From 1eeeb028f91490461435c5f2562939058eac8fc5 Mon Sep 17 00:00:00 2001 From: stamoor Date: Thu, 22 Oct 2015 19:05:46 +0000 Subject: [PATCH 01/31] Small tweak for compatibility with different versions of lscpu git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14162 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/USER-INTEL/fix_intel.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp index 9bd1a632cd..8bc3772509 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/USER-INTEL/fix_intel.cpp @@ -664,7 +664,7 @@ int FixIntel::set_host_affinity(const int nomp) FILE *p; char cmd[512]; char readbuf[INTEL_MAX_HOST_CORE_COUNT*5]; - sprintf(cmd, "lscpu -p=cpu,core,socket | grep -v '#' |" + sprintf(cmd, "lscpu -p | grep -v '#' |" "sort -t, -k 3,3n -k 2,2n | awk -F, '{print $1}'"); p = popen(cmd, "r"); if (p == NULL) return -1; From b229c719d0d31f8d3b637963747b2d77a12327c5 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 22 Oct 2015 21:48:05 +0000 Subject: [PATCH 02/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14163 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/atom.cpp | 30 ++++++++----- src/atom.h | 8 ++-- src/molecule.cpp | 81 +++++++++++++++++++++++++++-------- src/molecule.h | 3 +- src/read_data.cpp | 105 ++++++++++++++++++++++++++++++---------------- src/read_data.h | 3 +- 6 files changed, 160 insertions(+), 70 deletions(-) diff --git a/src/atom.cpp b/src/atom.cpp index eac098d953..6d7bb5b4ed 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -950,7 +950,8 @@ void Atom::data_vels(int n, char *buf, tagint id_offset) check that atom IDs are > 0 and <= map_tag_max ------------------------------------------------------------------------- */ -void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset) +void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset, + int type_offset) { int m,tmp,itype; tagint atom1,atom2; @@ -966,6 +967,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset) atom1 += id_offset; atom2 += id_offset; } + itype += type_offset; if (atom1 <= 0 || atom1 > map_tag_max || atom2 <= 0 || atom2 > map_tag_max) @@ -1001,7 +1003,8 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset) check that atom IDs are > 0 and <= map_tag_max ------------------------------------------------------------------------- */ -void Atom::data_angles(int n, char *buf, int *count, tagint id_offset) +void Atom::data_angles(int n, char *buf, int *count, tagint id_offset, + int type_offset) { int m,tmp,itype; tagint atom1,atom2,atom3; @@ -1018,6 +1021,7 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset) atom2 += id_offset; atom3 += id_offset; } + itype += type_offset; if (atom1 <= 0 || atom1 > map_tag_max || atom2 <= 0 || atom2 > map_tag_max || @@ -1068,7 +1072,8 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset) check that atom IDs are > 0 and <= map_tag_max ------------------------------------------------------------------------- */ -void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset) +void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset, + int type_offset) { int m,tmp,itype; tagint atom1,atom2,atom3,atom4; @@ -1087,6 +1092,7 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset) atom3 += id_offset; atom4 += id_offset; } + itype += type_offset; if (atom1 <= 0 || atom1 > map_tag_max || atom2 <= 0 || atom2 > map_tag_max || @@ -1153,7 +1159,8 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset) check that atom IDs are > 0 and <= map_tag_max ------------------------------------------------------------------------- */ -void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset) +void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset, + int type_offset) { int m,tmp,itype; tagint atom1,atom2,atom3,atom4; @@ -1172,6 +1179,7 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset) atom3 += id_offset; atom4 += id_offset; } + itype += type_offset; if (atom1 <= 0 || atom1 > map_tag_max || atom2 <= 0 || atom2 > map_tag_max || @@ -1496,17 +1504,17 @@ void Atom::add_molecule(int narg, char **arg) if (find_molecule(arg[0]) >= 0) error->all(FLERR,"Reuse of molecule template ID"); - // may over-allocate if not all args are mol files, but OK for srealloc - - molecules = (Molecule **) - memory->srealloc(molecules,(nmolecule+narg-1)*sizeof(Molecule *), - "atom::molecules"); - // 1st molecule in set stores nset = # of mols, others store nset = 0 + // ifile = count of molecules in set + // index = argument index where next molecule starts, updated by constructor int ifile = 1; + int index = 1; while (1) { - molecules[nmolecule] = new Molecule(lmp,narg,arg,ifile); + molecules = (Molecule **) + memory->srealloc(molecules,(nmolecule+1)*sizeof(Molecule *), + "atom::molecules"); + molecules[nmolecule] = new Molecule(lmp,narg,arg,index); molecules[nmolecule]->nset = 0; molecules[nmolecule-ifile+1]->nset++; nmolecule++; diff --git a/src/atom.h b/src/atom.h index 1583dada7e..dd0d9821a1 100644 --- a/src/atom.h +++ b/src/atom.h @@ -213,10 +213,10 @@ class Atom : protected Pointers { void data_atoms(int, char *, tagint, int, int, double *); void data_vels(int, char *, tagint); - void data_bonds(int, char *, int *, tagint); - void data_angles(int, char *, int *, tagint); - void data_dihedrals(int, char *, int *, tagint); - void data_impropers(int, char *, int *, tagint); + void data_bonds(int, char *, int *, tagint, int); + void data_angles(int, char *, int *, tagint, int); + void data_dihedrals(int, char *, int *, tagint, int); + void data_impropers(int, char *, int *, tagint, int); void data_bonus(int, char *, class AtomVec *, tagint); void data_bodies(int, char *, class AtomVecBody *, tagint); diff --git a/src/molecule.cpp b/src/molecule.cpp index ee8f9ae424..83157200eb 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -35,11 +35,12 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int ifile) : Pointers(lmp) +Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) : + Pointers(lmp) { me = comm->me; - if (ifile >= narg) error->all(FLERR,"Illegal molecule command"); + if (index >= narg) error->all(FLERR,"Illegal molecule command"); int n = strlen(arg[0]) + 1; id = new char[n]; @@ -50,21 +51,14 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int ifile) : Pointers(lmp) error->all(FLERR,"Molecule template ID must be " "alphanumeric or underscore characters"); - // scan args past ifile to reach optional args - // set last = 1 if no more files in list - - last = 0; - int iarg = ifile+1; - while (iarg < narg) { - if (strcmp(arg[iarg],"offset") == 0) break; - iarg++; - } - if (iarg == ifile+1) last = 1; - - // parse optional args + // parse args until reach unknown arg (next file) toffset = 0; boffset = aoffset = doffset = ioffset = 0; + sizescale = 1.0; + + int ifile = index; + int iarg = ifile+1; while (iarg < narg) { if (strcmp(arg[iarg],"offset") == 0) { @@ -78,9 +72,45 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int ifile) : Pointers(lmp) doffset < 0 || ioffset < 0) error->all(FLERR,"Illegal molecule command"); iarg += 6; - } else error->all(FLERR,"Illegal molecule command"); + } else if (strcmp(arg[iarg],"toff") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command"); + toffset = force->inumeric(FLERR,arg[iarg+1]); + if (toffset < 0) error->all(FLERR,"Illegal molecule command"); + iarg += 2; + } else if (strcmp(arg[iarg],"boff") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command"); + boffset = force->inumeric(FLERR,arg[iarg+1]); + if (boffset < 0) error->all(FLERR,"Illegal molecule command"); + iarg += 2; + } else if (strcmp(arg[iarg],"aoff") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command"); + aoffset = force->inumeric(FLERR,arg[iarg+1]); + if (aoffset < 0) error->all(FLERR,"Illegal molecule command"); + iarg += 2; + } else if (strcmp(arg[iarg],"doff") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command"); + doffset = force->inumeric(FLERR,arg[iarg+1]); + if (doffset < 0) error->all(FLERR,"Illegal molecule command"); + iarg += 2; + } else if (strcmp(arg[iarg],"ioff") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command"); + ioffset = force->inumeric(FLERR,arg[iarg+1]); + if (ioffset < 0) error->all(FLERR,"Illegal molecule command"); + iarg += 2; + } else if (strcmp(arg[iarg],"scale") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command"); + sizescale = force->numeric(FLERR,arg[iarg+1]); + if (sizescale <= 0.0) error->all(FLERR,"Illegal molecule command"); + iarg += 2; + } else break; } + index = iarg; + + // last molecule if have scanned all args + + if (iarg == narg) last = 1; + // initialize all fields to empty initialize(); @@ -392,10 +422,14 @@ void Molecule::read(int flag) else if (strstr(line,"mass")) { massflag = 1; sscanf(line,"%lg",&masstotal); + masstotal *= sizescale*sizescale*sizescale; } else if (strstr(line,"com")) { comflag = 1; sscanf(line,"%lg %lg %lg",&com[0],&com[1],&com[2]); + com[0] *= sizescale; + com[1] *= sizescale; + com[2] *= sizescale; if (domain->dimension == 2 && com[2] != 0.0) error->all(FLERR,"Molecule file z center-of-mass must be 0.0 for 2d"); } @@ -404,6 +438,12 @@ void Molecule::read(int flag) sscanf(line,"%lg %lg %lg %lg %lg %lg", &itensor[0],&itensor[1],&itensor[2], &itensor[3],&itensor[4],&itensor[5]); + itensor[0] *= sizescale*sizescale*sizescale*sizescale*sizescale; + itensor[1] *= sizescale*sizescale*sizescale*sizescale*sizescale; + itensor[2] *= sizescale*sizescale*sizescale*sizescale*sizescale; + itensor[3] *= sizescale*sizescale*sizescale*sizescale*sizescale; + itensor[4] *= sizescale*sizescale*sizescale*sizescale*sizescale; + itensor[5] *= sizescale*sizescale*sizescale*sizescale*sizescale; } else break; @@ -414,8 +454,10 @@ void Molecule::read(int flag) if (natoms < 1) error->all(FLERR,"No or invalid atom count in molecule file"); if (nbonds < 0) error->all(FLERR,"Invalid bond count in molecule file"); if (nangles < 0) error->all(FLERR,"Invalid angle count in molecule file"); - if (ndihedrals < 0) error->all(FLERR,"Invalid dihedral count in molecule file"); - if (nimpropers < 0) error->all(FLERR,"Invalid improper count in molecule file"); + if (ndihedrals < 0) + error->all(FLERR,"Invalid dihedral count in molecule file"); + if (nimpropers < 0) + error->all(FLERR,"Invalid improper count in molecule file"); // count = vector for tallying bonds,angles,etc per atom @@ -544,6 +586,9 @@ void Molecule::coords(char *line) error->all(FLERR,"Invalid Coords section in molecule file"); } sscanf(line,"%d %lg %lg %lg",&tmp,&x[i][0],&x[i][1],&x[i][2]); + x[i][0] *= sizescale; + x[i][1] *= sizescale; + x[i][2] *= sizescale; } if (domain->dimension == 2) { @@ -614,6 +659,7 @@ void Molecule::diameters(char *line) error->all(FLERR,"Invalid Diameters section in molecule file"); } sscanf(line,"%d %lg",&tmp,&radius[i]); + radius[i] *= sizescale; radius[i] *= 0.5; maxradius = MAX(maxradius,radius[i]); } @@ -638,6 +684,7 @@ void Molecule::masses(char *line) error->all(FLERR,"Invalid Masses section in molecule file"); } sscanf(line,"%d %lg",&tmp,&rmass[i]); + rmass[i] *= sizescale*sizescale*sizescale; } for (int i = 0; i < natoms; i++) diff --git a/src/molecule.h b/src/molecule.h index 81d13d4e26..9ecb86b202 100644 --- a/src/molecule.h +++ b/src/molecule.h @@ -102,7 +102,7 @@ class Molecule : protected Pointers { double **dxbody; // displacement of each atom relative to COM // in body frame (diagonalized interia tensor) - Molecule(class LAMMPS *, int, char **, int); + Molecule(class LAMMPS *, int, char **, int &); ~Molecule(); void compute_center(); void compute_mass(); @@ -116,6 +116,7 @@ class Molecule : protected Pointers { int *count; int toffset,boffset,aoffset,doffset,ioffset; int autospecial; + double sizescale; void read(int); void coords(char *); diff --git a/src/read_data.cpp b/src/read_data.cpp index 036e333bdb..7e4b70484b 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -279,7 +279,7 @@ void ReadData::command(int narg, char **arg) // ----------------------------------------------------------------- - // perform 1-pass read if no molecular topoogy in file + // perform 1-pass read if no molecular topology in file // perform 2-pass read if molecular topology, // first pass calculates max topology/atom @@ -301,7 +301,7 @@ void ReadData::command(int narg, char **arg) triclinic = 0; keyword[0] = '\0'; - int nlocal_previous = atom->nlocal; + nlocal_previous = atom->nlocal; int firstpass = 1; while (1) { @@ -315,7 +315,7 @@ void ReadData::command(int narg, char **arg) // read header info - header(); + header(firstpass); // problem setup using info from header // only done once, if firstpass and first data file @@ -648,7 +648,7 @@ void ReadData::command(int narg, char **arg) // will also observe extra settings even if bond/etc topology not in file // leaves other atom arrays unchanged, since already nmax in length - atom->deallocate_topology(); + if (addflag == NONE) atom->deallocate_topology(); atom->avec->grow(atom->nmax); } @@ -788,7 +788,7 @@ void ReadData::command(int narg, char **arg) some logic differs if adding atoms ------------------------------------------------------------------------- */ -void ReadData::header() +void ReadData::header(int firstpass) { int n; char *ptr; @@ -856,7 +856,7 @@ void ReadData::header() if (strstr(line,"atoms")) { sscanf(line,BIGINT_FORMAT,&natoms); if (addflag == NONE) atom->natoms = natoms; - else atom->natoms += natoms; + else if (firstpass) atom->natoms += natoms; // check for these first // otherwise "triangles" will be matched as "angles" @@ -1093,6 +1093,8 @@ void ReadData::velocities() void ReadData::bonds(int firstpass) { + int nchunk,eof; + if (me == 0) { if (firstpass) { if (screen) fprintf(screen," scanning bonds ...\n"); @@ -1114,32 +1116,38 @@ void ReadData::bonds(int firstpass) // read and process bonds - int nchunk,eof; bigint nread = 0; - bigint nbonds = atom->nbonds; while (nread < nbonds) { nchunk = MIN(nbonds-nread,CHUNK); eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); if (eof) error->all(FLERR,"Unexpected end of data file"); - atom->data_bonds(nchunk,buffer,count,id_offset); + atom->data_bonds(nchunk,buffer,count,id_offset,boffset); nread += nchunk; } // if firstpass: tally max bond/atom and return + // if addflag = NONE, store max bond/atom with extra + // else just check actual max does not exceed existing max if (firstpass) { int max = 0; - for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]); + for (int i = nlocal_previous; i < nlocal; i++) max = MAX(max,count[i]); int maxall; MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world); - maxall += atom->extra_bond_per_atom; + if (addflag == NONE) maxall += atom->extra_bond_per_atom; if (me == 0) { if (screen) fprintf(screen," %d = max bonds/atom\n",maxall); if (logfile) fprintf(logfile," %d = max bonds/atom\n",maxall); } - atom->bond_per_atom = maxall; + + if (addflag != NONE) { + if (maxall > atom->bond_per_atom) + error->all(FLERR,"Subsequent read data induced " + "too many bonds per atom"); + } else atom->bond_per_atom = maxall; + memory->destroy(count); return; } @@ -1147,7 +1155,7 @@ void ReadData::bonds(int firstpass) // if 2nd pass: check that bonds were assigned correctly bigint n = 0; - for (int i = 0; i < nlocal; i++) n += atom->num_bond[i]; + for (int i = nlocal_previous; i < nlocal; i++) n += atom->num_bond[i]; bigint sum; MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world); int factor = 1; @@ -1158,7 +1166,7 @@ void ReadData::bonds(int firstpass) if (logfile) fprintf(logfile," " BIGINT_FORMAT " bonds\n",sum/factor); } - if (sum != factor*atom->nbonds) + if (sum != factor*nbonds) error->all(FLERR,"Bonds assigned incorrectly"); } @@ -1168,6 +1176,8 @@ void ReadData::bonds(int firstpass) void ReadData::angles(int firstpass) { + int nchunk,eof; + if (me == 0) { if (firstpass) { if (screen) fprintf(screen," scanning angles ...\n"); @@ -1189,32 +1199,38 @@ void ReadData::angles(int firstpass) // read and process angles - int nchunk,eof; bigint nread = 0; - bigint nangles = atom->nangles; while (nread < nangles) { nchunk = MIN(nangles-nread,CHUNK); eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); if (eof) error->all(FLERR,"Unexpected end of data file"); - atom->data_angles(nchunk,buffer,count,id_offset); + atom->data_angles(nchunk,buffer,count,id_offset,aoffset); nread += nchunk; } // if firstpass: tally max angle/atom and return + // if addflag = NONE, store max angle/atom with extra + // else just check actual max does not exceed existing max if (firstpass) { int max = 0; - for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]); + for (int i = nlocal_previous; i < nlocal; i++) max = MAX(max,count[i]); int maxall; MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world); - maxall += atom->extra_angle_per_atom; + if (addflag == NONE) maxall += atom->extra_angle_per_atom; if (me == 0) { if (screen) fprintf(screen," %d = max angles/atom\n",maxall); if (logfile) fprintf(logfile," %d = max angles/atom\n",maxall); } - atom->angle_per_atom = maxall; + + if (addflag != NONE) { + if (maxall > atom->angle_per_atom) + error->all(FLERR,"Subsequent read data induced " + "too many angles per atom"); + } else atom->angle_per_atom = maxall; + memory->destroy(count); return; } @@ -1222,7 +1238,7 @@ void ReadData::angles(int firstpass) // if 2nd pass: check that angles were assigned correctly bigint n = 0; - for (int i = 0; i < nlocal; i++) n += atom->num_angle[i]; + for (int i = nlocal_previous; i < nlocal; i++) n += atom->num_angle[i]; bigint sum; MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world); int factor = 1; @@ -1233,7 +1249,7 @@ void ReadData::angles(int firstpass) if (logfile) fprintf(logfile," " BIGINT_FORMAT " angles\n",sum/factor); } - if (sum != factor*atom->nangles) + if (sum != factor*nangles) error->all(FLERR,"Angles assigned incorrectly"); } @@ -1243,6 +1259,8 @@ void ReadData::angles(int firstpass) void ReadData::dihedrals(int firstpass) { + int nchunk,eof; + if (me == 0) { if (firstpass) { if (screen) fprintf(screen," scanning dihedrals ...\n"); @@ -1264,31 +1282,38 @@ void ReadData::dihedrals(int firstpass) // read and process dihedrals - int nchunk,eof; bigint nread = 0; - bigint ndihedrals = atom->ndihedrals; while (nread < ndihedrals) { nchunk = MIN(ndihedrals-nread,CHUNK); eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); if (eof) error->all(FLERR,"Unexpected end of data file"); - atom->data_dihedrals(nchunk,buffer,count,id_offset); + atom->data_dihedrals(nchunk,buffer,count,id_offset,doffset); nread += nchunk; } // if firstpass: tally max dihedral/atom and return + // if addflag = NONE, store max dihedral/atom with extra + // else just check actual max does not exceed existing max if (firstpass) { int max = 0; for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]); int maxall; MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world); - maxall += atom->extra_dihedral_per_atom; + if (addflag == NONE) maxall += atom->extra_dihedral_per_atom; if (me == 0) { if (screen) fprintf(screen," %d = max dihedrals/atom\n",maxall); if (logfile) fprintf(logfile," %d = max dihedrals/atom\n",maxall); } + + if (addflag != NONE) { + if (maxall > atom->dihedral_per_atom) + error->all(FLERR,"Subsequent read data induced " + "too many dihedrals per atom"); + } else atom->dihedral_per_atom = maxall; + atom->dihedral_per_atom = maxall; memory->destroy(count); return; @@ -1297,7 +1322,7 @@ void ReadData::dihedrals(int firstpass) // if 2nd pass: check that dihedrals were assigned correctly bigint n = 0; - for (int i = 0; i < nlocal; i++) n += atom->num_dihedral[i]; + for (int i = nlocal_previous; i < nlocal; i++) n += atom->num_dihedral[i]; bigint sum; MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world); int factor = 1; @@ -1308,7 +1333,7 @@ void ReadData::dihedrals(int firstpass) if (logfile) fprintf(logfile," " BIGINT_FORMAT " dihedrals\n",sum/factor); } - if (sum != factor*atom->ndihedrals) + if (sum != factor*ndihedrals) error->all(FLERR,"Dihedrals assigned incorrectly"); } @@ -1318,6 +1343,8 @@ void ReadData::dihedrals(int firstpass) void ReadData::impropers(int firstpass) { + int nchunk,eof; + if (me == 0) { if (firstpass) { if (screen) fprintf(screen," scanning impropers ...