indenter pour: pouring of granular particles into a 3d box, then chute flow prd: parallel replica dynamics of vacancy diffusion in bulk Si python: use of PYTHON package to invoke Python code from input script @@ -107,6 +107,7 @@ srd: stochastic rotation dynamics (SRD) particles as solvent snap: NVE dynamics for BCC tantalum crystal using SNAP potential streitz: Streitz-Mintmire potential for Al2O3 tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si +threebody: regression test input for a variety of manybody potentials vashishta: models using the Vashishta potential voronoi: Voronoi tesselation via compute voronoi/atom command @@ -117,9 +118,7 @@ cp ../../src/lmp_mpi . # copy LAMMPS executable to this dir lmp_mpi -in in.indent # run the problem Running the simulation produces the files {dump.indent} and -{log.lammps}. You can visualize the dump file as follows: - -../../tools/xmovie/xmovie -scale dump.indent +{log.lammps}. If you uncomment the dump image line(s) in the input script a series of JPG images will be produced by the run. These can be viewed From d0c6484fb0daf67ecc8c193779a1e77e00363e8a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 20 May 2019 15:15:51 -0400 Subject: [PATCH 11/11] add false positive --- doc/utils/sphinx-config/false_positives.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 2d0575ca70..867d3028c6 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -2708,6 +2708,7 @@ Thiaville Thibaudeau Thijsse Thirumalai +threebody thrid ThunderX thylakoid