\n"); @@ -1339,32 +1366,38 @@ void ReadData::impropers(int firstpass) // read and process impropers - int nchunk,eof; bigint nread = 0; - bigint nimpropers = atom->nimpropers; while (nread < nimpropers) { nchunk = MIN(nimpropers-nread,CHUNK); eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); if (eof) error->all(FLERR,"Unexpected end of data file"); - atom->data_impropers(nchunk,buffer,count,id_offset); + atom->data_impropers(nchunk,buffer,count,id_offset,ioffset); nread += nchunk; } // if firstpass: tally max improper/atom and return + // if addflag = NONE, store max improper/atom + // else just check it does not exceed existing max if (firstpass) { int max = 0; - for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]); + for (int i = nlocal_previous; i < nlocal; i++) max = MAX(max,count[i]); int maxall; MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world); - maxall += atom->extra_improper_per_atom; + if (addflag == NONE) maxall += atom->extra_improper_per_atom; if (me == 0) { if (screen) fprintf(screen," %d = max impropers/atom\n",maxall); if (logfile) fprintf(logfile," %d = max impropers/atom\n",maxall); } - atom->improper_per_atom = maxall; + + if (addflag != NONE) { + if (maxall > atom->improper_per_atom) + error->all(FLERR,"Subsequent read data induced " + "too many impropers per atom"); + } else atom->improper_per_atom = maxall; + memory->destroy(count); return; } @@ -1372,7 +1405,7 @@ void ReadData::impropers(int firstpass) // if 2nd pass: check that impropers were assigned correctly bigint n = 0; - for (int i = 0; i < nlocal; i++) n += atom->num_improper[i]; + for (int i = nlocal_previous; i < nlocal; i++) n += atom->num_improper[i]; bigint sum; MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world); int factor = 1; @@ -1383,7 +1416,7 @@ void ReadData::impropers(int firstpass) if (logfile) fprintf(logfile," " BIGINT_FORMAT " impropers\n",sum/factor); } - if (sum != factor*atom->nimpropers) + if (sum != factor*nimpropers) error->all(FLERR,"Impropers assigned incorrectly"); } diff --git a/src/read_data.h b/src/read_data.h index 74c3e2c8b9..925ec1f07e 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -41,6 +41,7 @@ class ReadData : protected Pointers { bigint id_offset; + int nlocal_previous; bigint natoms; bigint nbonds,nangles,ndihedrals,nimpropers; int ntypes; @@ -81,7 +82,7 @@ class ReadData : protected Pointers { void open(char *); void scan(int &, int &, int &, int &); int reallocate(int **, int, int); - void header(); + void header(int); void parse_keyword(int); void skip_lines(bigint); void parse_coeffs(char *, const char *, int, int, int); From cee848f948653c39f50b5686a1926f373e30c458 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 22 Oct 2015 22:06:49 +0000 Subject: [PATCH 03/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14164 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/CORESHELL/pair_lj_cut_coul_long_cs.cpp | 3 +- src/DIPOLE/pair_lj_cut_dipole_long.cpp | 4 +- src/KOKKOS/verlet_kokkos.cpp | 18 +- src/KSPACE/pair_lj_cut_coul_long.cpp | 4 +- src/KSPACE/pair_lj_cut_coul_msm.cpp | 4 +- src/MANYBODY/pair_adp.cpp | 1 + src/MANYBODY/pair_airebo.cpp | 1 + src/MANYBODY/pair_comb.cpp | 2 + src/MANYBODY/pair_comb3.cpp | 2 + src/MANYBODY/pair_eam.cpp | 2 + src/MANYBODY/pair_eim.cpp | 1 + src/MANYBODY/pair_nb3b_harmonic.cpp | 1 + src/MANYBODY/pair_polymorphic.cpp | 2 +- src/MANYBODY/pair_sw.cpp | 1 + src/MANYBODY/pair_tersoff.cpp | 1 + src/PYTHON/python.cpp | 2 + src/REPLICA/verlet_split.cpp | 13 +- src/USER-AWPMD/pair_awpmd_cut.h | 2 +- src/USER-CUDA/verlet_cuda.cpp | 23 +- src/USER-DIFFRACTION/compute_saed.h | 1 - src/USER-DRUDE/pair_lj_cut_thole_long.cpp | 4 +- src/USER-DRUDE/pair_thole.cpp | 2 +- .../pair_lj_charmm_coul_long_soft.cpp | 2 + src/USER-FEP/pair_lj_cut_coul_long_soft.cpp | 2 + src/USER-FEP/pair_lj_cut_soft.cpp | 1 + src/USER-H5MD/dump_h5md.cpp | 2 +- src/USER-H5MD/dump_h5md.h | 1 - src/USER-INTEL/verlet_intel.cpp | 22 +- src/USER-MISC/fix_imd.cpp | 20 +- src/USER-MISC/fix_pimd.cpp | 7 +- src/USER-MISC/fix_srp.cpp | 12 +- src/USER-MISC/fix_ti_rs.cpp | 26 +- src/USER-MISC/fix_ti_rs.h | 6 +- src/USER-MISC/fix_ti_spring.cpp | 23 +- src/USER-MISC/fix_ti_spring.h | 6 +- src/USER-MISC/pair_tersoff_table.cpp | 11 - src/USER-MOLFILE/dump_molfile.cpp | 1 + src/USER-OMP/fix_omp.cpp | 40 +- src/USER-OMP/pair_tersoff_table_omp.cpp | 11 - src/USER-OMP/respa_omp.cpp | 17 + src/USER-REAXC/reaxc_bond_orders.cpp | 6 - src/USER-REAXC/reaxc_bond_orders.h | 17 - src/USER-REAXC/reaxc_ffield.cpp | 2 + src/USER-REAXC/reaxc_forces.cpp | 219 +-------- src/USER-REAXC/reaxc_io_tools.cpp | 428 ------------------ src/USER-REAXC/reaxc_io_tools.h | 74 --- src/USER-REAXC/reaxc_lookup.cpp | 24 - src/USER-REAXC/reaxc_reset_tools.cpp | 23 - src/USER-REAXC/reaxc_reset_tools.h | 5 - src/USER-REAXC/reaxc_system_props.cpp | 215 --------- src/USER-REAXC/reaxc_system_props.h | 12 - src/USER-REAXC/reaxc_tool_box.cpp | 120 ----- src/USER-REAXC/reaxc_tool_box.h | 24 - src/USER-REAXC/reaxc_vector.cpp | 76 ---- src/USER-REAXC/reaxc_vector.h | 9 - src/USER-SPH/atom_vec_meso.cpp | 26 +- src/fix.h | 4 +- src/info.cpp | 1 + src/input.cpp | 69 ++- src/lammps.cpp | 1 + src/min_cg.cpp | 1 + src/min_fire.cpp | 1 + src/min_quickmin.cpp | 1 + src/min_sd.cpp | 1 + src/modify.cpp | 19 +- src/modify.h | 5 +- src/read_restart.h | 2 - src/respa.cpp | 8 + src/set.cpp | 16 +- src/verlet.cpp | 8 + 70 files changed, 331 insertions(+), 1390 deletions(-) diff --git a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp index 6f068f4be7..fe9ba28696 100644 --- a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp +++ b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp @@ -555,9 +555,10 @@ void PairLJCutCoulLongCS::compute_outer(int eflag, int vflag) if (rsq <= cut_in_off_sq) { r6inv = r2inv*r2inv*r2inv; forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); - } else if (rsq <= cut_in_on_sq) + } else if (rsq <= cut_in_on_sq) { r6inv = r2inv*r2inv*r2inv; forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + } fpair = (forcecoul + factor_lj*forcelj) * r2inv; } diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp index 60190ce905..824bbf734a 100755 --- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp @@ -291,10 +291,10 @@ void PairLJCutDipoleLong::compute(int eflag, int vflag) } if (eflag) { - if (rsq < cut_coulsq) { + if (rsq < cut_coulsq && factor_coul > 0.0) { ecoul = qqrd2e*(b0*g0 + b1*g1 + b2*g2); if (factor_coul < 1.0) { - ecoul *= factor_coul; + ecoul *= factor_coul; ecoul += (1-factor_coul) * qqrd2e * (d0*g0 + d1*g1 + d2*g2); } } else ecoul = 0.0; diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index b63ca98ba4..cdd3cecf8e 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -53,8 +53,24 @@ VerletKokkos::VerletKokkos(LAMMPS *lmp, int narg, char **arg) : void VerletKokkos::setup() { + if (comm->me == 0 && screen) { + fprintf(screen,"Setting up Verlet run ...\n"); + fprintf(screen," Unit style : %s\n", update->unit_style); + fprintf(screen," Current step: " BIGINT_FORMAT "\n", update->ntimestep); + fprintf(screen," Time step : %g\n", update->dt); + if (update->max_wall > 0) { + char outtime[128]; + double totalclock = update->max_wall; + int seconds = fmod(totalclock,60.0); + totalclock = (totalclock - seconds) / 60.0; + int minutes = fmod(totalclock,60.0); + int hours = (totalclock - minutes) / 60.0; + sprintf(outtime," Max walltime: " + "%d:%02d:%02d\n", hours, minutes, seconds); + fputs(outtime,screen); + } + } - if (comm->me == 0 && screen) fprintf(screen,"Setting up run ...\n"); update->setupflag = 1; // setup domain, communication and neighboring diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp index aa19c7f533..c113aea83a 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.cpp +++ b/src/KSPACE/pair_lj_cut_coul_long.cpp @@ -550,10 +550,10 @@ void PairLJCutCoulLong::compute_outer(int eflag, int vflag) if (rsq <= cut_in_off_sq) { r6inv = r2inv*r2inv*r2inv; forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); - } else if (rsq <= cut_in_on_sq) + } else if (rsq <= cut_in_on_sq) { r6inv = r2inv*r2inv*r2inv; forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); - + } fpair = (forcecoul + factor_lj*forcelj) * r2inv; } diff --git a/src/KSPACE/pair_lj_cut_coul_msm.cpp b/src/KSPACE/pair_lj_cut_coul_msm.cpp index a503b54aa3..f9fc9be3fc 100644 --- a/src/KSPACE/pair_lj_cut_coul_msm.cpp +++ b/src/KSPACE/pair_lj_cut_coul_msm.cpp @@ -403,10 +403,10 @@ void PairLJCutCoulMSM::compute_outer(int eflag, int vflag) if (rsq <= cut_in_off_sq) { r6inv = r2inv*r2inv*r2inv; forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); - } else if (rsq <= cut_in_on_sq) + } else if (rsq <= cut_in_on_sq) { r6inv = r2inv*r2inv*r2inv; forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); - + } fpair = (forcecoul + factor_lj*forcelj) * r2inv; } diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index 369bcc8c9e..5cb861b563 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -44,6 +44,7 @@ PairADP::PairADP(LAMMPS *lmp) : Pair(lmp) fp = NULL; mu = NULL; lambda = NULL; + map = NULL; setfl = NULL; diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index 58bbeffbfc..f3a7be5a2d 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -59,6 +59,7 @@ PairAIREBO::PairAIREBO(LAMMPS *lmp) : Pair(lmp) pgsize = oneatom = 0; nC = nH = NULL; + map = NULL; manybody_flag = 1; } diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index da9c4a49aa..26ff69d564 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -56,6 +56,8 @@ PairComb::PairComb(LAMMPS *lmp) : Pair(lmp) nmax = 0; NCo = NULL; bbij = NULL; + map = NULL; + esm = NULL; nelements = 0; elements = NULL; diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index 95e6239bce..2d1a782070 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -54,6 +54,8 @@ PairComb3::PairComb3(LAMMPS *lmp) : Pair(lmp) nmax = 0; NCo = NULL; bbij = NULL; + map = NULL; + esm = NULL; nelements = 0; elements = NULL; diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index 82f69c76b6..5b832d0ab4 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -42,6 +42,8 @@ PairEAM::PairEAM(LAMMPS *lmp) : Pair(lmp) nmax = 0; rho = NULL; fp = NULL; + map = NULL; + type2frho = NULL; nfuncfl = 0; funcfl = NULL; diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index 9206229e9d..196e899534 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -45,6 +45,7 @@ PairEIM::PairEIM(LAMMPS *lmp) : Pair(lmp) nmax = 0; rho = NULL; fp = NULL; + map = NULL; nelements = 0; elements = NULL; diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index ef1432827d..a98bacd274 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -52,6 +52,7 @@ PairNb3bHarmonic::PairNb3bHarmonic(LAMMPS *lmp) : Pair(lmp) nparams = maxparam = 0; params = NULL; elem2param = NULL; + map = NULL; } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index 67342d91d6..b9d3755e6c 100755 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -51,7 +51,7 @@ PairPolymorphic::PairPolymorphic(LAMMPS *lmp) : Pair(lmp) tripletParameters = NULL; elem2param = NULL; elem3param = NULL; - + type_map = NULL; } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index 27394c7a67..5cdd8f778e 100755 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -50,6 +50,7 @@ PairSW::PairSW(LAMMPS *lmp) : Pair(lmp) nparams = maxparam = 0; params = NULL; elem2param = NULL; + map = NULL; } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index f725df0cc6..44712e691e 100755 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -51,6 +51,7 @@ PairTersoff::PairTersoff(LAMMPS *lmp) : Pair(lmp) nparams = maxparam = 0; params = NULL; elem2param = NULL; + map = NULL; } /* ---------------------------------------------------------------------- diff --git a/src/PYTHON/python.cpp b/src/PYTHON/python.cpp index 8c34098126..607181a1ec 100644 --- a/src/PYTHON/python.cpp +++ b/src/PYTHON/python.cpp @@ -117,6 +117,7 @@ void Python::command(int narg, char **arg) iarg += 2; } else if (strcmp(arg[iarg],"file") == 0) { if (iarg+2 > narg) error->all(FLERR,"Invalid python command"); + delete[] pyfile; int n = strlen(arg[iarg+1]) + 1; pyfile = new char[n]; strcpy(pyfile,arg[iarg+1]); @@ -173,6 +174,7 @@ void Python::command(int narg, char **arg) if (fp == NULL) error->all(FLERR,"Could not open Python file"); int err = PyRun_SimpleFile(fp,pyfile); if (err) error->all(FLERR,"Could not process Python file"); + fclose(fp); } else if (herestr) { int err = PyRun_SimpleString(herestr); if (err) error->all(FLERR,"Could not process Python string"); diff --git a/src/REPLICA/verlet_split.cpp b/src/REPLICA/verlet_split.cpp index 408821fe22..dbb2660eb5 100644 --- a/src/REPLICA/verlet_split.cpp +++ b/src/REPLICA/verlet_split.cpp @@ -241,7 +241,8 @@ void VerletSplit::init() void VerletSplit::setup() { - if (comm->me == 0 && screen) fprintf(screen,"Setting up run ...\n"); + if (comm->me == 0 && screen) + fprintf(screen,"Setting up Verlet/split run ...\n"); if (!master) force->kspace->setup(); else Verlet::setup(); @@ -298,6 +299,7 @@ void VerletSplit::run(int n) int n_pre_exchange = modify->n_pre_exchange; int n_pre_neighbor = modify->n_pre_neighbor; int n_pre_force = modify->n_pre_force; + int n_pre_reverse = modify->n_pre_reverse; int n_post_force = modify->n_post_force; int n_end_of_step = modify->n_end_of_step; @@ -374,6 +376,10 @@ void VerletSplit::run(int n) timer->stamp(Timer::BOND); } + if (n_pre_reverse) { + modify->pre_reverse(eflag,vflag); + timer->stamp(Timer::MODIFY); + } if (force->newton) { comm->reverse_comm(); timer->stamp(Timer::COMM); @@ -391,6 +397,11 @@ void VerletSplit::run(int n) timer->stamp(Timer::KSPACE); } + if (n_pre_reverse) { + modify->pre_reverse(eflag,vflag); + timer->stamp(Timer::MODIFY); + } + // TIP4P PPPM puts forces on ghost atoms, so must reverse_comm() if (tip4p_flag && force->newton) { diff --git a/src/USER-AWPMD/pair_awpmd_cut.h b/src/USER-AWPMD/pair_awpmd_cut.h index b07db3abbb..fb8b9c65dc 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.h +++ b/src/USER-AWPMD/pair_awpmd_cut.h @@ -69,7 +69,7 @@ class PairAWPMDCut : public Pair { void virial_eradius_compute(); - AWPMD_split *wpmd; // solver oblect + AWPMD_split *wpmd; // solver object double ermscale; // scale of width mass for motion double width_pbc; // setting for width pbc double half_box_length; // calculated by coeff function diff --git a/src/USER-CUDA/verlet_cuda.cpp b/src/USER-CUDA/verlet_cuda.cpp index eba4a0b09c..2a216b5b46 100644 --- a/src/USER-CUDA/verlet_cuda.cpp +++ b/src/USER-CUDA/verlet_cuda.cpp @@ -118,7 +118,23 @@ void VerletCuda::setup() cuda->allocate(); - if(comm->me == 0 && screen) fprintf(screen, "Setting up run ...\n"); + if (comm->me == 0 && screen) { + fprintf(screen,"Setting up Verlet run ...\n"); + fprintf(screen," Unit style : %s\n", update->unit_style); + fprintf(screen," Current step: " BIGINT_FORMAT "\n", update->ntimestep); + fprintf(screen," Time step : %g\n", update->dt); + if (update->max_wall > 0) { + char outtime[128]; + double totalclock = update->max_wall; + int seconds = fmod(totalclock,60.0); + totalclock = (totalclock - seconds) / 60.0; + int minutes = fmod(totalclock,60.0); + int hours = (totalclock - minutes) / 60.0; + sprintf(outtime," Max walltime: " + "%d:%02d:%02d\n", hours, minutes, seconds); + fputs(outtime,screen); + } + } // setup domain, communication and neighboring // acquire ghosts @@ -639,6 +655,11 @@ void VerletCuda::run(int n) int firstreneigh = 1; for(int i = 0; i < n; i++) { + if (update->time_expired()) { + update->nsteps = i; + break; + } + if(atom->nlocal == 0) error->warning(FLERR, "# CUDA: There are currently no atoms on one of the MPI processes. This is currently prone to encountering errors with USER-CUDA package. Please use the 'processors' keyword to use a more balanced processor layout."); diff --git a/src/USER-DIFFRACTION/compute_saed.h b/src/USER-DIFFRACTION/compute_saed.h index ba221125a0..0118b64811 100644 --- a/src/USER-DIFFRACTION/compute_saed.h +++ b/src/USER-DIFFRACTION/compute_saed.h @@ -42,7 +42,6 @@ class ComputeSAED : public Compute { double prd_inv[3]; // Inverse spacing of unit cell bool echo; // echo compute_array progress bool manual; // Turn on manual recpiprocal map - double *f; int nRows; // Number of relp explored double Zone[3]; // Zone axis to view SAED diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp index a31a3b29f7..d517eb7932 100644 --- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp +++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp @@ -637,7 +637,7 @@ double PairLJCutTholeLong::single(int i, int j, int itype, int jtype, if (drudetype[type[i]] != NOPOL_TYPE && drudetype[type[j]] != NOPOL_TYPE) { di = atom->map(drudeid[i]); di_closest = domain->closest_image(i, di); - if (di_closest != dj){ + if (j != di_closest){ if (drudetype[i] == CORE_TYPE) dqi = -atom->q[di]; else if (drudetype[i] == DRUDE_TYPE) dqi = atom->q[i]; if (drudetype[j] == CORE_TYPE) { @@ -672,7 +672,7 @@ double PairLJCutTholeLong::single(int i, int j, int itype, int jtype, } if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor; if (drudetype[type[i]] != NOPOL_TYPE && drudetype[type[j]] != NOPOL_TYPE && - di_closest != dj) + di_closest != j) phicoul += factor_e * dcoul; eng += phicoul; } diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp index f9a16267d0..5840dbc51b 100644 --- a/src/USER-DRUDE/pair_thole.cpp +++ b/src/USER-DRUDE/pair_thole.cpp @@ -364,7 +364,7 @@ double PairThole::single(int i, int j, int itype, int jtype, double rsq, double factor_coul, double factor_lj, double &fforce) { - double r2inv,rinv,r,forcecoul,phicoul; + double r2inv,rinv,r,phicoul; double qi,qj,factor_f,factor_e,dcoul,asr,exp_asr; int di, dj; diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp index 81464e3606..1f4a2529f5 100644 --- a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp @@ -533,6 +533,8 @@ void PairLJCharmmCoulLongSoft::compute_outer(int eflag, int vflag) } else ecoul = 0.0; if (rsq < cut_ljsq) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * (1.0/(denlj*denlj) - 1.0/denlj); if (rsq > cut_lj_innersq) { diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp index daeeffd28c..6bb9538023 100644 --- a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp @@ -498,6 +498,8 @@ void PairLJCutCoulLongSoft::compute_outer(int eflag, int vflag) } else ecoul = 0.0; if (rsq < cut_ljsq[itype][jtype]) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * (1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype]; evdwl *= factor_lj; diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp index 1979508224..95b74d0d1f 100644 --- a/src/USER-FEP/pair_lj_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_soft.cpp @@ -393,6 +393,7 @@ void PairLJCutSoft::compute_outer(int eflag, int vflag) } if (eflag) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; denlj = lj3[itype][jtype] + rsq*r4sig6; evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * (1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype]; diff --git a/src/USER-H5MD/dump_h5md.cpp b/src/USER-H5MD/dump_h5md.cpp index 1c35c0ca52..4af1e2ed4c 100644 --- a/src/USER-H5MD/dump_h5md.cpp +++ b/src/USER-H5MD/dump_h5md.cpp @@ -36,7 +36,7 @@ using namespace LAMMPS_NS; /** Scan common options for the dump elements */ -int element_args(int narg, char **arg, int *every) +static int element_args(int narg, char **arg, int *every) { int iarg=0; while (iargme == 0 && screen) fprintf(screen,"Setting up run ...\n"); + if (comm->me == 0 && screen) { + fprintf(screen,"Setting up Verlet run ...\n"); + fprintf(screen," Unit style : %s\n", update->unit_style); + fprintf(screen," Current step: " BIGINT_FORMAT "\n", update->ntimestep); + fprintf(screen," Time step : %g\n", update->dt); + if (update->max_wall > 0) { + char outtime[128]; + double totalclock = update->max_wall; + int seconds = fmod(totalclock,60.0); + totalclock = (totalclock - seconds) / 60.0; + int minutes = fmod(totalclock,60.0); + int hours = (totalclock - minutes) / 60.0; + sprintf(outtime," Max walltime: " + "%d:%02d:%02d\n", hours, minutes, seconds); + fputs(outtime,screen); + } + } update->setupflag = 1; @@ -266,6 +282,10 @@ void VerletIntel::run(int n) else sortflag = 0; for (int i = 0; i < n; i++) { + if (update->time_expired()) { + update->nsteps = i; + return; + } ntimestep = ++update->ntimestep; ev_set(ntimestep); diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp index a5c411bf88..b5bd8caf0b 100644 --- a/src/USER-MISC/fix_imd.cpp +++ b/src/USER-MISC/fix_imd.cpp @@ -1205,6 +1205,7 @@ void * imdsock_create(void) { s = (imdsocket *) malloc(sizeof(imdsocket)); if (s != NULL) memset(s, 0, sizeof(imdsocket)); + else return NULL; if ((s->sd = socket(PF_INET, SOCK_STREAM, 0)) == -1) { printf("Failed to open socket."); @@ -1344,19 +1345,6 @@ int imdsock_selwrite(void *v, int sec) { /*************************************************************************/ /* start of imd API code. */ -/* Only works with aligned 4-byte quantities, will cause a bus error */ -/* on some platforms if used on unaligned data. */ -void swap4_aligned(void *v, long ndata) { - int *data = (int *) v; - long i; - int *N; - for (i=0; i>24)&0xff) | ((*N&0xff)<<24) | - ((*N>>8)&0xff00) | ((*N&0xff00)<<8)); - } -} - /** structure used to perform byte swapping operations */ typedef union { @@ -1431,12 +1419,6 @@ static int32 imd_writen(void *s, const char *ptr, int32 n) { return n; } -int imd_disconnect(void *s) { - IMDheader header; - imd_fill_header(&header, IMD_DISCONNECT, 0); - return (imd_writen(s, (char *)&header, IMDHEADERSIZE) != IMDHEADERSIZE); -} - int imd_handshake(void *s) { IMDheader header; imd_fill_header(&header, IMD_HANDSHAKE, 1); diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp index 5ade11ce26..75662a8207 100644 --- a/src/USER-MISC/fix_pimd.cpp +++ b/src/USER-MISC/fix_pimd.cpp @@ -659,8 +659,11 @@ void FixPIMD::comm_exec(double **ptr) { char error_line[256]; - sprintf(error_line, "Atom %d is missing at world [%d] rank [%d] required by rank [%d] (%d, %d, %d).\n", - tag_send[i], universe->iworld, comm->me, plan_recv[iplan], atom->tag[0], atom->tag[1], atom->tag[2]); + sprintf(error_line, "Atom " TAGINT_FORMAT " is missing at world [%d] " + "rank [%d] required by rank [%d] (" TAGINT_FORMAT ", " + TAGINT_FORMAT ", " TAGINT_FORMAT ").\n",tag_send[i], + universe->iworld, comm->me, plan_recv[iplan], + atom->tag[0], atom->tag[1], atom->tag[2]); error->universe_one(FLERR,error_line); } diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp index 613204a55e..08224d2950 100644 --- a/src/USER-MISC/fix_srp.cpp +++ b/src/USER-MISC/fix_srp.cpp @@ -152,7 +152,8 @@ void FixSRP::setup_pre_force(int zz) double delx, dely, delz, rmax, rsq, rsqmax; double **x = atom->x; bigint nall = atom->nlocal + atom->nghost; - double xold[nall][3]; + double **xold; + memory->create(xold,nall,3,"fix_srp:xold"); // make a copy of all coordinates and tags // need this because create_atom overwrites ghost atoms @@ -163,7 +164,8 @@ void FixSRP::setup_pre_force(int zz) } tagint *tag = atom->tag; - tagint tagold[nall]; + tagint *tagold; + memory->create(tagold,nall,"fix_srp:tagold"); for(int i = 0; i < nall; i++){ tagold[i]=tag[i]; @@ -212,7 +214,11 @@ void FixSRP::setup_pre_force(int zz) array[atom->nlocal-1][1] = (double)tagold[j]; nadd++; } - } + } + + // free temporary storage + memory->destroy(xold); + memory->destroy(tagold); // new total # of atoms bigint nblocal = atom->nlocal; diff --git a/src/USER-MISC/fix_ti_rs.cpp b/src/USER-MISC/fix_ti_rs.cpp index f80fc4cb17..d5036eb520 100755 --- a/src/USER-MISC/fix_ti_rs.cpp +++ b/src/USER-MISC/fix_ti_rs.cpp @@ -25,6 +25,7 @@ #include "update.h" #include "respa.h" #include "error.h" +#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -45,18 +46,18 @@ FixTIRS::FixTIRS(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) extvector = 1; // Time variables. - t_switch = atoi(arg[5]); - t_equil = atoi(arg[6]); + t_switch = force->bnumeric(FLERR,arg[5]); + t_equil = force->bnumeric(FLERR,arg[6]); t0 = update->ntimestep; - if (t_switch < 0.0) error->all(FLERR,"Illegal fix ti/rs command"); - if (t_equil < 0.0) error->all(FLERR,"Illegal fix ti/rs command"); + if (t_switch <= 0) error->all(FLERR,"Illegal fix ti/rs command"); + if (t_equil <= 0) error->all(FLERR,"Illegal fix ti/rs command"); // Coupling parameter limits and initialization. - l_initial = atof(arg[3]); - l_final = atof(arg[4]); + l_initial = force->numeric(FLERR,arg[3]); + l_final = force->numeric(FLERR,arg[4]); sf = 1; if (narg > 7) { - if (strcmp(arg[7], "function") == 0) sf = atoi(arg[8]); + if (strcmp(arg[7], "function") == 0) sf = force->inumeric(FLERR,arg[8]); else error->all(FLERR,"Illegal fix ti/rs switching function"); if ((sf<1) || (sf>3)) error->all(FLERR,"Illegal fix ti/rs switching function"); @@ -151,16 +152,17 @@ void FixTIRS::min_post_force(int vflag) void FixTIRS::initial_integrate(int vflag) { // Update the coupling parameter value. - double t = update->ntimestep - (t0+t_equil); + const bigint t = update->ntimestep - (t0+t_equil); + const double r_switch = 1.0/t_switch; if( (t >= 0) && (t <= t_switch) ) { - lambda = switch_func(t/t_switch); - dlambda = dswitch_func(t/t_switch); + lambda = switch_func(t*r_switch); + dlambda = dswitch_func(t*r_switch); } if( (t >= t_equil+t_switch) && (t <= (t_equil+2*t_switch)) ) { - lambda = switch_func(1.0 - (t - t_switch - t_equil)/t_switch); - dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)/t_switch); + lambda = switch_func(1.0 - (t - t_switch - t_equil)*r_switch); + dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)*r_switch); } } diff --git a/src/USER-MISC/fix_ti_rs.h b/src/USER-MISC/fix_ti_rs.h index 58466501a9..6b5124f711 100755 --- a/src/USER-MISC/fix_ti_rs.h +++ b/src/USER-MISC/fix_ti_rs.h @@ -53,9 +53,9 @@ class FixTIRS : public Fix { double l_initial; // Lambda initial value. double l_final; // Lambda final value. double linfo[2]; // Current lambda status. - int t_switch; // Total switching steps. - int t_equil; // Equilibration time. - int t0; // Initial time. + bigint t_switch; // Total switching steps. + bigint t_equil; // Equilibration time. + bigint t0; // Initial time. int sf; // Switching function option. int nlevels_respa; }; diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp index 529e650978..3d10312720 100755 --- a/src/USER-MISC/fix_ti_spring.cpp +++ b/src/USER-MISC/fix_ti_spring.cpp @@ -73,16 +73,16 @@ FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) : } // Time variables. - t_switch = atoi(arg[4]); // Switching time. - t_equil = atoi(arg[5]); // Equilibration time. + t_switch = force->bnumeric(FLERR,arg[4]); // Number of steps for switching. + t_equil = force->bnumeric(FLERR,arg[5]); // Number of steps for equilibration. t0 = update->ntimestep; // Initial time. - if (t_switch <= 0.0) error->all(FLERR,"Illegal fix ti/spring command"); - if (t_equil <= 0.0) error->all(FLERR,"Illegal fix ti/spring command"); + if (t_switch <= 0) error->all(FLERR,"Illegal fix ti/spring command"); + if (t_equil <= 0) error->all(FLERR,"Illegal fix ti/spring command"); // Coupling parameter initialization. sf = 1; if (narg > 6) { - if (strcmp(arg[6], "function") == 0) sf = atoi(arg[7]); + if (strcmp(arg[6], "function") == 0) sf = force->inumeric(FLERR,arg[7]); else error->all(FLERR,"Illegal fix ti/spring switching function"); if ((sf!=1) && (sf!=2)) error->all(FLERR,"Illegal fix ti/spring switching function"); @@ -151,7 +151,7 @@ void FixTISpring::min_setup(int vflag) void FixTISpring::post_force(int vflag) { // If on the first equilibration do not calculate forces. - int t = update->ntimestep - t0; + bigint t = update->ntimestep - t0; if(t < t_equil) return; double **x = atom->x; @@ -199,16 +199,17 @@ void FixTISpring::min_post_force(int vflag) void FixTISpring::initial_integrate(int vflag) { // Update the coupling parameter value. - double t = update->ntimestep - (t0+t_equil); + const bigint t = update->ntimestep - (t0+t_equil); + const double r_switch = 1.0/t_switch; if( (t >= 0) && (t <= t_switch) ) { - lambda = switch_func(t/t_switch); - dlambda = dswitch_func(t/t_switch); + lambda = switch_func(t*r_switch); + dlambda = dswitch_func(t*r_switch); } if( (t >= t_equil+t_switch) && (t <= (t_equil+2*t_switch)) ) { - lambda = switch_func(1.0 - (t - t_switch - t_equil)/t_switch ); - dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)/t_switch ); + lambda = switch_func(1.0 - (t - t_switch - t_equil)*r_switch); + dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)*r_switch); } } diff --git a/src/USER-MISC/fix_ti_spring.h b/src/USER-MISC/fix_ti_spring.h index ce67968d56..a5ff1fb677 100755 --- a/src/USER-MISC/fix_ti_spring.h +++ b/src/USER-MISC/fix_ti_spring.h @@ -65,9 +65,9 @@ class FixTISpring : public Fix { double lambda; // Coupling parameter. double dlambda; // Lambda variation with t. double linfo[2]; // Current lambda status. - int t_switch; // Total switching steps. - int t_equil; // Equilibration time. - int t0; // Initial time. + bigint t_switch; // Total switching steps. + bigint t_equil; // Equilibration time. + bigint t0; // Initial time. int sf; // Switching function option. int nlevels_respa; }; diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp index 77002a5ba3..c5865c0a99 100644 --- a/src/USER-MISC/pair_tersoff_table.cpp +++ b/src/USER-MISC/pair_tersoff_table.cpp @@ -306,10 +306,6 @@ void PairTersoffTable::compute(int eflag, int vflag) if (r_ik > params[ikparam].cutsq) continue; - r_ik = sqrt(r_ik); - - invR_ik = 1.0 / r_ik; - gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k]; cutoffFunctionIK = preCutoffFunction[neighbor_k]; @@ -335,13 +331,6 @@ void PairTersoffTable::compute(int eflag, int vflag) if (r_ik > params[ikparam].cutsq) continue; - r_ik = sqrt(r_ik); - invR_ik = 1.0 / r_ik; - - directorCos_ik_x = invR_ik * dr_ik[0]; - directorCos_ik_y = invR_ik * dr_ik[1]; - directorCos_ik_z = invR_ik * dr_ik[2]; - gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k]; cutoffFunctionIK = preCutoffFunction[neighbor_k]; diff --git a/src/USER-MOLFILE/dump_molfile.cpp b/src/USER-MOLFILE/dump_molfile.cpp index add7bf695b..54e86f3bc5 100644 --- a/src/USER-MOLFILE/dump_molfile.cpp +++ b/src/USER-MOLFILE/dump_molfile.cpp @@ -387,6 +387,7 @@ void DumpMolfile::write_data(int n, double *mybuf) if (need_structure) { mf->property(MFI::P_NAME,types,typenames); + mf->property(MFI::P_TYPE,types,typenames); if (atom->molecule_flag) mf->property(MFI::P_RESI,molids); diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp index 2b3e2de299..7cb63bcc16 100644 --- a/src/USER-OMP/fix_omp.cpp +++ b/src/USER-OMP/fix_omp.cpp @@ -147,13 +147,9 @@ FixOMP::FixOMP(LAMMPS *lmp, int narg, char **arg) FixOMP::~FixOMP() { -#if defined(_OPENMP) -#pragma omp parallel default(none) -#endif - { - const int tid = get_tid(); - delete thr[tid]; - } + for (int i=0; i < _nthr; ++i) + delete thr[i]; + delete[] thr; } @@ -189,8 +185,30 @@ void FixOMP::init() error->all(FLERR,"USER-OMP package does not (yet) work with " "atom_style template"); + // adjust number of data objects when the number of OpenMP + // threads has been changed somehow + const int nthreads = comm->nthreads; + if (_nthr != nthreads) { + if (screen) fprintf(screen,"Re-init USER-OMP for %d OpenMP thread(s)\n", nthreads); + if (logfile) fprintf(logfile,"Re-init USER-OMP for %d OpenMP thread(s)\n", nthreads); + + for (int i=0; i < _nthr; ++i) + delete thr[i]; + + thr = new ThrData *[nthreads]; + _nthr = nthreads; +#if defined(_OPENMP) +#pragma omp parallel default(none) +#endif + { + const int tid = get_tid(); + Timer *t = new Timer(lmp); + thr[tid] = new ThrData(tid,t); + } + } + // reset per thread timer - for (int i=0; i < comm->nthreads; ++i) { + for (int i=0; i < nthreads; ++i) { thr[i]->_timer_active=1; thr[i]->timer(Timer::RESET); thr[i]->_timer_active=-1; @@ -323,7 +341,7 @@ void FixOMP::set_neighbor_omp() void FixOMP::setup(int) { // we are post the force compute in setup. turn on timers - for (int i=0; i < comm->nthreads; ++i) + for (int i=0; i < _nthr; ++i) thr[i]->_timer_active=0; } @@ -356,8 +374,8 @@ void FixOMP::pre_force(int) double FixOMP::memory_usage() { - double bytes = comm->nthreads * (sizeof(ThrData *) + sizeof(ThrData)); - bytes += comm->nthreads * thr[0]->memory_usage(); + double bytes = _nthr * (sizeof(ThrData *) + sizeof(ThrData)); + bytes += _nthr * thr[0]->memory_usage(); return bytes; } diff --git a/src/USER-OMP/pair_tersoff_table_omp.cpp b/src/USER-OMP/pair_tersoff_table_omp.cpp index bd786c7ca9..ece331abd9 100644 --- a/src/USER-OMP/pair_tersoff_table_omp.cpp +++ b/src/USER-OMP/pair_tersoff_table_omp.cpp @@ -297,10 +297,6 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr) if (r_ik > params[ikparam].cutsq) continue; - r_ik = sqrt(r_ik); - - invR_ik = 1.0 / r_ik; - gtetaFunctionIJK = thrGtetaFunction[tid][neighbor_j][neighbor_k]; cutoffFunctionIK = thrCutoffFunction[tid][neighbor_k]; @@ -326,13 +322,6 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr) if (r_ik > params[ikparam].cutsq) continue; - r_ik = sqrt(r_ik); - invR_ik = 1.0 / r_ik; - - directorCos_ik_x = invR_ik * dr_ik[0]; - directorCos_ik_y = invR_ik * dr_ik[1]; - directorCos_ik_z = invR_ik * dr_ik[2]; - gtetaFunctionIJK = thrGtetaFunction[tid][neighbor_j][neighbor_k]; cutoffFunctionIK = thrCutoffFunction[tid][neighbor_k]; diff --git a/src/USER-OMP/respa_omp.cpp b/src/USER-OMP/respa_omp.cpp index ed08f019fb..f5603adf92 100644 --- a/src/USER-OMP/respa_omp.cpp +++ b/src/USER-OMP/respa_omp.cpp @@ -74,6 +74,17 @@ void RespaOMP::setup() fprintf(screen," Unit style : %s\n", update->unit_style); fprintf(screen," Current step : " BIGINT_FORMAT "\n", update->ntimestep); fprintf(screen," OuterTime step: %g\n", update->dt); + if (update->max_wall > 0) { + char outtime[128]; + double totalclock = update->max_wall; + int seconds = fmod(totalclock,60.0); + totalclock = (totalclock - seconds) / 60.0; + int minutes = fmod(totalclock,60.0); + int hours = (totalclock - minutes) / 60.0; + sprintf(outtime," Max walltime: " + "%d:%02d:%02d\n", hours, minutes, seconds); + fputs(outtime,screen); + } } update->setupflag = 1; @@ -150,6 +161,7 @@ void RespaOMP::setup() fix->did_reduce(); } + modify->pre_reverse(eflag,vflag); if (newton[ilevel]) comm->reverse_comm(); copy_f_flevel(ilevel); } @@ -243,6 +255,7 @@ void RespaOMP::setup_minimal(int flag) fix->did_reduce(); } + modify->pre_reverse(eflag,vflag); if (newton[ilevel]) comm->reverse_comm(); copy_f_flevel(ilevel); } @@ -391,6 +404,10 @@ void RespaOMP::recurse(int ilevel) fix->did_reduce(); } + if (modify->n_pre_reverse) { + modify->pre_reverse(eflag,vflag); + timer->stamp(Timer::MODIFY); + } if (newton[ilevel]) { comm->reverse_comm(); timer->stamp(Timer::COMM); diff --git a/src/USER-REAXC/reaxc_bond_orders.cpp b/src/USER-REAXC/reaxc_bond_orders.cpp index e524c75e87..0b4ca21adf 100644 --- a/src/USER-REAXC/reaxc_bond_orders.cpp +++ b/src/USER-REAXC/reaxc_bond_orders.cpp @@ -359,12 +359,6 @@ int BOp( storage *workspace, reax_list *bonds, double bo_cut, } -int compare_bonds( const void *p1, const void *p2 ) -{ - return ((bond_data *)p1)->nbr - ((bond_data *)p2)->nbr; -} - - void BO( reax_system *system, control_params *control, simulation_data *data, storage *workspace, reax_list **lists, output_controls *out_control ) { diff --git a/src/USER-REAXC/reaxc_bond_orders.h b/src/USER-REAXC/reaxc_bond_orders.h index 8f1e182aa2..3631d90c89 100644 --- a/src/USER-REAXC/reaxc_bond_orders.h +++ b/src/USER-REAXC/reaxc_bond_orders.h @@ -36,23 +36,6 @@ typedef struct{ double C1dDelta, C2dDelta, C3dDelta; }dbond_coefficients; -#ifdef TEST_FORCES -void Get_dBO( reax_system*, reax_list**, int, int, double, rvec* ); -void Get_dBOpinpi2( reax_system*, reax_list**, - int, int, double, double, rvec*, rvec* ); - -void Add_dBO( reax_system*, reax_list**, int, int, double, rvec* ); -void Add_dBOpinpi2( reax_system*, reax_list**, - int, int, double, double, rvec*, rvec* ); - -void Add_dBO_to_Forces( reax_system*, reax_list**, int, int, double ); -void Add_dBOpinpi2_to_Forces( reax_system*, reax_list**, - int, int, double, double ); - -void Add_dDelta( reax_system*, reax_list**, int, double, rvec* ); -void Add_dDelta_to_Forces( reax_system *, reax_list**, int, double ); -#endif - void Add_dBond_to_Forces( reax_system*, int, int, storage*, reax_list** ); void Add_dBond_to_Forces_NPT( int, int, simulation_data*, storage*, reax_list** ); diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp index 34ac121856..6007cb7344 100644 --- a/src/USER-REAXC/reaxc_ffield.cpp +++ b/src/USER-REAXC/reaxc_ffield.cpp @@ -60,6 +60,8 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, if (n < 1) { fprintf( stderr, "WARNING: number of globals in ffield file is 0!\n" ); fclose(fp); + free(s); + free(tmp); return 1; } diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp index 84bb86e5d2..7f11f5565f 100644 --- a/src/USER-REAXC/reaxc_forces.cpp +++ b/src/USER-REAXC/reaxc_forces.cpp @@ -171,213 +171,6 @@ void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists, } -double Compute_H( double r, double gamma, double *ctap ) -{ - double taper, dr3gamij_1, dr3gamij_3; - - taper = ctap[7] * r + ctap[6]; - taper = taper * r + ctap[5]; - taper = taper * r + ctap[4]; - taper = taper * r + ctap[3]; - taper = taper * r + ctap[2]; - taper = taper * r + ctap[1]; - taper = taper * r + ctap[0]; - - dr3gamij_1 = ( r*r*r + gamma ); - dr3gamij_3 = pow( dr3gamij_1 , 0.33333333333333 ); - return taper * EV_to_KCALpMOL / dr3gamij_3; -} - - -double Compute_tabH( double r_ij, int ti, int tj ) -{ - int r, tmin, tmax; - double val, dif, base; - LR_lookup_table *t; - - tmin = MIN( ti, tj ); - tmax = MAX( ti, tj ); - t = &( LR[tmin][tmax] ); - - /* cubic spline interpolation */ - r = (int)(r_ij * t->inv_dx); - if( r == 0 ) ++r; - base = (double)(r+1) * t->dx; - dif = r_ij - base; - val = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif + - t->ele[r].a; - val *= EV_to_KCALpMOL / C_ele; - - return val; -} - - -void Init_Forces( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, reax_list **lists, - output_controls *out_control, MPI_Comm comm ) { - int i, j, pj; - int start_i, end_i; - int type_i, type_j; - int Htop, btop_i, btop_j, num_bonds, num_hbonds; - int ihb, jhb, ihb_top, jhb_top; - int local, flag, renbr; - double r_ij, cutoff; - sparse_matrix *H; - reax_list *far_nbrs, *bonds, *hbonds; - single_body_parameters *sbp_i, *sbp_j; - two_body_parameters *twbp; - far_neighbor_data *nbr_pj; - reax_atom *atom_i, *atom_j; - - far_nbrs = *lists + FAR_NBRS; - bonds = *lists + BONDS; - hbonds = *lists + HBONDS; - - for( i = 0; i < system->n; ++i ) - workspace->bond_mark[i] = 0; - for( i = system->n; i < system->N; ++i ) { - workspace->bond_mark[i] = 1000; // put ghost atoms to an infinite distance - } - - H = workspace->H; - H->n = system->n; - Htop = 0; - num_bonds = 0; - num_hbonds = 0; - btop_i = btop_j = 0; - renbr = (data->step-data->prev_steps) % control->reneighbor == 0; - - for( i = 0; i < system->N; ++i ) { - atom_i = &(system->my_atoms[i]); - type_i = atom_i->type; - if (type_i < 0) continue; - start_i = Start_Index(i, far_nbrs); - end_i = End_Index(i, far_nbrs); - btop_i = End_Index( i, bonds ); - sbp_i = &(system->reax_param.sbp[type_i]); - - if( i < system->n ) { - local = 1; - cutoff = control->nonb_cut; - } - else { - local = 0; - cutoff = control->bond_cut; - } - - ihb = -1; - ihb_top = -1; - if( local ) { - H->start[i] = Htop; - H->entries[Htop].j = i; - H->entries[Htop].val = sbp_i->eta; - ++Htop; - - if( control->hbond_cut > 0 ) { - ihb = sbp_i->p_hbond; - if( ihb == 1 ) - ihb_top = End_Index( atom_i->Hindex, hbonds ); - else ihb_top = -1; - } - } - - /* update i-j distance - check if j is within cutoff */ - for( pj = start_i; pj < end_i; ++pj ) { - nbr_pj = &( far_nbrs->select.far_nbr_list[pj] ); - j = nbr_pj->nbr; - atom_j = &(system->my_atoms[j]); - if( renbr ) { - if(nbr_pj->d <= cutoff) - flag = 1; - else flag = 0; - } - else{ - nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0]; - nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1]; - nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2]; - nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec ); - if( nbr_pj->d <= SQR(cutoff) ) { - nbr_pj->d = sqrt(nbr_pj->d); - flag = 1; - } - else { - flag = 0; - } - } - - if( flag ){ - type_j = atom_j->type; - if (type_j < 0) continue; - r_ij = nbr_pj->d; - sbp_j = &(system->reax_param.sbp[type_j]); - twbp = &(system->reax_param.tbp[type_i][type_j]); - - if( local ) { - /* H matrix entry */ - if( j < system->n || atom_i->orig_id < atom_j->orig_id ) {//tryQEq||1 - H->entries[Htop].j = j; - if( control->tabulate == 0 ) - H->entries[Htop].val = Compute_H(r_ij,twbp->gamma,workspace->Tap); - else H->entries[Htop].val = Compute_tabH(r_ij, type_i, type_j); - ++Htop; - } - - /* hydrogen bond lists */ - if( control->hbond_cut > 0 && (ihb==1 || ihb==2) && - nbr_pj->d <= control->hbond_cut ) { - jhb = sbp_j->p_hbond; - if( ihb == 1 && jhb == 2 ) { - hbonds->select.hbond_list[ihb_top].nbr = j; - hbonds->select.hbond_list[ihb_top].scl = 1; - hbonds->select.hbond_list[ihb_top].ptr = nbr_pj; - ++ihb_top; - ++num_hbonds; - } - else if( j < system->n && ihb == 2 && jhb == 1 ) { - jhb_top = End_Index( atom_j->Hindex, hbonds ); - hbonds->select.hbond_list[jhb_top].nbr = i; - hbonds->select.hbond_list[jhb_top].scl = -1; - hbonds->select.hbond_list[jhb_top].ptr = nbr_pj; - Set_End_Index( atom_j->Hindex, jhb_top+1, hbonds ); - ++num_hbonds; - } - } - } - - /* uncorrected bond orders */ - if( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) && - nbr_pj->d <= control->bond_cut && - BOp( workspace, bonds, control->bo_cut, - i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) { - num_bonds += 2; - ++btop_i; - - if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 ) - workspace->bond_mark[j] = workspace->bond_mark[i] + 1; - else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 ) { - workspace->bond_mark[i] = workspace->bond_mark[j] + 1; - } - } - } - } - - Set_End_Index( i, btop_i, bonds ); - if( local ) { - H->end[i] = Htop; - if( ihb == 1 ) - Set_End_Index( atom_i->Hindex, ihb_top, hbonds ); - } - } - - workspace->realloc.Htop = Htop; - workspace->realloc.num_bonds = num_bonds; - workspace->realloc.num_hbonds = num_hbonds; - - Validate_Lists( system, workspace, lists, data->step, - system->n, system->N, system->numH, comm ); -} - - void Init_Forces_noQEq( reax_system *system, control_params *control, simulation_data *data, storage *workspace, reax_list **lists, output_controls *out_control, @@ -647,19 +440,11 @@ void Compute_Forces( reax_system *system, control_params *control, reax_list **lists, output_controls *out_control, mpi_datatypes *mpi_data ) { - MPI_Comm comm; - int qeq_flag; + MPI_Comm comm = mpi_data->world; - comm = mpi_data->world; - qeq_flag = 0; - - if( qeq_flag ) - Init_Forces( system, control, data, workspace, lists, out_control, comm ); - else - Init_Forces_noQEq( system, control, data, workspace, + Init_Forces_noQEq( system, control, data, workspace, lists, out_control, comm ); - /********* bonded interactions ************/ Compute_Bonded_Forces( system, control, data, workspace, lists, out_control, mpi_data->world ); diff --git a/src/USER-REAXC/reaxc_io_tools.cpp b/src/USER-REAXC/reaxc_io_tools.cpp index 1a978d0073..0c14dad5d4 100644 --- a/src/USER-REAXC/reaxc_io_tools.cpp +++ b/src/USER-REAXC/reaxc_io_tools.cpp @@ -34,8 +34,6 @@ #include "reaxc_traj.h" #include "reaxc_vector.h" -print_interaction Print_Interactions[NUM_INTRS]; - int Init_Output_Files( reax_system *system, control_params *control, output_controls *out_control, mpi_datatypes *mpi_data, char *msg ) @@ -109,432 +107,6 @@ int Close_Output_Files( reax_system *system, control_params *control, } - -void Print_Box( simulation_box* box, char *name, FILE *out ) -{ - // int i, j; - - fprintf( out, "%s:\n", name ); - fprintf( out, "\tmin[%8.3f %8.3f %8.3f]\n", - box->min[0], box->min[1], box->min[2] ); - fprintf( out, "\tmax[%8.3f %8.3f %8.3f]\n", - box->max[0], box->max[1], box->max[2] ); - fprintf( out, "\tdims[%8.3f%8.3f%8.3f]\n", - box->box_norms[0], box->box_norms[1], box->box_norms[2] ); - -} - - - -void Print_Grid( grid* g, FILE *out ) -{ - int x, y, z, gc_type; - ivec gc_str; - char gcell_type_text[10][12] = - { "NO_NBRS", "NEAR_ONLY", "HBOND_ONLY", "FAR_ONLY", - "NEAR_HBOND", "NEAR_FAR", "HBOND_FAR", "FULL_NBRS", "NATIVE" }; - - fprintf( out, "\tnumber of grid cells: %d %d %d\n", - g->ncells[0], g->ncells[1], g->ncells[2] ); - fprintf( out, "\tgcell lengths: %8.3f %8.3f %8.3f\n", - g->cell_len[0], g->cell_len[1], g->cell_len[2] ); - fprintf( out, "\tinverses of gcell lengths: %8.3f %8.3f %8.3f\n", - g->inv_len[0], g->inv_len[1], g->inv_len[2] ); - fprintf( out, "\t---------------------------------\n" ); - fprintf( out, "\tnumber of native gcells: %d %d %d\n", - g->native_cells[0], g->native_cells[1], g->native_cells[2] ); - fprintf( out, "\tnative gcell span: %d-%d %d-%d %d-%d\n", - g->native_str[0], g->native_end[0], - g->native_str[1], g->native_end[1], - g->native_str[2], g->native_end[2] ); - fprintf( out, "\t---------------------------------\n" ); - fprintf( out, "\tvlist gcell stretch: %d %d %d\n", - g->vlist_span[0], g->vlist_span[1], g->vlist_span[2] ); - fprintf( out, "\tnonbonded nbrs gcell stretch: %d %d %d\n", - g->nonb_span[0], g->nonb_span[1], g->nonb_span[2] ); - fprintf( out, "\tbonded nbrs gcell stretch: %d %d %d\n", - g->bond_span[0], g->bond_span[1], g->bond_span[2] ); - fprintf( out, "\t---------------------------------\n" ); - fprintf( out, "\tghost gcell span: %d %d %d\n", - g->ghost_span[0], g->ghost_span[1], g->ghost_span[2] ); - fprintf( out, "\tnonbonded ghost gcell span: %d %d %d\n", - g->ghost_nonb_span[0],g->ghost_nonb_span[1],g->ghost_nonb_span[2]); - fprintf(out, "\thbonded ghost gcell span: %d %d %d\n", - g->ghost_hbond_span[0],g->ghost_hbond_span[1],g->ghost_hbond_span[2]); - fprintf( out, "\tbonded ghost gcell span: %d %d %d\n", - g->ghost_bond_span[0],g->ghost_bond_span[1],g->ghost_bond_span[2]); - fprintf( out, "\t---------------------------------\n" ); - - fprintf( stderr, "GCELL MARKS:\n" ); - gc_type = g->cells[0][0][0].type; - ivec_MakeZero( gc_str ); - - x = y = z = 0; - for( x = 0; x < g->ncells[0]; ++x ) - for( y = 0; y < g->ncells[1]; ++y ) - for( z = 0; z < g->ncells[2]; ++z ) - if( g->cells[x][y][z].type != gc_type ){ - fprintf( stderr, - "\tgcells from(%2d %2d %2d) to (%2d %2d %2d): %d - %s\n", - gc_str[0], gc_str[1], gc_str[2], x, y, z, - gc_type, gcell_type_text[gc_type] ); - gc_type = g->cells[x][y][z].type; - gc_str[0] = x; - gc_str[1] = y; - gc_str[2] = z; - } - fprintf( stderr, "\tgcells from(%2d %2d %2d) to (%2d %2d %2d): %d - %s\n", - gc_str[0], gc_str[1], gc_str[2], x, y, z, - gc_type, gcell_type_text[gc_type] ); - fprintf( out, "-------------------------------------\n" ); -} - -void Print_Native_GCells( reax_system *system ) -{ - int i, j, k, l; - char fname[100]; - FILE *f; - grid *g; - grid_cell *gc; - char gcell_type_text[10][12] = - { "NO_NBRS", "NEAR_ONLY", "HBOND_ONLY", "FAR_ONLY", - "NEAR_HBOND", "NEAR_FAR", "HBOND_FAR", "FULL_NBRS", "NATIVE" }; - - sprintf( fname, "native_gcells.%d", system->my_rank ); - f = fopen( fname, "w" ); - g = &(system->my_grid); - - for( i = g->native_str[0]; i < g->native_end[0]; i++ ) - for( j = g->native_str[1]; j < g->native_end[1]; j++ ) - for( k = g->native_str[2]; k < g->native_end[2]; k++ ) - { - gc = &( g->cells[i][j][k] ); - - fprintf( f, "p%d gcell(%2d %2d %2d) of type %d(%s)\n", - system->my_rank, i, j, k, - gc->type, gcell_type_text[gc->type] ); - - fprintf( f, "\tatom list start: %d, end: %d\n\t", gc->str, gc->end ); - - for( l = gc->str; l < gc->end; ++l ) - fprintf( f, TAGINT_FORMAT, system->my_atoms[l].orig_id ); - fprintf( f, "\n" ); - } - - fclose(f); -} - - - -void Print_All_GCells( reax_system *system ) -{ - int i, j, k, l; - char fname[100]; - FILE *f; - grid *g; - grid_cell *gc; - char gcell_type_text[10][12] = - { "NO_NBRS", "NEAR_ONLY", "HBOND_ONLY", "FAR_ONLY", - "NEAR_HBOND", "NEAR_FAR", "HBOND_FAR", "FULL_NBRS", "NATIVE" }; - - sprintf( fname, "all_gcells.%d", system->my_rank ); - f = fopen( fname, "w" ); - g = &(system->my_grid); - - for( i = 0; i < g->ncells[0]; i++ ) - for( j = 0; j < g->ncells[1]; j++ ) - for( k = 0; k < g->ncells[2]; k++ ) - { - gc = &( g->cells[i][j][k] ); - - fprintf( f, "p%d gcell(%2d %2d %2d) of type %d(%s)\n", - system->my_rank, i, j, k, - gc->type, gcell_type_text[gc->type] ); - - fprintf( f, "\tatom list start: %d, end: %d\n\t", gc->str, gc->end ); - - for( l = gc->str; l < gc->end; ++l ) - fprintf( f, TAGINT_FORMAT, system->my_atoms[l].orig_id ); - fprintf( f, "\n" ); - } - - fclose(f); -} - - - -void Print_My_Atoms( reax_system *system ) -{ - int i; - char fname[100]; - FILE *fh; - - sprintf( fname, "my_atoms.%d", system->my_rank ); - if( (fh = fopen( fname, "w" )) == NULL ) - { - fprintf( stderr, "error in opening my_atoms file" ); - MPI_Abort( MPI_COMM_WORLD, FILE_NOT_FOUND ); - } - - for( i = 0; i < system->n; ++i ) - fprintf( fh, "p%-2d %-5d %2d %24.15e%24.15e%24.15e\n", - system->my_rank, - system->my_atoms[i].orig_id, system->my_atoms[i].type, - system->my_atoms[i].x[0], - system->my_atoms[i].x[1], - system->my_atoms[i].x[2] ); - - fclose( fh ); -} - - -void Print_My_Ext_Atoms( reax_system *system ) -{ - int i; - char fname[100]; - FILE *fh; - - sprintf( fname, "my_ext_atoms.%d", system->my_rank ); - if( (fh = fopen( fname, "w" )) == NULL ) - { - fprintf( stderr, "error in opening my_ext_atoms file" ); - MPI_Abort( MPI_COMM_WORLD, FILE_NOT_FOUND ); - } - - for( i = 0; i < system->N; ++i ) - fprintf( fh, "p%-2d %-5d imprt%-5d %2d %24.15e%24.15e%24.15e\n", - system->my_rank, system->my_atoms[i].orig_id, - system->my_atoms[i].imprt_id, system->my_atoms[i].type, - system->my_atoms[i].x[0], - system->my_atoms[i].x[1], - system->my_atoms[i].x[2] ); - - fclose( fh ); -} - - -void Print_Far_Neighbors( reax_system *system, reax_list **lists, - control_params *control ) -{ - char fname[100]; - int i, j, nbr, natoms; - rc_tagint id_i, id_j; - FILE *fout; - reax_list *far_nbrs; - - sprintf( fname, "%s.far_nbrs.%d", control->sim_name, system->my_rank ); - fout = fopen( fname, "w" ); - far_nbrs = (*lists) + FAR_NBRS; - natoms = system->N; - - for( i = 0; i < natoms; ++i ) { - id_i = system->my_atoms[i].orig_id; - - for( j = Start_Index(i,far_nbrs); j < End_Index(i,far_nbrs); ++j ) { - nbr = far_nbrs->select.far_nbr_list[j].nbr; - id_j = system->my_atoms[nbr].orig_id; - - fprintf( fout, "%6d%6d%24.15e%24.15e%24.15e%24.15e\n", - id_i, id_j, far_nbrs->select.far_nbr_list[j].d, - far_nbrs->select.far_nbr_list[j].dvec[0], - far_nbrs->select.far_nbr_list[j].dvec[1], - far_nbrs->select.far_nbr_list[j].dvec[2] ); - - fprintf( fout, "%6d%6d%24.15e%24.15e%24.15e%24.15e\n", - id_j, id_i, far_nbrs->select.far_nbr_list[j].d, - -far_nbrs->select.far_nbr_list[j].dvec[0], - -far_nbrs->select.far_nbr_list[j].dvec[1], - -far_nbrs->select.far_nbr_list[j].dvec[2] ); - } - } - - fclose( fout ); -} - - -void Print_Sparse_Matrix( reax_system *system, sparse_matrix *A ) -{ - int i, j; - - for( i = 0; i < A->n; ++i ) - for( j = A->start[i]; j < A->end[i]; ++j ) - fprintf( stderr, "%d %d %.15e\n", - system->my_atoms[i].orig_id, - system->my_atoms[A->entries[j].j].orig_id, - A->entries[j].val ); -} - - -void Print_Sparse_Matrix2( reax_system *system, sparse_matrix *A, char *fname ) -{ - int i, j; - FILE *f = fopen( fname, "w" ); - - for( i = 0; i < A->n; ++i ) - for( j = A->start[i]; j < A->end[i]; ++j ) - fprintf( f, "%d %d %.15e\n", - system->my_atoms[i].orig_id, - system->my_atoms[A->entries[j].j].orig_id, - A->entries[j].val ); - - fclose(f); -} - - -void Print_Symmetric_Sparse(reax_system *system, sparse_matrix *A, char *fname) -{ - int i, j; - reax_atom *ai, *aj; - FILE *f = fopen( fname, "w" ); - - for( i = 0; i < A->n; ++i ) { - ai = &(system->my_atoms[i]); - for( j = A->start[i]; j < A->end[i]; ++j ) { - aj = &(system->my_atoms[A->entries[j].j]); - fprintf( f, "%d %d %.15e\n", - ai->renumber, aj->renumber, A->entries[j].val ); - if( A->entries[j].j < system->n && ai->renumber != aj->renumber ) - fprintf( f, "%d %d %.15e\n", - aj->renumber, ai->renumber, A->entries[j].val ); - } - } - - fclose(f); -} - - -void Print_Linear_System( reax_system *system, control_params *control, - storage *workspace, int step ) -{ - int i; - char fname[100]; - reax_atom *ai; - FILE *out; - - // print rhs and init guesses for QEq - sprintf( fname, "%s.p%dstate%d", control->sim_name, system->my_rank, step ); - out = fopen( fname, "w" ); - for( i = 0; i < system->n; i++ ) { - ai = &(system->my_atoms[i]); - fprintf( out, "%6d%2d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n", - ai->renumber, ai->type, ai->x[0], ai->x[1], ai->x[2], - workspace->s[i], workspace->b_s[i], - workspace->t[i], workspace->b_t[i] ); - } - fclose( out ); - - // print QEq coef matrix - sprintf( fname, "%s.p%dH%d", control->sim_name, system->my_rank, step ); - Print_Symmetric_Sparse( system, workspace->H, fname ); - -} - - -void Print_LinSys_Soln( reax_system *system, double *x, double *b_prm, double *b ) -{ - int i; - char fname[100]; - FILE *fout; - - sprintf( fname, "qeq.%d.out", system->my_rank ); - fout = fopen( fname, "w" ); - - for( i = 0; i < system->n; ++i ) - fprintf( fout, "%6d%10.4f%10.4f%10.4f\n", - system->my_atoms[i].orig_id, x[i], b_prm[i], b[i] ); - - fclose( fout ); -} - - -void Print_Charges( reax_system *system ) -{ - int i; - char fname[100]; - FILE *fout; - - sprintf( fname, "q.%d.out", system->my_rank ); - fout = fopen( fname, "w" ); - - for( i = 0; i < system->n; ++i ) - fprintf( fout, "%6d %10.7f %10.7f %10.7f\n", - system->my_atoms[i].orig_id, - system->my_atoms[i].s[0], - system->my_atoms[i].t[0], - system->my_atoms[i].q ); - - fclose( fout ); -} - - -void Print_Bonds( reax_system *system, reax_list *bonds, char *fname ) -{ - int i, j, pj; - bond_data *pbond; - bond_order_data *bo_ij; - FILE *f = fopen( fname, "w" ); - - for( i = 0; i < system->N; ++i ) - for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) { - pbond = &(bonds->select.bond_list[pj]); - bo_ij = &(pbond->bo_data); - j = pbond->nbr; - fprintf( f, "%8d%8d %24.15f %24.15f\n", - i, j,//system->my_atoms[i].orig_id, system->my_atoms[j].orig_id, - pbond->d, bo_ij->BO ); - } - - fclose(f); -} - - -int fn_qsort_intcmp( const void *a, const void *b ) -{ - return( *(int *)a - *(int *)b ); -} - -void Print_Bond_List2( reax_system *system, reax_list *bonds, char *fname ) -{ - int i,j, nbr, pj; - rc_tagint id_i, id_j; - FILE *f = fopen( fname, "w" ); - int temp[500]; - int num=0; - - for( i = 0; i < system->n; ++i ) { - num=0; - id_i = system->my_atoms[i].orig_id; - fprintf( f, "%6d:", id_i); - for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) { - nbr = bonds->select.bond_list[pj].nbr; - id_j = system->my_atoms[nbr].orig_id; - if( id_i < id_j ) - temp[num++] = id_j; - } - - qsort(&temp, num, sizeof(int), fn_qsort_intcmp); - for(j=0; j < num; j++) - fprintf(f, "%6d", temp[j] ); - fprintf(f, "\n"); - } -} - - -void Print_Total_Force( reax_system *system, simulation_data *data, - storage *workspace ) -{ - int i; - - fprintf( stderr, "step: %d\n", data->step ); - fprintf( stderr, "%6s\t%-38s\n", "atom", "atom.f[0,1,2]"); - - for( i = 0; i < system->N; ++i ) - fprintf( stderr, "%6d %f %f %f\n", - //"%6d%24.15e%24.15e%24.15e\n", - system->my_atoms[i].orig_id, - workspace->f[i][0], workspace->f[i][1], workspace->f[i][2] ); -} - void Output_Results( reax_system *system, control_params *control, simulation_data *data, reax_list **lists, output_controls *out_control, mpi_datatypes *mpi_data ) diff --git a/src/USER-REAXC/reaxc_io_tools.h b/src/USER-REAXC/reaxc_io_tools.h index 12312d344e..a3f22fccc2 100644 --- a/src/USER-REAXC/reaxc_io_tools.h +++ b/src/USER-REAXC/reaxc_io_tools.h @@ -33,80 +33,6 @@ int Init_Output_Files( reax_system*, control_params*, output_controls*, mpi_datatypes*, char* ); int Close_Output_Files( reax_system*, control_params*, output_controls*, mpi_datatypes* ); - -void Print_Box( simulation_box*, char*, FILE* ); - -void Print_Grid( grid*, FILE* ); -void Print_GCell_Exchange_Bounds( int, neighbor_proc* ); -void Print_Native_GCells( reax_system* ); -void Print_All_GCells( reax_system*); - -void Print_Init_Atoms( reax_system*, storage* ); -void Print_My_Atoms( reax_system* ); -void Print_My_Ext_Atoms( reax_system* ); - -void Print_Far_Neighbors( reax_system*, reax_list**, control_params *); -void Print_Sparse_Matrix( reax_system*, sparse_matrix* ); -void Print_Sparse_Matrix2( reax_system*, sparse_matrix*, char* ); -void Print_Linear_System( reax_system*, control_params*, storage*, int ); -void Print_LinSys_Soln( reax_system*, double*, double*, double* ); -void Print_Charges( reax_system* ); -void Print_Bonds( reax_system*, reax_list*, char* ); -void Print_Bond_List2( reax_system*, reax_list*, char* ); -void Print_Total_Force( reax_system*, simulation_data*, storage* ); void Output_Results( reax_system*, control_params*, simulation_data*, reax_list**, output_controls*, mpi_datatypes* ); - -#if defined(DEBUG_FOCUS) || defined(TEST_FORCES) || defined(TEST_ENERGY) -void Debug_Marker_Bonded( output_controls*, int ); -void Debug_Marker_Nonbonded( output_controls*, int ); -void Print_Near_Neighbors_List( reax_system*, reax_list**, control_params*, - simulation_data*, output_controls* ); -void Print_Far_Neighbors_List( reax_system*, reax_list**, control_params*, - simulation_data*, output_controls* ); -void Print_Bond_List( reax_system*, control_params*, simulation_data*, - reax_list**, output_controls* ); -/*void Dummy_Printer( reax_system*, control_params*, simulation_data*, - storage*, reax_list**, output_controls* ); -void Print_Bond_Orders( reax_system*, control_params*, simulation_data*, - storage*, reax_list**, output_controls* ); -void Print_Bond_Forces( reax_system*, control_params*, simulation_data*, - storage*, reax_list**, output_controls* ); -void Print_LonePair_Forces( reax_system*, control_params*, simulation_data*, - storage*, reax_list**, output_controls* ); -void Print_OverUnderCoor_Forces( reax_system*, control_params*, - simulation_data*, storage*, reax_list**, - output_controls* ); -void Print_Three_Body_Forces( reax_system*, control_params*, simulation_data*, - storage*, reax_list**, output_controls* ); -void Print_Hydrogen_Bond_Forces( reax_system*, control_params*, - simulation_data*, storage*, reax_list**, - output_controls* ); -void Print_Four_Body_Forces( reax_system*, control_params*, simulation_data*, - storage*, reax_list**, output_controls* ); -void Print_vdW_Coulomb_Forces( reax_system*, control_params*, - simulation_data*, storage*, reax_list**, - output_controls* ); -void Print_Total_Force( reax_system*, control_params*, simulation_data*, - storage*, reax_list**, output_controls* ); -void Compare_Total_Forces( reax_system*, control_params*, simulation_data*, -storage*, reax_list**, output_controls* );*/ -//void Print_Total_Force( reax_system*, control_params* ); -void Print_Force_Files( reax_system*, control_params*, simulation_data*, - storage*, reax_list**, output_controls*, - mpi_datatypes * ); -//void Init_Force_Test_Functions( ); - -int fn_qsort_intcmp( const void *, const void * ); - -void Print_Far_Neighbors_List( reax_system*, reax_list**, control_params*, - simulation_data*, output_controls* ); - -void Print_Near_Neighbors_List( reax_system*, reax_list**, control_params*, - simulation_data*, output_controls* ); - -void Print_Bond_List( reax_system*, control_params*, simulation_data*, - reax_list**, output_controls*); - -#endif #endif diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/USER-REAXC/reaxc_lookup.cpp index 7497a5c096..903e54962d 100644 --- a/src/USER-REAXC/reaxc_lookup.cpp +++ b/src/USER-REAXC/reaxc_lookup.cpp @@ -150,30 +150,6 @@ void Complete_Cubic_Spline( const double *h, const double *f, double v0, double } -void LR_Lookup( LR_lookup_table *t, double r, LR_data *y ) -{ - int i; - double base, dif; - - i = (int)(r * t->inv_dx); - if( i == 0 ) ++i; - base = (double)(i+1) * t->dx; - dif = r - base; - - y->e_vdW = ((t->vdW[i].d*dif + t->vdW[i].c)*dif + t->vdW[i].b)*dif + - t->vdW[i].a; - y->CEvd = ((t->CEvd[i].d*dif + t->CEvd[i].c)*dif + - t->CEvd[i].b)*dif + t->CEvd[i].a; - - y->e_ele = ((t->ele[i].d*dif + t->ele[i].c)*dif + t->ele[i].b)*dif + - t->ele[i].a; - y->CEclmb = ((t->CEclmb[i].d*dif + t->CEclmb[i].c)*dif + t->CEclmb[i].b)*dif + - t->CEclmb[i].a; - - y->H = y->e_ele * EV_to_KCALpMOL / C_ele; -} - - int Init_Lookup_Tables( reax_system *system, control_params *control, storage *workspace, mpi_datatypes *mpi_data, char *msg ) { diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/USER-REAXC/reaxc_reset_tools.cpp index 7d9e9deb76..1e6aeab475 100644 --- a/src/USER-REAXC/reaxc_reset_tools.cpp +++ b/src/USER-REAXC/reaxc_reset_tools.cpp @@ -119,29 +119,6 @@ void Reset_Workspace( reax_system *system, storage *workspace ) } -void Reset_Grid( grid *g ) -{ - int i, j, k; - - for( i = 0; i < g->ncells[0]; i++ ) - for( j = 0; j < g->ncells[1]; j++ ) - for( k = 0; k < g->ncells[2]; k++ ) { - g->cells[i][j][k].top = 0; - g->cells[i][j][k].str = 0; - g->cells[i][j][k].end = 0; - } -} - - -void Reset_Out_Buffers( mpi_out_data *out_buf, int n ) -{ - int i; - - for( i = 0; i < n; ++i ) - out_buf[i].cnt = 0; -} - - void Reset_Neighbor_Lists( reax_system *system, control_params *control, storage *workspace, reax_list **lists, MPI_Comm comm ) diff --git a/src/USER-REAXC/reaxc_reset_tools.h b/src/USER-REAXC/reaxc_reset_tools.h index adc562735c..c2a90072d5 100644 --- a/src/USER-REAXC/reaxc_reset_tools.h +++ b/src/USER-REAXC/reaxc_reset_tools.h @@ -33,13 +33,8 @@ void Reset_Pressures( simulation_data* ); void Reset_Simulation_Data( simulation_data*, int ); void Reset_Timing( reax_timing* ); void Reset_Workspace( reax_system*, storage* ); -void Reset_Grid( grid* ); -void Reset_Out_Buffers( mpi_out_data*, int ); void Reset_Neighbor_Lists( reax_system*, control_params*, storage*, reax_list**, MPI_Comm ); void Reset( reax_system*, control_params*, simulation_data*, storage*, reax_list**, MPI_Comm ); -#ifdef TEST_FORCES -void Reset_Test_Forces( reax_system*, storage* ); -#endif #endif diff --git a/src/USER-REAXC/reaxc_system_props.cpp b/src/USER-REAXC/reaxc_system_props.cpp index 554151ba82..6b4551a03f 100644 --- a/src/USER-REAXC/reaxc_system_props.cpp +++ b/src/USER-REAXC/reaxc_system_props.cpp @@ -29,55 +29,6 @@ #include "reaxc_tool_box.h" #include "reaxc_vector.h" -void Temperature_Control( control_params *control, simulation_data *data ) -{ - double tmp; - - if( control->T_mode == 1 ) {// step-wise temperature control - if((data->step-data->prev_steps) % ((int)(control->T_freq/control->dt))==0){ - if( fabs( control->T - control->T_final ) >= fabs( control->T_rate ) ) - control->T += control->T_rate; - else control->T = control->T_final; - } - } - else if( control->T_mode == 2 ) { // constant slope control - tmp = control->T_rate * control->dt / control->T_freq; - - if( fabs( control->T - control->T_final ) >= fabs( tmp ) ) - control->T += tmp; - } -} - - - -void Compute_Kinetic_Energy( reax_system* system, simulation_data* data, - MPI_Comm comm ) -{ - int i; - rvec p; - double m; - - data->my_en.e_kin = 0.0; - data->sys_en.e_kin = 0.0; - data->therm.T = 0; - - for( i = 0; i < system->n; i++ ) { - m = system->reax_param.sbp[system->my_atoms[i].type].mass; - - rvec_Scale( p, m, system->my_atoms[i].v ); - data->my_en.e_kin += 0.5 * rvec_Dot( p, system->my_atoms[i].v ); - } - - MPI_Allreduce( &data->my_en.e_kin, &data->sys_en.e_kin, - 1, MPI_DOUBLE, MPI_SUM, comm ); - - data->therm.T = (2. * data->sys_en.e_kin) / (data->N_f * K_B); - - // avoid T being an absolute zero, might cause F.P.E! - if( fabs(data->therm.T) < ALMOST_ZERO ) - data->therm.T = ALMOST_ZERO; -} - void Compute_System_Energy( reax_system *system, simulation_data *data, MPI_Comm comm ) @@ -135,169 +86,3 @@ void Compute_System_Energy( reax_system *system, simulation_data *data, data->sys_en.e_tot = data->sys_en.e_pot + E_CONV * data->sys_en.e_kin; } } - - -void Compute_Total_Mass( reax_system *system, simulation_data *data, - MPI_Comm comm ) -{ - int i; - double tmp; - - tmp = 0; - for( i = 0; i < system->n; i++ ) - tmp += system->reax_param.sbp[ system->my_atoms[i].type ].mass; - - MPI_Allreduce( &tmp, &data->M, 1, MPI_DOUBLE, MPI_SUM, comm ); - - data->inv_M = 1. / data->M; -} - - - -void Compute_Center_of_Mass( reax_system *system, simulation_data *data, - mpi_datatypes *mpi_data, MPI_Comm comm ) -{ - int i; - double m, det; //xx, xy, xz, yy, yz, zz; - double tmp_mat[6], tot_mat[6]; - rvec my_xcm, my_vcm, my_amcm, my_avcm; - rvec tvec, diff; - rtensor mat, inv; - - rvec_MakeZero( my_xcm ); // position of CoM - rvec_MakeZero( my_vcm ); // velocity of CoM - rvec_MakeZero( my_amcm ); // angular momentum of CoM - rvec_MakeZero( my_avcm ); // angular velocity of CoM - - /* Compute the position, vel. and ang. momentum about the centre of mass */ - for( i = 0; i < system->n; ++i ) { - m = system->reax_param.sbp[ system->my_atoms[i].type ].mass; - - rvec_ScaledAdd( my_xcm, m, system->my_atoms[i].x ); - rvec_ScaledAdd( my_vcm, m, system->my_atoms[i].v ); - - rvec_Cross( tvec, system->my_atoms[i].x, system->my_atoms[i].v ); - rvec_ScaledAdd( my_amcm, m, tvec ); - } - - MPI_Allreduce( my_xcm, data->xcm, 3, MPI_DOUBLE, MPI_SUM, comm ); - MPI_Allreduce( my_vcm, data->vcm, 3, MPI_DOUBLE, MPI_SUM, comm ); - MPI_Allreduce( my_amcm, data->amcm, 3, MPI_DOUBLE, MPI_SUM, comm ); - - rvec_Scale( data->xcm, data->inv_M, data->xcm ); - rvec_Scale( data->vcm, data->inv_M, data->vcm ); - rvec_Cross( tvec, data->xcm, data->vcm ); - rvec_ScaledAdd( data->amcm, -data->M, tvec ); - data->etran_cm = 0.5 * data->M * rvec_Norm_Sqr( data->vcm ); - - /* Calculate and then invert the inertial tensor */ - for( i = 0; i < 6; ++i ) - tmp_mat[i] = 0; - //my_xx = my_xy = my_xz = my_yy = my_yz = my_zz = 0; - - for( i = 0; i < system->n; ++i ){ - m = system->reax_param.sbp[ system->my_atoms[i].type ].mass; - rvec_ScaledSum( diff, 1., system->my_atoms[i].x, -1., data->xcm ); - - tmp_mat[0]/*my_xx*/ += diff[0] * diff[0] * m; - tmp_mat[1]/*my_xy*/ += diff[0] * diff[1] * m; - tmp_mat[2]/*my_xz*/ += diff[0] * diff[2] * m; - tmp_mat[3]/*my_yy*/ += diff[1] * diff[1] * m; - tmp_mat[4]/*my_yz*/ += diff[1] * diff[2] * m; - tmp_mat[5]/*my_zz*/ += diff[2] * diff[2] * m; - } - - MPI_Reduce( tmp_mat, tot_mat, 6, MPI_DOUBLE, MPI_SUM, MASTER_NODE, comm ); - - if( system->my_rank == MASTER_NODE ) { - mat[0][0] = tot_mat[3] + tot_mat[5]; // yy + zz; - mat[0][1] = mat[1][0] = -tot_mat[1]; // -xy; - mat[0][2] = mat[2][0] = -tot_mat[2]; // -xz; - mat[1][1] = tot_mat[0] + tot_mat[5]; // xx + zz; - mat[2][1] = mat[1][2] = -tot_mat[4]; // -yz; - mat[2][2] = tot_mat[0] + tot_mat[3]; // xx + yy; - - /* invert the inertial tensor */ - det = ( mat[0][0] * mat[1][1] * mat[2][2] + - mat[0][1] * mat[1][2] * mat[2][0] + - mat[0][2] * mat[1][0] * mat[2][1] ) - - ( mat[0][0] * mat[1][2] * mat[2][1] + - mat[0][1] * mat[1][0] * mat[2][2] + - mat[0][2] * mat[1][1] * mat[2][0] ); - - inv[0][0] = mat[1][1] * mat[2][2] - mat[1][2] * mat[2][1]; - inv[0][1] = mat[0][2] * mat[2][1] - mat[0][1] * mat[2][2]; - inv[0][2] = mat[0][1] * mat[1][2] - mat[0][2] * mat[1][1]; - inv[1][0] = mat[1][2] * mat[2][0] - mat[1][0] * mat[2][2]; - inv[1][1] = mat[0][0] * mat[2][2] - mat[0][2] * mat[2][0]; - inv[1][2] = mat[0][2] * mat[1][0] - mat[0][0] * mat[1][2]; - inv[2][0] = mat[1][0] * mat[2][1] - mat[2][0] * mat[1][1]; - inv[2][1] = mat[2][0] * mat[0][1] - mat[0][0] * mat[2][1]; - inv[2][2] = mat[0][0] * mat[1][1] - mat[1][0] * mat[0][1]; - - if( det > ALMOST_ZERO ) - rtensor_Scale( inv, 1./det, inv ); - else rtensor_MakeZero( inv ); - - /* Compute the angular velocity about the centre of mass */ - rtensor_MatVec( data->avcm, inv, data->amcm ); - } - - MPI_Bcast( data->avcm, 3, MPI_DOUBLE, MASTER_NODE, comm ); - - /* Compute the rotational energy */ - data->erot_cm = 0.5 * E_CONV * rvec_Dot( data->avcm, data->amcm ); - -} - -void Compute_Pressure(reax_system* system, control_params *control, - simulation_data* data, mpi_datatypes *mpi_data) -{ - int i; - reax_atom *p_atom; - rvec tmp, tx, int_press; - simulation_box *big_box = &(system->big_box); - - /* Calculate internal pressure */ - rvec_MakeZero( int_press ); - - // 0: both int and ext, 1: ext only, 2: int only - if( control->press_mode == 0 || control->press_mode == 2 ) { - for( i = 0; i < system->n; ++i ) { - p_atom = &( system->my_atoms[i] ); - - /* transform x into unitbox coordinates */ - Transform_to_UnitBox( p_atom->x, big_box, 1, tx ); - - /* this atom's contribution to internal pressure */ - rvec_Multiply( tmp, p_atom->f, tx ); - rvec_Add( int_press, tmp ); - - } - } - - /* sum up internal and external pressure */ - MPI_Allreduce( int_press, data->int_press, - 3, MPI_DOUBLE, MPI_SUM, mpi_data->comm_mesh3D ); - MPI_Allreduce( data->my_ext_press, data->ext_press, - 3, MPI_DOUBLE, MPI_SUM, mpi_data->comm_mesh3D ); - - /* kinetic contribution */ - data->kin_press = 2.*(E_CONV*data->sys_en.e_kin) / (3.*big_box->V*P_CONV); - - /* Calculate total pressure in each direction */ - data->tot_press[0] = data->kin_press - - (( data->int_press[0] + data->ext_press[0] ) / - ( big_box->box_norms[1] * big_box->box_norms[2] * P_CONV )); - - data->tot_press[1] = data->kin_press - - (( data->int_press[1] + data->ext_press[1] ) / - ( big_box->box_norms[0] * big_box->box_norms[2] * P_CONV )); - - data->tot_press[2] = data->kin_press - - (( data->int_press[2] + data->ext_press[2] ) / - ( big_box->box_norms[0] * big_box->box_norms[1] * P_CONV )); - - data->iso_bar.P = - ( data->tot_press[0] + data->tot_press[1] + data->tot_press[2] ) / 3.; -} diff --git a/src/USER-REAXC/reaxc_system_props.h b/src/USER-REAXC/reaxc_system_props.h index 544b051dce..161060e184 100644 --- a/src/USER-REAXC/reaxc_system_props.h +++ b/src/USER-REAXC/reaxc_system_props.h @@ -29,18 +29,6 @@ #include "reaxc_types.h" -void Temperature_Control( control_params*, simulation_data* ); - -void Compute_Kinetic_Energy( reax_system*, simulation_data*, MPI_Comm ); - void Compute_System_Energy( reax_system*, simulation_data*, MPI_Comm ); -void Compute_Total_Mass( reax_system*, simulation_data*, MPI_Comm ); - -void Compute_Center_of_Mass( reax_system*, simulation_data*, - mpi_datatypes*, MPI_Comm ); - -void Compute_Pressure( reax_system*, control_params*, - simulation_data*, mpi_datatypes* ); -//void Compute_Pressure( reax_system*, simulation_data* ); #endif diff --git a/src/USER-REAXC/reaxc_tool_box.cpp b/src/USER-REAXC/reaxc_tool_box.cpp index 4096c75118..fa1f8b8a75 100644 --- a/src/USER-REAXC/reaxc_tool_box.cpp +++ b/src/USER-REAXC/reaxc_tool_box.cpp @@ -27,57 +27,6 @@ #include "pair_reax_c.h" #include "reaxc_tool_box.h" -void Transform( rvec x1, simulation_box *box, char flag, rvec x2 ) -{ - int i, j; - double tmp; - - if (flag > 0) { - for (i=0; i < 3; i++) { - tmp = 0.0; - for (j=0; j < 3; j++) - tmp += box->trans[i][j]*x1[j]; - x2[i] = tmp; - } - } - else { - for (i=0; i < 3; i++) { - tmp = 0.0; - for (j=0; j < 3; j++) - tmp += box->trans_inv[i][j]*x1[j]; - x2[i] = tmp; - } - } -} - - -void Transform_to_UnitBox( rvec x1, simulation_box *box, char flag, rvec x2 ) -{ - Transform( x1, box, flag, x2 ); - - x2[0] /= box->box_norms[0]; - x2[1] /= box->box_norms[1]; - x2[2] /= box->box_norms[2]; -} - -void Fit_to_Periodic_Box( simulation_box *box, rvec *p ) -{ - int i; - - for( i = 0; i < 3; ++i ) { - if( (*p)[i] < box->min[i] ) { - /* handle lower coords */ - while( (*p)[i] < box->min[i] ) - (*p)[i] += box->box_norms[i]; - } - else if( (*p)[i] >= box->max[i] ) { - /* handle higher coords */ - while( (*p)[i] >= box->max[i] ) - (*p)[i] -= box->box_norms[i]; - } - } -} - struct timeval tim; double t_end; @@ -87,75 +36,6 @@ double Get_Time( ) return( tim.tv_sec + (tim.tv_usec / 1000000.0) ); } - -double Get_Timing_Info( double t_start ) -{ - gettimeofday(&tim, NULL ); - t_end = tim.tv_sec + (tim.tv_usec / 1000000.0); - return (t_end - t_start); -} - - -void Update_Timing_Info( double *t_start, double *timing ) -{ - gettimeofday(&tim, NULL ); - t_end = tim.tv_sec + (tim.tv_usec / 1000000.0); - *timing += (t_end - *t_start); - *t_start = t_end; -} - -int Get_Atom_Type( reax_interaction *reax_param, char *s, MPI_Comm comm ) -{ - int i; - - for( i = 0; i < reax_param->num_atom_types; ++i ) - if( !strcmp( reax_param->sbp[i].name, s ) ) - return i; - - fprintf( stderr, "Unknown atom type %s. Terminating...\n", s ); - MPI_Abort( comm, UNKNOWN_ATOM_TYPE ); - - return -1; -} - - - -char *Get_Element( reax_system *system, int i ) -{ - return &( system->reax_param.sbp[system->my_atoms[i].type].name[0] ); -} - - - -char *Get_Atom_Name( reax_system *system, int i ) -{ - return &(system->my_atoms[i].name[0]); -} - - - -int Allocate_Tokenizer_Space( char **line, char **backup, char ***tokens ) -{ - int i; - - if( (*line = (char*) malloc( sizeof(char) * MAX_LINE )) == NULL ) - return FAILURE; - - if( (*backup = (char*) malloc( sizeof(char) * MAX_LINE )) == NULL ) - return FAILURE; - - if( (*tokens = (char**) malloc( sizeof(char*) * MAX_TOKENS )) == NULL ) - return FAILURE; - - for( i = 0; i < MAX_TOKENS; i++ ) - if( ((*tokens)[i] = (char*) malloc(sizeof(char) * MAX_TOKEN_LEN)) == NULL ) - return FAILURE; - - return SUCCESS; -} - - - int Tokenize( char* s, char*** tok ) { char test[MAX_LINE]; diff --git a/src/USER-REAXC/reaxc_tool_box.h b/src/USER-REAXC/reaxc_tool_box.h index 2a5ea1d6db..90a711fdb7 100644 --- a/src/USER-REAXC/reaxc_tool_box.h +++ b/src/USER-REAXC/reaxc_tool_box.h @@ -30,34 +30,10 @@ #include "reaxc_types.h" #include "reaxc_defs.h" -/* from comm_tools.h */ -int SumScan( int, int, int, MPI_Comm ); -void SumScanB( int, int, int, int, MPI_Comm, int* ); - -/* from box.h */ -void Transform_to_UnitBox( rvec, simulation_box*, char, rvec ); -void Fit_to_Periodic_Box( simulation_box*, rvec* ); -void Box_Touch_Point( simulation_box*, ivec, rvec ); -int is_Inside_Box( simulation_box*, rvec ); -int iown_midpoint( simulation_box*, rvec, rvec ); - -/* from grid.h */ -void GridCell_Closest_Point( grid_cell*, grid_cell*, ivec, ivec, rvec ); -void GridCell_to_Box_Points( grid_cell*, ivec, rvec, rvec ); -double DistSqr_between_Special_Points( rvec, rvec ); -double DistSqr_to_Special_Point( rvec, rvec ); -int Relative_Coord_Encoding( ivec ); - /* from system_props.h */ double Get_Time( ); -double Get_Timing_Info( double ); -void Update_Timing_Info( double*, double* ); /* from io_tools.h */ -int Get_Atom_Type( reax_interaction*, char*, MPI_Comm ); -char *Get_Element( reax_system*, int ); -char *Get_Atom_Name( reax_system*, int ); -int Allocate_Tokenizer_Space( char**, char**, char*** ); int Tokenize( char*, char*** ); /* from lammps */ diff --git a/src/USER-REAXC/reaxc_vector.cpp b/src/USER-REAXC/reaxc_vector.cpp index 17a2851b00..ee63e94280 100644 --- a/src/USER-REAXC/reaxc_vector.cpp +++ b/src/USER-REAXC/reaxc_vector.cpp @@ -52,14 +52,6 @@ void rvec_ScaledAdd( rvec ret, double c, rvec v ) } -void rvec_Sum( rvec ret, rvec v1 ,rvec v2 ) -{ - ret[0] = v1[0] + v2[0]; - ret[1] = v1[1] + v2[1]; - ret[2] = v1[2] + v2[2]; -} - - void rvec_ScaledSum( rvec ret, double c1, rvec v1 ,double c2, rvec v2 ) { ret[0] = c1 * v1[0] + c2 * v2[0]; @@ -74,20 +66,6 @@ double rvec_Dot( rvec v1, rvec v2 ) } -double rvec_ScaledDot( double c1, rvec v1, double c2, rvec v2 ) -{ - return (c1*c2) * (v1[0]*v2[0] + v1[1]*v2[1] + v1[2]*v2[2]); -} - - -void rvec_Multiply( rvec r, rvec v1, rvec v2 ) -{ - r[0] = v1[0] * v2[0]; - r[1] = v1[1] * v2[1]; - r[2] = v1[2] * v2[2]; -} - - void rvec_iMultiply( rvec r, ivec v1, rvec v2 ) { r[0] = v1[0] * v2[0]; @@ -96,30 +74,6 @@ void rvec_iMultiply( rvec r, ivec v1, rvec v2 ) } -void rvec_Divide( rvec r, rvec v1, rvec v2 ) -{ - r[0] = v1[0] / v2[0]; - r[1] = v1[1] / v2[1]; - r[2] = v1[2] / v2[2]; -} - - -void rvec_iDivide( rvec r, rvec v1, ivec v2 ) -{ - r[0] = v1[0] / v2[0]; - r[1] = v1[1] / v2[1]; - r[2] = v1[2] / v2[2]; -} - - -void rvec_Invert( rvec r, rvec v ) -{ - r[0] = 1. / v[0]; - r[1] = 1. / v[1]; - r[2] = 1. / v[2]; -} - - void rvec_Cross( rvec ret, rvec v1, rvec v2 ) { ret[0] = v1[1] * v2[2] - v1[2] * v2[1]; @@ -128,16 +82,6 @@ void rvec_Cross( rvec ret, rvec v1, rvec v2 ) } -void rvec_OuterProduct( rtensor r, rvec v1, rvec v2 ) -{ - int i, j; - - for( i = 0; i < 3; ++i ) - for( j = 0; j < 3; ++j ) - r[i][j] = v1[i] * v2[j]; -} - - double rvec_Norm_Sqr( rvec v ) { return SQR(v[0]) + SQR(v[1]) + SQR(v[2]); @@ -150,16 +94,6 @@ double rvec_Norm( rvec v ) } -int rvec_isZero( rvec v ) -{ - if( fabs(v[0]) > ALMOST_ZERO || - fabs(v[1]) > ALMOST_ZERO || - fabs(v[2]) > ALMOST_ZERO ) - return 0; - return 1; -} - - void rvec_MakeZero( rvec v ) { v[0] = v[1] = v[2] = 0.000000000000000e+00; @@ -187,16 +121,6 @@ void rtensor_MatVec( rvec ret, rtensor m, rvec v ) } -void rtensor_Scale( rtensor ret, double c, rtensor m ) -{ - int i, j; - - for( i = 0; i < 3; ++i ) - for( j = 0; j < 3; ++j ) - ret[i][j] = c * m[i][j]; -} - - void rtensor_MakeZero( rtensor t ) { t[0][0] = t[0][1] = t[0][2] = 0; diff --git a/src/USER-REAXC/reaxc_vector.h b/src/USER-REAXC/reaxc_vector.h index 4aafff87e9..906b200dc9 100644 --- a/src/USER-REAXC/reaxc_vector.h +++ b/src/USER-REAXC/reaxc_vector.h @@ -35,26 +35,17 @@ void rvec_Copy( rvec, rvec ); void rvec_Scale( rvec, double, rvec ); void rvec_Add( rvec, rvec ); void rvec_ScaledAdd( rvec, double, rvec ); -void rvec_Sum( rvec, rvec, rvec ); void rvec_ScaledSum( rvec, double, rvec, double, rvec ); double rvec_Dot( rvec, rvec ); -double rvec_ScaledDot( double, rvec, double, rvec ); -void rvec_Multiply( rvec, rvec, rvec ); void rvec_iMultiply( rvec, ivec, rvec ); -void rvec_Divide( rvec, rvec, rvec ); -void rvec_iDivide( rvec, rvec, ivec ); -void rvec_Invert( rvec, rvec ); void rvec_Cross( rvec, rvec, rvec ); -void rvec_OuterProduct( rtensor, rvec, rvec ); double rvec_Norm_Sqr( rvec ); double rvec_Norm( rvec ); -int rvec_isZero( rvec ); void rvec_MakeZero( rvec ); void rvec_Random( rvec ); void rtensor_MakeZero( rtensor ); void rtensor_MatVec( rvec, rtensor, rvec ); -void rtensor_Scale( rtensor, double, rtensor ); void ivec_MakeZero( ivec ); void ivec_Copy( ivec, ivec ); diff --git a/src/USER-SPH/atom_vec_meso.cpp b/src/USER-SPH/atom_vec_meso.cpp index e4677703db..947139e791 100644 --- a/src/USER-SPH/atom_vec_meso.cpp +++ b/src/USER-SPH/atom_vec_meso.cpp @@ -482,7 +482,7 @@ int AtomVecMeso::pack_border_vel(int n, int *list, double *buf, int pbc_flag, int *pbc) { int i,j,m; - double dx,dy,dz; + double dx,dy,dz,dvx,dvy,dvz; m = 0; if (pbc_flag == 0) { @@ -534,6 +534,9 @@ int AtomVecMeso::pack_border_vel(int n, int *list, double *buf, int pbc_flag, buf[m++] = vest[j][2]; } } else { + dvx = pbc[0] * h_rate[0] + pbc[5] * h_rate[5] + pbc[4] * h_rate[4]; + dvy = pbc[1] * h_rate[1] + pbc[3] * h_rate[3]; + dvz = pbc[2] * h_rate[2]; for (i = 0; i < n; i++) { j = list[i]; buf[m++] = x[j][0] + dx; @@ -543,20 +546,23 @@ int AtomVecMeso::pack_border_vel(int n, int *list, double *buf, int pbc_flag, buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; if (mask[i] & deform_groupbit) { - buf[m++] = v[j][0]; - buf[m++] = v[j][1]; - buf[m++] = v[j][2]; + buf[m++] = v[j][0] + dvx; + buf[m++] = v[j][1] + dvy; + buf[m++] = v[j][2] + dvz; + buf[m++] = vest[j][0] + dvx; + buf[m++] = vest[j][1] + dvy; + buf[m++] = vest[j][2] + dvz; } else { buf[m++] = v[j][0]; buf[m++] = v[j][1]; buf[m++] = v[j][2]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; } buf[m++] = rho[j]; buf[m++] = e[j]; buf[m++] = cv[j]; - buf[m++] = vest[j][0]; - buf[m++] = vest[j][1]; - buf[m++] = vest[j][2]; } } } @@ -619,12 +625,12 @@ void AtomVecMeso::unpack_border_vel(int n, int first, double *buf) { v[i][0] = buf[m++]; v[i][1] = buf[m++]; v[i][2] = buf[m++]; - rho[i] = buf[m++]; - e[i] = buf[m++]; - cv[i] = buf[m++]; vest[i][0] = buf[m++]; vest[i][1] = buf[m++]; vest[i][2] = buf[m++]; + rho[i] = buf[m++]; + e[i] = buf[m++]; + cv[i] = buf[m++]; } if (atom->nextra_border) diff --git a/src/fix.h b/src/fix.h index f0836de021..24d209f019 100644 --- a/src/fix.h +++ b/src/fix.h @@ -120,6 +120,7 @@ class Fix : protected Pointers { virtual void pre_exchange() {} virtual void pre_neighbor() {} virtual void pre_force(int) {} + virtual void pre_reverse(int,int) {} virtual void post_force(int) {} virtual void final_integrate() {} virtual void end_of_step() {} @@ -251,7 +252,8 @@ namespace FixConst { static const int MIN_POST_FORCE = 1<<17; static const int MIN_ENERGY = 1<<18; static const int POST_RUN = 1<<19; - static const int FIX_CONST_LAST = 1<<20; + static const int PRE_REVERSE = 1<<20; + static const int FIX_CONST_LAST = 1<<21; } } diff --git a/src/info.cpp b/src/info.cpp index c34eb401cd..1eba5a8b92 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -109,6 +109,7 @@ void Info::command(int narg, char **arg) idx += 2; } else if ((idx+1 < narg) && (strncmp(arg[idx],"out",3) == 0) && (strncmp(arg[idx+1],"log",3) == 0)) { + if ((out != screen) && (out != logfile)) fclose(out); out = logfile; idx += 2; } else if ((idx+2 < narg) && (strncmp(arg[idx],"out",3) == 0) diff --git a/src/input.cpp b/src/input.cpp index 5b0c27e603..b048389c3c 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -15,6 +15,7 @@ #include "stdio.h" #include "stdlib.h" #include "string.h" +#include "errno.h" #include "ctype.h" #include "unistd.h" #include "sys/stat.h" @@ -1086,48 +1087,96 @@ void Input::quit() /* ---------------------------------------------------------------------- */ +char *shell_failed_message(const char* cmd, int errnum) +{ + const char *errmsg = strerror(errnum); + int len = strlen(cmd)+strlen(errmsg)+64; + char *msg = new char[len]; + sprintf(msg,"shell command '%s' failed with error '%s'", cmd, errmsg); + return msg; +} + void Input::shell() { + int rv,err; + if (narg < 1) error->all(FLERR,"Illegal shell command"); if (strcmp(arg[0],"cd") == 0) { if (narg != 2) error->all(FLERR,"Illegal shell cd command"); - chdir(arg[1]); + rv = (chdir(arg[1]) < 0) ? errno : 0; + MPI_Reduce(&rv,&err,1,MPI_INT,MPI_MAX,0,world); + if (me == 0 && err != 0) { + char *message = shell_failed_message("cd",err); + error->warning(FLERR,message); + delete [] message; + } } else if (strcmp(arg[0],"mkdir") == 0) { if (narg < 2) error->all(FLERR,"Illegal shell mkdir command"); if (me == 0) for (int i = 1; i < narg; i++) { #if defined(_WIN32) - _mkdir(arg[i]); + rv = _mkdir(arg[i]); #else - mkdir(arg[i], S_IRWXU | S_IRGRP | S_IXGRP); + rv = mkdir(arg[i], S_IRWXU | S_IRGRP | S_IXGRP); #endif + if (rv < 0) { + char *message = shell_failed_message("mkdir",errno); + error->warning(FLERR,message); + delete [] message; + } } } else if (strcmp(arg[0],"mv") == 0) { if (narg != 3) error->all(FLERR,"Illegal shell mv command"); - if (me == 0) rename(arg[1],arg[2]); + rv = (rename(arg[1],arg[2]) < 0) ? errno : 0; + MPI_Reduce(&rv,&err,1,MPI_INT,MPI_MAX,0,world); + if (me == 0 && err != 0) { + char *message = shell_failed_message("mv",err); + error->warning(FLERR,message); + delete [] message; + } } else if (strcmp(arg[0],"rm") == 0) { if (narg < 2) error->all(FLERR,"Illegal shell rm command"); if (me == 0) - for (int i = 1; i < narg; i++) unlink(arg[i]); + for (int i = 1; i < narg; i++) { + if (unlink(arg[i]) < 0) { + char *message = shell_failed_message("rm",errno); + error->warning(FLERR,message); + delete [] message; + } + } } else if (strcmp(arg[0],"rmdir") == 0) { if (narg < 2) error->all(FLERR,"Illegal shell rmdir command"); if (me == 0) - for (int i = 1; i < narg; i++) rmdir(arg[i]); + for (int i = 1; i < narg; i++) { + if (rmdir(arg[i]) < 0) { + char *message = shell_failed_message("rmdir",errno); + error->warning(FLERR,message); + delete [] message; + } + } } else if (strcmp(arg[0],"putenv") == 0) { if (narg < 2) error->all(FLERR,"Illegal shell putenv command"); for (int i = 1; i < narg; i++) { char *ptr = strdup(arg[i]); + rv = 0; #ifdef _WIN32 - if (ptr != NULL) _putenv(ptr); + if (ptr != NULL) rv = _putenv(ptr); #else - if (ptr != NULL) putenv(ptr); + if (ptr != NULL) rv = putenv(ptr); #endif + rv = (rv < 0) ? errno : 0; + MPI_Reduce(&rv,&err,1,MPI_INT,MPI_MAX,0,world); + if (me == 0 && err != 0) { + char *message = shell_failed_message("putenv",err); + error->warning(FLERR,message); + delete [] message; + } } // use work string to concat args back into one string separated by spaces @@ -1144,7 +1193,9 @@ void Input::shell() strcat(work,arg[i]); } - if (me == 0) system(work); + if (me == 0) + if (system(work) != 0) + error->warning(FLERR,"shell command returned with non-zero status"); } } diff --git a/src/lammps.cpp b/src/lammps.cpp index 4014090aac..95d925b6cb 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -195,6 +195,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) error->universe_all(FLERR,"Invalid command-line argument"); delete [] suffix; delete [] suffix2; + suffix2 = NULL; suffix_enable = 1; // hybrid option to set fall-back for suffix2 if (strcmp(arg[iarg+1],"hybrid") == 0) { diff --git a/src/min_cg.cpp b/src/min_cg.cpp index 4953370562..af3ef5b7a4 100644 --- a/src/min_cg.cpp +++ b/src/min_cg.cpp @@ -66,6 +66,7 @@ int MinCG::iterate(int maxiter) gg = fnorm_sqr(); for (int iter = 0; iter < maxiter; iter++) { + ntimestep = ++update->ntimestep; niter++; diff --git a/src/min_fire.cpp b/src/min_fire.cpp index 8d0debf349..115e91e63c 100644 --- a/src/min_fire.cpp +++ b/src/min_fire.cpp @@ -92,6 +92,7 @@ int MinFire::iterate(int maxiter) alpha_final = 0.0; for (int iter = 0; iter < maxiter; iter++) { + ntimestep = ++update->ntimestep; niter++; diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp index 124b5bf575..84abf5487f 100644 --- a/src/min_quickmin.cpp +++ b/src/min_quickmin.cpp @@ -87,6 +87,7 @@ int MinQuickMin::iterate(int maxiter) alpha_final = 0.0; for (int iter = 0; iter < maxiter; iter++) { + ntimestep = ++update->ntimestep; niter++; diff --git a/src/min_sd.cpp b/src/min_sd.cpp index 44936ce32a..1394f379fa 100644 --- a/src/min_sd.cpp +++ b/src/min_sd.cpp @@ -57,6 +57,7 @@ int MinSD::iterate(int maxiter) for (i = 0; i < nextra_global; i++) hextra[i] = fextra[i]; for (int iter = 0; iter < maxiter; iter++) { + ntimestep = ++update->ntimestep; niter++; diff --git a/src/modify.cpp b/src/modify.cpp index 0745c1c6ca..9ca992738a 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -42,7 +42,7 @@ Modify::Modify(LAMMPS *lmp) : Pointers(lmp) nfix = maxfix = 0; n_initial_integrate = n_post_integrate = 0; n_pre_exchange = n_pre_neighbor = 0; - n_pre_force = n_post_force = 0; + n_pre_force = n_pre_reverse = n_post_force = 0; n_final_integrate = n_end_of_step = n_thermo_energy = 0; n_initial_integrate_respa = n_post_integrate_respa = 0; n_pre_force_respa = n_post_force_respa = n_final_integrate_respa = 0; @@ -52,7 +52,7 @@ Modify::Modify(LAMMPS *lmp) : Pointers(lmp) fmask = NULL; list_initial_integrate = list_post_integrate = NULL; list_pre_exchange = list_pre_neighbor = NULL; - list_pre_force = list_post_force = NULL; + list_pre_force = list_pre_reverse = list_post_force = NULL; list_final_integrate = list_end_of_step = NULL; list_thermo_energy = NULL; list_initial_integrate_respa = list_post_integrate_respa = NULL; @@ -119,6 +119,7 @@ Modify::~Modify() delete [] list_pre_exchange; delete [] list_pre_neighbor; delete [] list_pre_force; + delete [] list_pre_reverse; delete [] list_post_force; delete [] list_final_integrate; delete [] list_end_of_step; @@ -162,6 +163,7 @@ void Modify::init() list_init(PRE_EXCHANGE,n_pre_exchange,list_pre_exchange); list_init(PRE_NEIGHBOR,n_pre_neighbor,list_pre_neighbor); list_init(PRE_FORCE,n_pre_force,list_pre_force); + list_init(PRE_REVERSE,n_pre_reverse,list_pre_reverse); list_init(POST_FORCE,n_post_force,list_post_force); list_init(FINAL_INTEGRATE,n_final_integrate,list_final_integrate); list_init_end_of_step(END_OF_STEP,n_end_of_step,list_end_of_step); @@ -382,6 +384,15 @@ void Modify::pre_force(int vflag) for (int i = 0; i < n_pre_force; i++) fix[list_pre_force[i]]->pre_force(vflag); } +/* ---------------------------------------------------------------------- + pre_reverse call, only for relevant fixes +------------------------------------------------------------------------- */ + +void Modify::pre_reverse(int eflag, int vflag) +{ + for (int i = 0; i < n_pre_reverse; i++) + fix[list_pre_reverse[i]]->pre_reverse(eflag,vflag); +} /* ---------------------------------------------------------------------- post_force call, only for relevant fixes @@ -789,8 +800,8 @@ void Modify::add_fix(int narg, char **arg, int trysuffix) strcmp(style_restart_global[i],fix[ifix]->style) == 0) { fix[ifix]->restart(state_restart_global[i]); if (comm->me == 0) { - char *str = (char *) ("Resetting global state of Fix %s Style %s " - "from restart file info\n"); + const char *str = (const char *) ("Resetting global state of Fix %s " + "Style %s from restart file info\n"); if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style); if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style); } diff --git a/src/modify.h b/src/modify.h index 7c11714a74..12a475cf0b 100644 --- a/src/modify.h +++ b/src/modify.h @@ -26,7 +26,7 @@ class Modify : protected Pointers { public: int nfix,maxfix; int n_initial_integrate,n_post_integrate,n_pre_exchange,n_pre_neighbor; - int n_pre_force,n_post_force; + int n_pre_force,n_pre_reverse,n_post_force; int n_final_integrate,n_end_of_step,n_thermo_energy; int n_initial_integrate_respa,n_post_integrate_respa; int n_pre_force_respa,n_post_force_respa,n_final_integrate_respa; @@ -55,6 +55,7 @@ class Modify : protected Pointers { virtual void pre_exchange(); virtual void pre_neighbor(); virtual void pre_force(int); + virtual void pre_reverse(int,int); virtual void post_force(int); virtual void final_integrate(); virtual void end_of_step(); @@ -111,7 +112,7 @@ class Modify : protected Pointers { int *list_initial_integrate,*list_post_integrate; int *list_pre_exchange,*list_pre_neighbor; - int *list_pre_force,*list_post_force; + int *list_pre_force,*list_pre_reverse,*list_post_force; int *list_final_integrate,*list_end_of_step,*list_thermo_energy; int *list_initial_integrate_respa,*list_post_integrate_respa; int *list_pre_force_respa,*list_post_force_respa; diff --git a/src/read_restart.h b/src/read_restart.h index 1d84cf238e..586a13c210 100644 --- a/src/read_restart.h +++ b/src/read_restart.h @@ -33,7 +33,6 @@ class ReadRestart : protected Pointers { private: int me,nprocs,nprocs_file,multiproc_file; FILE *fp; - int nfix_restart_global,nfix_restart_peratom; int multiproc; // 0 = proc 0 writes for all // else # of procs writing files @@ -42,7 +41,6 @@ class ReadRestart : protected Pointers { int mpiioflag; // 1 for MPIIO output, else 0 class RestartMPIIO *mpiio; // MPIIO for restart file input - int numChunksAssigned; bigint assignedChunkSize; MPI_Offset assignedChunkOffset,headerOffset; diff --git a/src/respa.cpp b/src/respa.cpp index 632d2a109f..dbd3effb63 100644 --- a/src/respa.cpp +++ b/src/respa.cpp @@ -453,6 +453,7 @@ void Respa::setup() if (kspace_compute_flag) force->kspace->compute(eflag,vflag); } + modify->pre_reverse(eflag,vflag); if (newton[ilevel]) comm->reverse_comm(); copy_f_flevel(ilevel); } @@ -527,6 +528,8 @@ void Respa::setup_minimal(int flag) force->kspace->setup(); if (kspace_compute_flag) force->kspace->compute(eflag,vflag); } + + modify->pre_reverse(eflag,vflag); if (newton[ilevel]) comm->reverse_comm(); copy_f_flevel(ilevel); } @@ -711,6 +714,11 @@ void Respa::recurse(int ilevel) timer->stamp(Timer::KSPACE); } + if (modify->n_pre_reverse) { + modify->pre_reverse(eflag,vflag); + timer->stamp(Timer::MODIFY); + } + if (newton[ilevel]) { comm->reverse_comm(); timer->stamp(Timer::COMM); diff --git a/src/set.cpp b/src/set.cpp index 914d725d81..9919518294 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -565,14 +565,16 @@ void Set::set(int keyword) // overwrite dvalue, ivalue, xyzw value if variables defined // else the input script scalar value remains in place - - if (varflag1) { - dvalue = xvalue = vec1[i]; - ivalue = static_cast (dvalue); + + if (varflag) { + if (varflag1) { + dvalue = xvalue = vec1[i]; + ivalue = static_cast (dvalue); + } + if (varflag2) yvalue = vec2[i]; + if (varflag3) zvalue = vec3[i]; + if (varflag4) wvalue = vec4[i]; } - if (varflag2) yvalue = vec2[i]; - if (varflag3) zvalue = vec3[i]; - if (varflag4) wvalue = vec4[i]; // set values in per-atom arrays // error check here in case atom-style variables generated bogus value diff --git a/src/verlet.cpp b/src/verlet.cpp index 345549d914..e5a067777e 100644 --- a/src/verlet.cpp +++ b/src/verlet.cpp @@ -139,6 +139,7 @@ void Verlet::setup() else force->kspace->compute_dummy(eflag,vflag); } + modify->pre_reverse(eflag,vflag); if (force->newton) comm->reverse_comm(); modify->setup(vflag); @@ -199,6 +200,7 @@ void Verlet::setup_minimal(int flag) else force->kspace->compute_dummy(eflag,vflag); } + modify->pre_reverse(eflag,vflag); if (force->newton) comm->reverse_comm(); modify->setup(vflag); @@ -218,6 +220,7 @@ void Verlet::run(int n) int n_pre_exchange = modify->n_pre_exchange; int n_pre_neighbor = modify->n_pre_neighbor; int n_pre_force = modify->n_pre_force; + int n_pre_reverse = modify->n_pre_reverse; int n_post_force = modify->n_post_force; int n_end_of_step = modify->n_end_of_step; @@ -303,6 +306,11 @@ void Verlet::run(int n) timer->stamp(Timer::KSPACE); } + if (n_pre_reverse) { + modify->pre_reverse(eflag,vflag); + timer->stamp(Timer::MODIFY); + } + // reverse communication of forces if (force->newton) { From 449f373db533fc8ace45a8acac4a34d86b3b9e3a Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 22 Oct 2015 22:08:30 +0000 Subject: [PATCH 04/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14165 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- lib/colvars/colvar.cpp | 109 +++++++++++++++++++++-------------- lib/colvars/colvarmodule.h | 24 ++++---- lib/colvars/colvarscript.cpp | 2 + 3 files changed, 78 insertions(+), 57 deletions(-) diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp index 1a42f85eea..158ff7a4f1 100644 --- a/lib/colvars/colvar.cpp +++ b/lib/colvars/colvar.cpp @@ -638,6 +638,7 @@ int colvar::enable(colvar::task const &t) case task_output_system_force: enable(task_system_force); + tasks[t] = true; break; case task_report_Jacobian_force: @@ -646,6 +647,7 @@ int colvar::enable(colvar::task const &t) if (cvm::debug()) cvm::log("Adding the Jacobian force to the system force, " "rather than applying its opposite silently.\n"); + tasks[t] = true; break; case task_Jacobian_force: @@ -669,6 +671,7 @@ int colvar::enable(colvar::task const &t) "on this colvar.\n"); } fj.type(value()); + tasks[t] = true; break; case task_system_force: @@ -683,6 +686,7 @@ int colvar::enable(colvar::task const &t) } ft.type(value()); ft_reported.type(value()); + tasks[t] = true; break; case task_output_applied_force: @@ -690,16 +694,19 @@ int colvar::enable(colvar::task const &t) case task_upper_wall: // all of the above require gradients enable(task_gradients); + tasks[t] = true; break; case task_fdiff_velocity: x_old.type(value()); v_fdiff.type(value()); v_reported.type(value()); + tasks[t] = true; break; case task_output_velocity: enable(task_fdiff_velocity); + tasks[t] = true; break; case task_grid: @@ -708,11 +715,13 @@ int colvar::enable(colvar::task const &t) this->name+"\", because its value is not a scalar number.\n", INPUT_ERROR); } + tasks[t] = true; break; case task_extended_lagrangian: enable(task_gradients); v_reported.type(value()); + tasks[t] = true; break; case task_lower_boundary: @@ -722,16 +731,17 @@ int colvar::enable(colvar::task const &t) "and cannot produce a grid.\n", INPUT_ERROR); } + tasks[t] = true; break; case task_output_value: case task_runave: case task_corrfunc: - case task_ntot: case task_langevin: case task_output_energy: case task_scripted: case task_gradients: + tasks[t] = true; break; case task_collect_gradients: @@ -745,10 +755,13 @@ int colvar::enable(colvar::task const &t) if (atom_ids.size() == 0) { build_atom_list(); } + tasks[t] = true; + break; + + default: break; } - tasks[t] = true; return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); } @@ -763,23 +776,28 @@ void colvar::disable(colvar::task const &t) disable(task_output_applied_force); disable(task_system_force); disable(task_Jacobian_force); + tasks[t] = false; break; case task_system_force: disable(task_output_system_force); + tasks[t] = false; break; case task_Jacobian_force: disable(task_report_Jacobian_force); + tasks[t] = false; break; case task_fdiff_velocity: disable(task_output_velocity); + tasks[t] = false; break; case task_lower_boundary: case task_upper_boundary: disable(task_grid); + tasks[t] = false; break; case task_extended_lagrangian: @@ -793,15 +811,17 @@ void colvar::disable(colvar::task const &t) case task_grid: case task_lower_wall: case task_upper_wall: - case task_ntot: case task_langevin: case task_output_energy: case task_collect_gradients: case task_scripted: + tasks[t] = false; + break; + + default: break; } - tasks[t] = false; } @@ -1106,44 +1126,6 @@ cvm::real colvar::update() f += fb; - if (tasks[task_lower_wall] || tasks[task_upper_wall]) { - - // wall force - colvarvalue fw(value()); - fw.reset(); - - if (cvm::debug()) - cvm::log("Calculating wall forces for colvar \""+this->name+"\".\n"); - - // if the two walls are applied concurrently, decide which is the - // closer one (on a periodic colvar, both walls may be applicable - // at the same time) - if ( (!tasks[task_upper_wall]) || - (this->dist2(x_reported, lower_wall) < this->dist2(x_reported, upper_wall)) ) { - - cvm::real const grad = this->dist2_lgrad(x_reported, lower_wall); - if (grad < 0.0) { - fw = -0.5 * lower_wall_k * grad; - if (cvm::debug()) - cvm::log("Applying a lower wall force("+ - cvm::to_str(fw)+") to \""+this->name+"\".\n"); - f += fw; - - } - - } else { - - cvm::real const grad = this->dist2_lgrad(x_reported, upper_wall); - if (grad > 0.0) { - fw = -0.5 * upper_wall_k * grad; - if (cvm::debug()) - cvm::log("Applying an upper wall force("+ - cvm::to_str(fw)+") to \""+this->name+"\".\n"); - f += fw; - } - } - } - if (tasks[task_Jacobian_force]) { size_t i; for (i = 0; i < cvcs.size(); i++) { @@ -1178,10 +1160,11 @@ cvm::real colvar::update() // the total force is applied to the fictitious mass, while the // atoms only feel the harmonic force - // fr: extended coordinate force (without harmonic spring), for output in trajectory + // fr: bias force on extended coordinate (without harmonic spring), for output in trajectory // f_ext: total force on extended coordinate (including harmonic spring) // f: - initially, external biasing force - // - after this code block, colvar force to be applied to atomic coordinates, ie. spring force + // - after this code block, colvar force to be applied to atomic coordinates, ie. spring force + // (note: wall potential is added to f after this block) fr = f; f_ext = f + (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x); f = (-0.5 * ext_force_k) * this->dist2_rgrad(xr, x); @@ -1203,6 +1186,44 @@ cvm::real colvar::update() } + // Adding wall potential to "true" colvar force, whether or not an extended coordinate is in use + if (tasks[task_lower_wall] || tasks[task_upper_wall]) { + + // Wall force + colvarvalue fw(x); + fw.reset(); + + if (cvm::debug()) + cvm::log("Calculating wall forces for colvar \""+this->name+"\".\n"); + + // For a periodic colvar, both walls may be applicable at the same time + // in which case we pick the closer one + if ( (!tasks[task_upper_wall]) || + (this->dist2(x, lower_wall) < this->dist2(x, upper_wall)) ) { + + cvm::real const grad = this->dist2_lgrad(x, lower_wall); + if (grad < 0.0) { + fw = -0.5 * lower_wall_k * grad; + f += fw; + if (cvm::debug()) + cvm::log("Applying a lower wall force("+ + cvm::to_str(fw)+") to \""+this->name+"\".\n"); + } + + } else { + + cvm::real const grad = this->dist2_lgrad(x, upper_wall); + if (grad > 0.0) { + fw = -0.5 * upper_wall_k * grad; + f += fw; + if (cvm::debug()) + cvm::log("Applying an upper wall force("+ + cvm::to_str(fw)+") to \""+this->name+"\".\n"); + } + } + } + + if (tasks[task_fdiff_velocity]) { // set it for the next step x_old = x; diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h index d9f6a03d7c..ee6ec3ea35 100644 --- a/lib/colvars/colvarmodule.h +++ b/lib/colvars/colvarmodule.h @@ -4,7 +4,7 @@ #define COLVARMODULE_H #ifndef COLVARS_VERSION -#define COLVARS_VERSION "2015-09-03" +#define COLVARS_VERSION "2015-09-16" #endif #ifndef COLVARS_DEBUG @@ -20,19 +20,17 @@ /// shared between all object instances) to be accessed from other /// objects. -// Internal method return codes -#define COLVARS_NOT_IMPLEMENTED -2 -#define COLVARS_ERROR -1 +// Error codes #define COLVARS_OK 0 - -// On error, values of the colvars module error register -#define GENERAL_ERROR 1 -#define FILE_ERROR (1<<1) -#define MEMORY_ERROR (1<<2) -#define BUG_ERROR (1<<3) // Inconsistent state indicating bug -#define INPUT_ERROR (1<<4) // out of bounds or inconsistent input -#define DELETE_COLVARS (1<<5) // Instruct the caller to delete cvm -#define FATAL_ERROR (1<<6) // Should be set, or not, together with other bits +#define COLVARS_ERROR -1 +#define GENERAL_ERROR -1 // TODO this can be simply merged with COLVARS_ERROR +#define COLVARS_NOT_IMPLEMENTED (-1<<1) +#define INPUT_ERROR (-1<<2) // out of bounds or inconsistent input +#define BUG_ERROR (-1<<3) // Inconsistent state indicating bug +#define FILE_ERROR (-1<<4) +#define MEMORY_ERROR (-1<<5) +#define FATAL_ERROR (-1<<6) // Should be set, or not, together with other bits +#define DELETE_COLVARS (-1<<7) // Instruct the caller to delete cvm #include diff --git a/lib/colvars/colvarscript.cpp b/lib/colvars/colvarscript.cpp index 0c23faf519..4c999eee84 100644 --- a/lib/colvars/colvarscript.cpp +++ b/lib/colvars/colvarscript.cpp @@ -388,6 +388,7 @@ Input and output:\n\ list -- return a list of all variables\n\ list biases -- return a list of all biases\n\ load -- load a state file (requires configuration)\n\ + save -- save a state file (requires configuration)\n\ update -- recalculate colvars and biases based\n\ printframe -- return a summary of the current frame\n\ printframelabels -- return labels to annotate printframe's output\n"; @@ -406,6 +407,7 @@ Accessing collective variables:\n\ colvar delete -- delete colvar \n\ colvar addforce -- apply given force on colvar \n\ colvar getconfig -- return config string of colvar \n\ + colvar cvcflags -- enable or disable cvcs according to 0/1 flags\n\ \n\ Accessing biases:\n\ bias energy -- return the current energy of bias \n\ From 0068c45c803d127fe04539bafec86693c6e1c9bf Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 22 Oct 2015 22:09:41 +0000 Subject: [PATCH 05/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14166 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/version.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/version.h b/src/version.h index c4415eb1bf..6439ed804a 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "22 Oct 2015" +#define LAMMPS_VERSION "23 Oct 2015" From 36b3880e392a1d53e0b48b3c3a78976e0de91fdd Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 22 Oct 2015 22:09:44 +0000 Subject: [PATCH 06/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14167 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Manual.html | 882 +++++++++++++++++++++++++----------------------- doc/Manual.txt | 10 +- 2 files changed, 458 insertions(+), 434 deletions(-) diff --git a/doc/Manual.html b/doc/Manual.html index dd72c5f5fa..bb284d114d 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -1,454 +1,478 @@ + + + +LAMMPS Users Manual + + + + + + + + + +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
- - - - - - - - - LAMMPS Documentation — LAMMPS 15 May 2015 version documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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LAMMPS Documentation¶

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10 Aug 2015 version¶

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Version info:¶

-

The LAMMPS “version” is the date when it was released, such as 1 May + + +

+ +

+ +

LAMMPS Documentation +

+

23 Oct 2015 version +

+

Version info: +

+

The LAMMPS "version" is the date when it was released, such as 1 May 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a -feature, we release it immediately, and post a notice on this page of the WWW site. Each dated copy of LAMMPS contains all the +feature, we release it immediately, and post a notice on this page of +the WWW site. Each dated copy of LAMMPS contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run LAMMPS. It is also in the file src/version.h and in the LAMMPS directory name created when you unpack a tarball, and at the top of -the first page of the manual (this page).

-
    -
  • If you browse the HTML doc pages on the LAMMPS WWW site, they always -describe the most current version of LAMMPS.
    • -
  • If you browse the HTML doc pages included in your tarball, they -describe the version you have.
    • -
  • The PDF file on the WWW site or in the tarball is updated -about once per month. This is because it is large, and we don’t want -it to be part of every patch.
    • -
  • There is also a Developer.pdf file in the doc +the first page of the manual (this page). +

    +
    • If you browse the HTML doc pages on the LAMMPS WWW site, they always +describe the most current version of LAMMPS. + +
    • If you browse the HTML doc pages included in your tarball, they +describe the version you have. + +
    • The PDF file on the WWW site or in the tarball is updated +about once per month. This is because it is large, and we don't want +it to be part of every patch. + +
    • There is also a Developer.pdf file in the doc directory, which describes the internal structure and algorithms of -LAMMPS.
      • -
    -

    LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel -Simulator.

    -

    LAMMPS is a classical molecular dynamics simulation code designed to +LAMMPS. +

+

LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel +Simulator. +

+

LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely -under the terms of the GNU Public License (GPL).

-

The primary developers of LAMMPS are Steve Plimpton, Aidan +under the terms of the GNU Public License (GPL). +

+

The primary developers of LAMMPS are Steve Plimpton, Aidan Thompson, and Paul Crozier who can be contacted at -sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at -http://lammps.sandia.gov has more information about the code and its -uses.

-
-

The LAMMPS documentation is organized into the following sections. If +sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at +http://lammps.sandia.gov has more information about the code and its +uses. +

+ + + + +
+ +

The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for useful information to add, please send an email to the developers so -we can improve the LAMMPS documentation.

-

Once you are familiar with LAMMPS, you may want to bookmark this page at Section_commands.html#comm since -it gives quick access to documentation for all LAMMPS commands.

-

PDF file of the entire manual, generated by -htmldoc

-
- -
-
-
-
-

Indices and tables¶

- -
+we can improve the LAMMPS documentation. +

+

Once you are familiar with LAMMPS, you may want to bookmark this +page at Section_commands.html#comm since +it gives quick access to documentation for all LAMMPS commands. +

+

PDF file of the entire manual, generated by +htmldoc +

+

+

+
  1. +Introduction + + +
  2. Getting started + + +
  3. Commands + + +
  4. Packages + + +
  5. Accelerating LAMMPS performance + + +
  6. How-to discussions + + +
  7. Example problems + +
  8. Performance & scalability + +
  9. Additional tools + +
  10. Modifying & extending LAMMPS + + +
  11. Python interface + + +
  12. Errors + + +
  13. Future and history + + + +
-
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - \ No newline at end of file + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/doc/Manual.txt b/doc/Manual.txt index b0857e6c32..db95040025 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation :c,h3 -10 Aug 2015 version :c,h4 +23 Oct 2015 version :c,h4 Version info: :h4 @@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands. .. toctree:: :maxdepth: 2 - :numbered: + :numbered: // comment Section_intro Section_start @@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands. Indices and tables ================== -* :ref:`genindex` -* :ref:`search` +* :ref:`genindex` // comment +* :ref:`search` // comment END_RST --> From 0a4b0ced3336202194c561fc444ee55ea6af45d0 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 22 Oct 2015 22:17:09 +0000 Subject: [PATCH 07/31] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14169 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/doc2/Manual.html.html | 4 ++-- doc/doc2/temper.html | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/doc2/Manual.html.html b/doc/doc2/Manual.html.html index f766895045..0ddcdedea4 100644 --- a/doc/doc2/Manual.html.html +++ b/doc/doc2/Manual.html.html @@ -3,7 +3,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation

-

22 Oct 2015 version +

23 Oct 2015 version

Version info:

diff --git a/doc/doc2/temper.html b/doc/doc2/temper.html index fd5727b883..6523d13037 100644 --- a/doc/doc2/temper.html +++ b/doc/doc2/temper.html @@ -54,7 +54,7 @@ assigned a different temperature. See the variable 
variable t world 300.0 310.0 320.0 330.0
-fix myfix all nvt $t $t 100.0
+fix myfix all nvt temp $t $t 100.0
 temper 100000 100 $t myfix 3847 58382

would define 4 temperatures, and assign one of them to the thermostat From 01acc93029251dbf7bc10fb4e9cb37e4a4b4d82b Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 22 Oct 2015 22:17:18 +0000 Subject: [PATCH 08/31] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14170 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Manual.html | 900 +++++++++++++++++++++---------------------- doc/Manual.html.html | 4 +- doc/Manual.txt | 10 +- doc/temper.html | 2 +- doc/temper.txt | 2 +- 5 files changed, 447 insertions(+), 471 deletions(-) diff --git a/doc/Manual.html b/doc/Manual.html index bb284d114d..dd72c5f5fa 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -1,478 +1,454 @@ - - - -LAMMPS Users Manual - - - - - - - - - -

LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
+ + + + + + + + + LAMMPS Documentation — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+ + + - - -
- -

- -

LAMMPS Documentation -

-

23 Oct 2015 version -

-

Version info: -

-

The LAMMPS "version" is the date when it was released, such as 1 May + +

+
+
+ +
+ + + +
+
+
+ +

+

LAMMPS Documentation¶

+
+

10 Aug 2015 version¶

+
+
+

Version info:¶

+

The LAMMPS “version” is the date when it was released, such as 1 May 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a -feature, we release it immediately, and post a notice on this page of -the WWW site. Each dated copy of LAMMPS contains all the +feature, we release it immediately, and post a notice on this page of the WWW site. Each dated copy of LAMMPS contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run LAMMPS. It is also in the file src/version.h and in the LAMMPS directory name created when you unpack a tarball, and at the top of -the first page of the manual (this page). -

-
  • If you browse the HTML doc pages on the LAMMPS WWW site, they always -describe the most current version of LAMMPS. - -
  • If you browse the HTML doc pages included in your tarball, they -describe the version you have. - -
  • The PDF file on the WWW site or in the tarball is updated -about once per month. This is because it is large, and we don't want -it to be part of every patch. - -
  • There is also a Developer.pdf file in the doc +the first page of the manual (this page).

    +
      +
    • If you browse the HTML doc pages on the LAMMPS WWW site, they always +describe the most current version of LAMMPS.
      • +
    • If you browse the HTML doc pages included in your tarball, they +describe the version you have.
      • +
    • The PDF file on the WWW site or in the tarball is updated +about once per month. This is because it is large, and we don’t want +it to be part of every patch.
      • +
    • There is also a Developer.pdf file in the doc directory, which describes the internal structure and algorithms of -LAMMPS. -
    -

    LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel -Simulator. -

    -

    LAMMPS is a classical molecular dynamics simulation code designed to +LAMMPS.

    • +
+

LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel +Simulator.

+

LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely -under the terms of the GNU Public License (GPL). -

-

The primary developers of LAMMPS are Steve Plimpton, Aidan +under the terms of the GNU Public License (GPL).

+

The primary developers of LAMMPS are Steve Plimpton, Aidan Thompson, and Paul Crozier who can be contacted at -sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at -http://lammps.sandia.gov has more information about the code and its -uses. -

- - - - -
- -

The LAMMPS documentation is organized into the following sections. If +sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at +http://lammps.sandia.gov has more information about the code and its +uses.

+
+

The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for useful information to add, please send an email to the developers so -we can improve the LAMMPS documentation. -

-

Once you are familiar with LAMMPS, you may want to bookmark this -page at Section_commands.html#comm since -it gives quick access to documentation for all LAMMPS commands. -

-

PDF file of the entire manual, generated by -htmldoc -

-

-

-
  1. -Introduction - - -
  2. Getting started - - -
  3. Commands - - -
  4. Packages - - -
  5. Accelerating LAMMPS performance - - -
  6. How-to discussions - - -
  7. Example problems - -
  8. Performance & scalability - -
  9. Additional tools - -
  10. Modifying & extending LAMMPS - - -
  11. Python interface - - -
  12. Errors - - -
  13. Future and history - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +we can improve the LAMMPS documentation.

+

Once you are familiar with LAMMPS, you may want to bookmark this page at Section_commands.html#comm since +it gives quick access to documentation for all LAMMPS commands.

+

PDF file of the entire manual, generated by +htmldoc

+
+ +
+
+
+
+

Indices and tables¶

+ +
+ + +
+
+ + +
+
+ +
+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/Manual.html.html b/doc/Manual.html.html index f766895045..0ddcdedea4 100644 --- a/doc/Manual.html.html +++ b/doc/Manual.html.html @@ -3,7 +3,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation

-

22 Oct 2015 version +

23 Oct 2015 version

Version info:

diff --git a/doc/Manual.txt b/doc/Manual.txt index db95040025..b0857e6c32 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation :c,h3 -23 Oct 2015 version :c,h4 +10 Aug 2015 version :c,h4 Version info: :h4 @@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands. .. toctree:: :maxdepth: 2 - :numbered: // comment + :numbered: Section_intro Section_start @@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands. Indices and tables ================== -* :ref:`genindex` // comment -* :ref:`search` // comment +* :ref:`genindex` +* :ref:`search` END_RST --> diff --git a/doc/temper.html b/doc/temper.html index f4956cc540..f41a33509d 100644 --- a/doc/temper.html +++ b/doc/temper.html @@ -170,7 +170,7 @@ variable previously set in the input script, so that each partition is assigned a different temperature. See the variable command for more details. For example:

variable t world 300.0 310.0 320.0 330.0
-fix myfix all nvt $t $t 100.0
+fix myfix all nvt temp $t $t 100.0
 temper 100000 100 $t myfix 3847 58382
diff --git a/doc/temper.txt b/doc/temper.txt index 6283c2b460..48c90cf909 100644 --- a/doc/temper.txt +++ b/doc/temper.txt @@ -51,7 +51,7 @@ assigned a different temperature. See the "variable"_variable.html command for more details. For example: variable t world 300.0 310.0 320.0 330.0 -fix myfix all nvt $t $t 100.0 +fix myfix all nvt temp $t $t 100.0 temper 100000 100 $t myfix 3847 58382 :pre would define 4 temperatures, and assign one of them to the thermostat From d8c16fb28dfc53ec5c1aa2181bd0f4762c33dc1e Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 22 Oct 2015 22:56:04 +0000 Subject: [PATCH 09/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14171 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- potentials/README | 1 + potentials/ffield.smtbq.Al | 34 +++++++++++++++++++++ potentials/ffield.smtbq.Al2O3 | 56 +++++++++++++++++++++++++++++++++++ potentials/ffield.smtbq.TiO2 | 53 +++++++++++++++++++++++++++++++++ 4 files changed, 144 insertions(+) create mode 100755 potentials/ffield.smtbq.Al create mode 100755 potentials/ffield.smtbq.Al2O3 create mode 100755 potentials/ffield.smtbq.TiO2 diff --git a/potentials/README b/potentials/README index d4dba824ca..599432ce8d 100644 --- a/potentials/README +++ b/potentials/README @@ -92,6 +92,7 @@ meam.sw.spline modified EAM (MEAM) Stillinger-Weber spline potential nb3b.harmonic nonbonded 3-body harmonic potential poly polymorphic 3-body potential reax ReaxFF potential (see README.reax for more info) +smtbq Second Moment Tight Binding - QEq potential snap SNAP potential snapcoeff SNAP potential snapparam SNAP potential diff --git a/potentials/ffield.smtbq.Al b/potentials/ffield.smtbq.Al new file mode 100755 index 0000000000..b8fd478a09 --- /dev/null +++ b/potentials/ffield.smtbq.Al @@ -0,0 +1,34 @@ +# +# SMTBQ parameter for Al-Al interaction. +# Edited by N. Salles Univ. Bourgogne and E. Maras from Aalto Univ. +# year: 2014 +# ========================================================================= +' Nombre.de.type.d.atome..........:' 1 +' ====== atomic parameters ======= ' +' Cation.de.l.oxyde..Stoechio.....:' 'Al' 1 +' Qform.....masse.................:' 3.0 26.98 +' Param.QEq.(ne,.Chi,.J,.R_eff)...:' 3 1.19258 11.05345 0.57701 +' Nbre.d.etats.partage.par.cation.:' 3 +' ===== potential Parameter ======' +' Atom1..atom2..potential..mode....' 'Al' 'Al' 'second_moment' 'metal' +' Potentiel.Cat-Ox.(A,.p,.Ksi,.q).:' 0.1221 8.612 1.316 2.516 +' Pot..Cat-Ox.(rc1,.rc2,.r0).Iota.:' 5.6 7.0 2.863 2.0 +' ======== Parametre tab ========= ' +' Rcoul...........................:' 11.1714 +' rmin...dr.......................:' 1.18845 0.001 +' ======== IFQM Parameter ======== ' +' Frenquency.Q.resolution..........' 0 +' loopmax.-.precision..............' 5000 0.0002 +' ==== Coordination parameters ====' +' .r1n................r2n..........' 2.5 3.2 +' ========== QInitMode ========= ' +' QInitMode....QInit(if.needed)....' 'false' 0.0 +' ======== Mode for QEq ======== ' +' mode(see.end.of.this.file.)......' 'QEqAllParallel' +' parameters.for.mode..............' +' ========== Verbose ============ ' +' Verbose(true.or.false)...........' 'false' +' Print.Energy.components..........' 'false' 300.0 +' Print.electroneg...components....' 'false' 300.0 +# =========================== END's parameters ========================= + diff --git a/potentials/ffield.smtbq.Al2O3 b/potentials/ffield.smtbq.Al2O3 new file mode 100755 index 0000000000..9c26ade9ec --- /dev/null +++ b/potentials/ffield.smtbq.Al2O3 @@ -0,0 +1,56 @@ +# DATE: 2015-10-22 CONTRIBUTOR: Nicolas Salles, nsalles@laas.fr CITATION: N. Salles, O. Politano, E. Amzallag and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189 +# SMTBQ parameter for AlO interaction with a limit length 'rc2sm=dc2**2'. +# Edited by N. Salles from Univ Bourgogne and E. Maras from Aalto Univ. +# +# Presentation atom : nature +# q, qmin, qmax, masse +# parameter QEq : Chi, J, R_eff +# Parameter SM : A, p, Ksi, q +# CutOff SM : dc1, dc2, r0 +# ========================================================================= +# -------------------------- Begin's parameters --------------------------- +' Number.of.atoms.type............:' 2 +' ====== atomic parameters ======= ' +' 1st.element.(Oxygen).Stoechio...:' 'O' 3 +' Qform.....mass..................:' -2.0 16.00 +' Param.QEq.(ne,.Chi0,.JiO).......:' 2 6.57 10.22 +' coordBB.coordB.coordS.rBB.rB.rS.:' 6. 4. 3.00 0.529 0.529 0.529 +' Number.of.shared.state.by.ions..:' 3 +' -------------------------------- ' +' 2nd.element.(metal).Stoechio....:' 'Al' 2 +' Qform.....mass..................:' 3.0 26.98 +' Param.QEq.(ne,.Chi0,.Ji0,.R_eff):' 3 1.19009 11.1903 0.56619 +' Number.of.shared.state.by.ions..:' 4 +' ===== potential Parameter ======' +' Atom1..atom2..potential..mode....' 'Al' 'O' 'second_moment' 'oxide' +' Pot.CatOx.(A,.p,.Ksi(ref=O),.q).:' 0.18176 8.80041 0.26044 1.58851 +' Pot..Cat-Ox.(rc1,.rc2,.r0)......:' 4. 5.6 1.91 +' -------------------------------- ' +' atom1..atom2..potential..........' 'O' 'O' 'buck' +' Potentiel.O-O...(C,.Rho)........:' 580.440 0.3540 +' ======== Parametre tab ========= ' +' Rcoul=a*rc(SMASH)...............:' 11.1714 +' rmin...dr.......................:' 1.18845 0.001 +' ======== IFQM Parameter ======== ' +' Nevery.charge.calculation........' 1 +' loopmax....precision.............' 7000 0.000001 +' ==== Coordination parameters ====' +' .r1n................r2n..........' 2.5 3.2 +' ========== QInitMode ========= ' +' QInitMode....QInit(if.needed)....' 'false' -1.8 +' ======== Mode for QEq ======== ' +' mode(see.end.of.this.file.)......' 'QEqAll' +' parameters.for.mode..............' +' ========== Verbose ============ ' +' Verbose(true.or.false)...........' 'false' +' Print.Energy.components..........' 'false' 300.0 +' Print.electroneg...components....' 'false' 300.0 +# =========================== FIN des parametres ========================= + +#Possible QInit modes +# true (then initialize all the oxygen charges to QOxInit and set the cation charge in order to keep the charge balance (neutrality of the box) +#any other name would lead to either 0 charges or charge read from the lammps atomic position file +#Possible QEq modes | parameters +# QEqAll | no parameters +# QEqAllParallel | no parameters +# Surface | zlim (QEq only for z>zlim) diff --git a/potentials/ffield.smtbq.TiO2 b/potentials/ffield.smtbq.TiO2 new file mode 100755 index 0000000000..4c8d9df535 --- /dev/null +++ b/potentials/ffield.smtbq.TiO2 @@ -0,0 +1,53 @@ +# DATE: 2015-10-22 CONTRIBUTOR: Nicolas Salles, nsalles@laas.fr CITATION: N. Salles, O. Politano, E. Amzallag and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189 +# ======================================================================== +# SMTBQ parameter for Ti-O interaction with a limit length 'rc2sm=dc2**2'. +# Edited by N. Salles from Univ Bourgogne and E. Maras from Aalto Univ +# september 2014 +# ======================================================================== +' Number.of.atoms.type............:' 2 +' ====== atomic parameters ======= ' +' 1st.element.(Oxygen).Stoechio...:' 'O' 2 +' Qform.....mass..................:' -2.0 16.00 +' Param.QEq.(ne,.Chi0,.JiO).......:' 2 6.57 10.22 +' coordBB.coordB.coordS.rBB.rB.rS.:' 6. 3. 2.00 0.52 0.54348 0.58 +' Number.of.shared.state.by.ions..:' 3 +' -------------------------------- ' +' 2nd.element.(metal).Stoechio....:' 'Ti' 1 +' Qform.....mass..................:' 4.0 26.98 +' Param.QEq.(nq,.Chi0,.Ji0,.R_eff):' 3 0.00 10.572 0.734 +' Number.of.shared.state.by.ions..:' 5 +' ===== potential Parameter ======' +' Atom1..atom2..potential..mode....' 'Ti' 'O' 'second_moment' 'oxide' +' Pot.CatOx.(A,.p,.Ksi(ref=O),.q).:' 0.134 12.609 0.5434 2.0965 +' Pot..Cat-Ox.(rc1,.rc2,.r0)......:' 3.6 6.0 1.95 +' -------------------------------- ' +' atom1..atom2..potential..........' 'O' 'O' 'buckPlusAttr' +' Potential.O-O...(C,.Rho)........:' 580.440 0.3540 +' Potential.O-O...(D.B.r1OO.r2OO).:' -20.86 -0.916 1.4 1.8 +' ======== Tab Parameter ========= ' +' Rcoul=a*rc(SMASH)...............:' 12.1744 +' rmin...dr.......................:' 1.0675 0.001 +' ======== IFQM Parameter ======== ' +' Nevery.charge.calculation........' 1 +' loopmax....precision.............' 7000 0.000001 +' ==== Coordination parameters ====' +' .r1n................r2n..........' 2.0 3.5 +' ========== QInitMode ========= ' +' QInitMode....QInit(if.needed)....' 'false' -1.0 +' ======== Mode for QEq ======== ' +' mode(see.end.of.this.file.)......' 'QEqAll' +' parameters.for.mode..............' +' ========== Verbose ============ ' +' Verbose(true.or.false)...........' 'false' +' Print.Energy.components..........' 'false' 300.0 +' Print.electroneg...components....' 'false' 300.0 +# =========================== END's parameters ========================= + +#Possible QInit modes +# true (then initialize all the oxygen charges to QOxInit and set the cation charge in order to keep the charge balance (neutrality of the box) +#any other name would lead to either 0 charges or charge read from the lammps atomic position file +#Possible QEq modes | parameters +# QEqAll | no parameters +# QEqAllParallel | no parameters +# Surface | zlim (QEq only for z>zlim) +# BulkFromSlab | zlim1 zlim2 (QEq only for zlim1 Date: Thu, 22 Oct 2015 22:56:21 +0000 Subject: [PATCH 10/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14172 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/Makefile | 2 +- src/USER-SMTBQ/README | 13 + src/USER-SMTBQ/pair_smtbq.cpp | 4241 +++++++++++++++++++++++++++++++++ src/USER-SMTBQ/pair_smtbq.h | 197 ++ 4 files changed, 4452 insertions(+), 1 deletion(-) create mode 100644 src/USER-SMTBQ/README create mode 100644 src/USER-SMTBQ/pair_smtbq.cpp create mode 100644 src/USER-SMTBQ/pair_smtbq.h diff --git a/src/Makefile b/src/Makefile index 2d6cd12180..25184d998f 100755 --- a/src/Makefile +++ b/src/Makefile @@ -50,7 +50,7 @@ PACKUSER = user-atc user-awpmd user-cg-cmm user-colvars user-cuda \ user-diffraction user-drude user-eff user-fep user-h5md \ user-intel user-lb \ user-misc user-molfile user-omp user-phonon user-qmmm user-qtb \ - user-quip user-reaxc user-smd user-sph user-tally + user-quip user-reaxc user-smd user-smtbq user-sph user-tally PACKLIB = compress gpu kim kokkos meam poems python reax voronoi \ user-atc user-awpmd user-colvars user-cuda user-h5md user-molfile \ diff --git a/src/USER-SMTBQ/README b/src/USER-SMTBQ/README new file mode 100644 index 0000000000..19fac74388 --- /dev/null +++ b/src/USER-SMTBQ/README @@ -0,0 +1,13 @@ +This package implements the Second Moment Tight Binding - QEq (SMTB-Q) +potential for the description of the ionocovalent bond in oxides. + +Authors: Nicolas Salles, Emile Maras, Olivier Politano, Robert T\'e9tot + +Contact email: lammps@u-bourgogne.fr + +See the doc page for the pair_style smtbq command to get started. + +There are potential files for this potential in the potentials dir. + +There are example scripts for using this package in +examples/USER/smtbq. diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp new file mode 100644 index 0000000000..52b431a8c2 --- /dev/null +++ b/src/USER-SMTBQ/pair_smtbq.cpp @@ -0,0 +1,4241 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + The SMTBQ code has been developed with the financial support of CNRS and + of the Regional Council of Burgundy (Convention n¡ 2010-9201AAO037S03129) + + Copyright (2015) + Universite de Bourgogne : Nicolas SALLES, Olivier POLITANO + Universite de Paris-Sud Orsay : R. Tetot + Aalto University (Finland) : E. Maras + + Please cite the related publication: + N. Salles, O. Politano, E. Amzallag and R. Tetot, + Comput. Mater. Sci., 111 (2016) 181-189 + + Contact : lammps@u-bourgogne.fr + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + See the GNU General Public License for more details: + . + ------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "pair_smtbq.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "group.h" +#include "update.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" +#include "domain.h" + +#include +#include +#include +#include + +//to DELETE +//#include +//#include +//#include +//#include +//to DELETE +using namespace std; + +using namespace LAMMPS_NS; +using namespace MathConst; + +#define MAXLINE 2048 +#define MAXTOKENS 2048 +#define DELTA 4 +#define PGDELTA 1 +#define MAXNEIGH 24 +#define Pi 4*atan(1) + +/* ---------------------------------------------------------------------- */ + +PairSMTBQ::PairSMTBQ(LAMMPS *lmp) : Pair(lmp) +{ + MPI_Comm_rank(world,&me); + MPI_Comm_size(world,&nproc); + + single_enable = 0; + restartinfo = 0; + one_coeff = 1; + + nmax = 0; + rmin = 0.0; + dr = 0.0; + ds = 0.0; + kmax = 0; + + nelements = 0; + elements = NULL; + nparams = 0; + maxparam = 0; + params = NULL; + intparams = NULL; + + intype = NULL; + coultype = NULL; + fafb = NULL; + dfafb = NULL; + potqn = NULL; + dpotqn = NULL; + Vself = 0.0; + tabsmb = NULL; + tabsmr = NULL; + dtabsmb = NULL; + dtabsmr = NULL; + + sbcov = NULL; + coord = NULL; + sbmet = NULL; + chimet = NULL; + ecov = NULL; + + potmad = NULL; + potself = NULL; + potcov = NULL; + qf = NULL; + q1 = NULL; + q2 = NULL; + tab_comm = NULL; + + nvsm = NULL; + vsm = NULL; + flag_QEq = NULL; + nQEqaall = NULL; + nQEqcall = NULL; + nQEqall = NULL; + nteam = 0; + cluster = 0; + + Nevery = 0.0; + Neverypot = 0.0; + + fct = NULL; + + + maxpage = 0; + + // set comm size needed by this Pair + + comm_forward = 1; + comm_reverse = 1; +} + +/* ---------------------------------------------------------------------- + check if allocated, since class can be destructed when incomplete + ------------------------------------------------------------------------- */ + +PairSMTBQ::~PairSMTBQ() +{ + int i; + if (elements) { + for ( i = 0; i < nelements; i++) delete [] elements[i]; + + for( i = 0; i < atom->ntypes ; i++ ) free( params[i].nom ); + for( i = 1; i <= maxintparam ; i++ ) free( intparams[i].typepot ); + for( i = 1; i <= maxintparam ; i++ ) free( intparams[i].mode ); + } + + free(QEqMode); + free(QInitMode); + free(writepot); + free(writeenerg); + free(Bavard); + + delete [] elements; + memory->sfree(params); + memory->sfree(intparams); + + memory->destroy(intype); + memory->destroy(coultype); + memory->destroy(fafb); + memory->destroy(dfafb); + memory->destroy(potqn); + memory->destroy(dpotqn); + + memory->destroy(ecov); + memory->destroy(sbcov); + memory->destroy(coord); + memory->destroy(sbmet); + memory->destroy(tabsmb); + memory->destroy(tabsmr); + memory->destroy(dtabsmb); + memory->destroy(dtabsmr); + + memory->destroy(potmad); + memory->destroy(potself); + memory->destroy(potcov); + memory->destroy(chimet); + + memory->destroy(nvsm); + memory->destroy(vsm);; + memory->destroy(flag_QEq); + + memory->destroy(nQEqall); + memory->destroy(nQEqcall); + memory->destroy(nQEqaall); + + memory->destroy(qf); + memory->destroy(q1); + memory->destroy(q2); + memory->destroy(tab_comm); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + delete [] map; + delete [] esm; + } + + memory->destroy(fct); +} + +/* ---------------------------------------------------------------------- */ + +void PairSMTBQ::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + map = new int[n+1]; + esm = new double[n]; +} + +/* ---------------------------------------------------------------------- + global settings + ------------------------------------------------------------------------- */ + +void PairSMTBQ::settings(int narg, char **arg) +{ + if (narg > 0) error->all(FLERR,"Illegal pair_style command"); +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs + ------------------------------------------------------------------------- */ + +void PairSMTBQ::coeff(int narg, char **arg) +{ + int i,j,n; + + if (!allocated) allocate(); + + if (narg != 3 + atom->ntypes) + error->all(FLERR,"Incorrect args for pair coefficients"); + + // insure I,J args are * * + + if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) + error->all(FLERR,"Incorrect args for pair coefficients"); + + // read args that map atom types to elements in potential file + // map[i] = which element the Ith atom type is, -1 if NULL + // nelements = # of unique elements + // elements = list of element names + + if (elements) { + for (i = 0; i < nelements; i++) delete [] elements[i]; + delete [] elements; + } + elements = new char*[atom->ntypes]; + for (i = 0; i < atom->ntypes; i++) elements[i] = NULL; + + nelements = 0; + for (i = 3; i < narg; i++) { + if (strcmp(arg[i],"NULL") == 0) { + map[i-2] = -1; + continue; + } + for (j = 0; j < nelements; j++) + if (strcmp(arg[i],elements[j]) == 0) break; + map[i-2] = j; + if (j == nelements) { + n = strlen(arg[i]) + 1; + elements[j] = new char[n]; + strcpy(elements[j],arg[i]); + nelements++; + } + } + + // read potential file and initialize potential parameters + + read_file(arg[2]); + + n = atom->ntypes; + + // generate Coulomb 1/r energy look-up table + + if (comm->me == 0 && screen) fprintf(screen,"Pair SMTBQ:\n"); + if (comm->me == 0 && screen) + fprintf(screen," generating Coulomb integral lookup table ...\n"); + + tabqeq(); + + // ------------ + + + if (comm->me == 0 && screen) + fprintf(screen," generating Second Moment integral lookup table ...\n"); + + tabsm(); + + // ------------ + + // clear setflag since coeff() called once with I,J = * * + + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + + // set setflag i,j for type pairs where both are mapped to elements + + int count = 0; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + if (map[i] >= 0 && map[j] >= 0) { + setflag[i][j] = 1; + count++; + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style + ------------------------------------------------------------------------- */ + +void PairSMTBQ::init_style() +{ + if (atom->tag_enable == 0) + error->all(FLERR,"Pair style SMTBQ requires atom IDs"); + if (force->newton_pair == 0) + error->all(FLERR,"Pair style SMTBQ requires newton pair on"); + if (!atom->q_flag) + error->all(FLERR,"Pair style SMTBQ requires atom attribute q"); + + + // need a full neighbor list + + int irequest = neighbor->request(this); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + + pgsize = neighbor->pgsize; + oneatom = neighbor->oneatom; + // if (maxpage == 0) add_pages(); + +} + +/* ---------------------------------------------------------------------- */ + +double PairSMTBQ::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + return cutmax; +} + +/* ---------------------------------------------------------------------- + ---------------------------------------------------------------------- */ + +void PairSMTBQ::read_file(char *file) +{ + int c, num_atom_types,i,k,m,test,j,verbose; + char **words; + + memory->sfree(params); + params = NULL; + memory->sfree(intparams); + intparams = NULL; + nparams = 0; + maxparam = 0; + maxintparam = 0; + + verbose = 1; + verbose = 0; + + // open file on proc 0 + FILE *fp; + fp = fopen( file, "r" ); + if ( fp == NULL ) { + fprintf( stderr, "error opening the force filed file! terminating...\n" ); + } + + + // read each line out of file, skipping blank lines or leading '#' + // store line of params if all 3 element tags are in element list + + char *ptr; + + ptr = (char*) malloc(sizeof(char)*MAXLINE); + words = (char**) malloc(sizeof(char*)*MAXTOKENS); + for (i=0; i < MAXTOKENS; i++) + words[i] = (char*) malloc(sizeof(char)*MAXTOKENS); + + + /* strip comment, skip line if blank */ + + if (verbose) printf ("\n"); + fgets(ptr,MAXLINE,fp); + while (strchr(ptr,'#')) { + if (verbose) printf ("%s",ptr); + fgets(ptr,MAXLINE,fp); + } + + + // Nombre d'atome different dans la structure + // =============================================== + c = Tokenize( ptr, &words ); + num_atom_types = atoi(words[1]); + if (verbose) printf (" %s %d\n", words[0], num_atom_types); + + memory->create(intype,num_atom_types,num_atom_types,"pair:intype"); + + m = 0; + for (i = 0; i < num_atom_types; i++) { + for (j = 0; j < num_atom_types; j++) { + if (j < i) { intype[i][j] = intype[j][i];} + else { intype[i][j] = 0; + m = m + 1; } + if (verbose) printf ("i %d, j %d, intype %d - nb pair %d\n",i,j,intype[i][j],m); + } + } + + // load up parameter settings and error check their values + + if (nparams == maxparam) { + maxparam += DELTA; + params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), + "pair:params"); + maxintparam += m; + intparams = (Intparam *) memory->srealloc(intparams,(maxintparam+1)*sizeof(Intparam), + "pair:intparams"); + } + + for (i=0; i < num_atom_types; i++) + params[i].nom = (char*) malloc(sizeof(char)*3); + + for (i=1; i <= maxintparam; i++) + intparams[i].typepot = (char*) malloc(sizeof(char)*15); + + for (i=1; i <= maxintparam; i++) + intparams[i].mode = (char*) malloc(sizeof(char)*6); + + QEqMode = (char*) malloc(sizeof(char)*18); + Bavard = (char*) malloc(sizeof(char)*5); + QInitMode = (char*) malloc(sizeof(char)*18); + writepot = (char*) malloc(sizeof(char)*5); + writeenerg = (char*) malloc(sizeof(char)*5); + + + // Little loop for ion's parameters + // ================================================ + for (i=0; i %d = %s\n",words[1],i,params[i].nom); + + for (j = 0; j %d = %s\n",words[2],j,params[j].nom); + + + if ( test == 1 ) { + if (verbose) printf ("========== fin des interaction ==========\n"); + break ; } + + + intype[i][j] = m; + intype[j][i] = intype[i][j]; + strcpy( intparams[m].typepot , words[3] ); + intparams[m].intsm = 0; + if (verbose) printf (" itype %d jtype %d - intype %d\n",i,j,intype[i][j]); + + if (strcmp(intparams[m].typepot,"second_moment") !=0 && + strcmp(intparams[m].typepot,"buck") != 0 && + strcmp(intparams[m].typepot,"buckPlusAttr") != 0) { + error->all(FLERR,"the potential other than second_moment or buckingham have not treated here\n");} + + + // On detemrine le type d'interaction + // ----------------------------------- + if (strcmp(intparams[m].typepot,"second_moment") == 0) { + maxintsm += 1; + strcpy( intparams[m].mode , words[4] ); + intparams[m].intsm = maxintsm; + + if (strcmp(intparams[m].mode,"oxide") != 0 && + strcmp(intparams[m].mode,"metal") != 0){ + error->all(FLERR,"needs mode to second moment interaction : oxide or metal"); } + +// if (strcmp(intparams[m].mode,"oxide") == 0) +// intparams[m].ncov = min((params[i].sto)*(params[i].n0),(params[j].sto)*(params[j].n0)); + + if (verbose) printf(" %s %s %s %s %s \n",words[0],words[1],words[2], + intparams[m].typepot,intparams[m].mode); + + fgets( ptr, MAXLINE, fp); + c= Tokenize( ptr, &words ); + + intparams[m].a = atof(words[1]) ; + intparams[m].p = atof(words[2]) ; + intparams[m].ksi = atof(words[3]) ; + intparams[m].q = atof(words[4]) ; + if (verbose) printf (" %s %f %f %f %f\n",words[0], + intparams[m].a,intparams[m].p,intparams[m].ksi,intparams[m].q); + + // Ligne 6 - rayon de coupure potentiel SM + + fgets( ptr, MAXLINE, fp); + c= Tokenize( ptr, &words ); + + intparams[m].dc1 = atof(words[1]) ; + intparams[m].dc2 = atof(words[2]) ; + intparams[m].r0 = atof(words[3]) ; + + + if (strcmp(intparams[m].mode,"metal") == 0) { + if (verbose) printf (" %s %f %f %f\n",words[0], + intparams[m].dc1,intparams[m].dc2,intparams[m].r0); + } else { + if (verbose) printf (" %s %f %f %f\n",words[0], + intparams[m].dc1,intparams[m].dc2,intparams[m].r0); + } + + + } else if (strcmp(intparams[m].typepot,"buck") == 0) { + + if (verbose) printf(" %s %s %s %s\n",words[0],words[1],words[2], + intparams[m].typepot); + + fgets( ptr, MAXLINE, fp); + c= Tokenize( ptr, &words ); + + intparams[m].abuck = atof(words[1]) ; intparams[m].rhobuck = atof(words[2]) ; + if (verbose) printf (" %s %f %f\n",words[0],intparams[m].abuck,intparams[m].rhobuck); + + } + + else if (strcmp(intparams[m].typepot,"buckPlusAttr") == 0) { + + if (verbose) printf(" %s %s %s %s\n",words[0],words[1],words[2], + intparams[m].typepot); + + fgets( ptr, MAXLINE, fp); + c= Tokenize( ptr, &words ); + + intparams[m].abuck = atof(words[1]) ; intparams[m].rhobuck = atof(words[2]) ; + if (verbose) printf (" %s %f %f\n",words[0],intparams[m].abuck,intparams[m].rhobuck); + + + fgets( ptr, MAXLINE, fp); + c= Tokenize( ptr, &words ); + + intparams[m].aOO = atof(words[1]) ; intparams[m].bOO = atof(words[2]) ; + intparams[m].r1OO = atof(words[3]) ;intparams[m].r2OO = atof(words[4]) ; + if (verbose) printf (" %s %f %f %f %f \n",words[0],intparams[m].aOO, + intparams[m].bOO,intparams[m].r1OO,intparams[m].r2OO); + + } + if (verbose) printf (" intsm %d \n",intparams[m].intsm); + + } // for maxintparam + + + /* ==================================================================== + tables Parameters + ==================================================================== */ + + // Ligne 9 - rayon de coupure Electrostatique + if (test == 0) { + fgets(ptr,MAXLINE,fp); + if (verbose) printf ("%s\n",ptr); + + fgets( ptr, MAXLINE, fp); + } + c= Tokenize( ptr, &words ); + + for (i=0 ; iall(FLERR,"The QEq Mode is not known. QEq mode should be :\n Possible QEq modes | parameters\n QEqAll | no parameters\n QEqAllParallel | no parameters\n Surface | zlim (QEq only for z>zlim)\n BulkFromSlab | zlim1 zlim2 (QEq only for zlim1 %f Ang\n", + intparams[m].typepot,intparams[m].neig_cut); + } + } + + //A adapter au STO + ncov = min((params[0].sto)*(params[0].n0),(params[1].sto)*(params[1].n0)); + + if (verbose) printf (" Parametre ncov = %f\n",ncov); + if (verbose) printf (" ********************************************* \n"); + + + +} + +/* ---------------------------------------------------------------------- + * COMPUTE + ---------------------------------------------------------------------- */ + +void PairSMTBQ::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,m,gp; + int itag,jtag,itype,jtype; + int *ilist,*jlist,*numneigh,**firstneigh; + + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double rsq,iq,jq,Eself,natom; + double ecovtot,ErepOO,ErepMO,Eion,Ecoh; + double **tmp,**tmpAll,*nmol; + double dq,dqcov; + + + int bavard; + + + if (atom->nmax > nmax) { + memory->destroy(ecov); + memory->destroy(potmad); + memory->destroy(potself); + memory->destroy(potcov); + memory->destroy(sbcov); + memory->destroy(coord); + memory->destroy(sbmet); + memory->destroy(chimet); + memory->destroy(flag_QEq); + memory->destroy(qf); + memory->destroy(q1); + memory->destroy(q2); + memory->destroy(tab_comm); + + nmax = atom->nmax; + + memory->create(ecov,nmax,"pair:ecov"); + memory->create(potmad,nmax,"pair:potmad"); + memory->create(potself,nmax,"pair:potself"); + memory->create(potcov,nmax,"pair:potcov"); + memory->create(sbcov,nmax,"pair:sbcov"); + memory->create(coord,nmax,"pair:coord"); + memory->create(sbmet,nmax,"pair:sbmet"); + memory->create(chimet,nmax,"pair:chimet"); + memory->create(flag_QEq,nmax,"pair:flag_QEq"); + memory->create(qf,nmax,"pair:qf"); + memory->create(q1,nmax,"pair:q1"); + memory->create(q2,nmax,"pair:q2"); + memory->create(tab_comm,nmax,"pair:tab_comm"); + } + + + evdwl = ecoul = ecovtot = ErepOO = ErepMO = Eion = 0.0; + Eself = 0.0; + + if (eflag || vflag) { ev_setup(eflag,vflag); } + else { evflag = vflag_fdotr = vflag_atom = 0; } + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *tag = atom->tag; + int *type = atom->type; + int newton_pair = force->newton_pair; + int nlocal = atom->nlocal; + int step = update->ntimestep; + struct timeval start, end; + + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + if (step == 0 || (Qstep !=0 && fmod(double(step), double(Qstep)) == 0.0 )) Charge(); +// :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: +// this is necessary to get sbcov or sbmet table in order to caclulate the covalent or metal bonding + if (Qstep == 0 || fmod(double(step), double(Qstep)) != 0.0 ) QForce_charge(0); + + + // Charges Communication + // ---------------------- + forward(q) ; reverse(q); + + memory->create(nmol,nteam+1,"pair:nmol"); + memory->create(tmp,nteam+1,7,"pair:tmp"); + memory->create(tmpAll,nteam+1,7,"pair:tmpAll"); + + + for (i=0; i ionic energy + 1 -> coulombian energy + 2 -> Electrosatic energy (ionic + Coulombian) + 3 -> Short int. Ox-Ox + 4 -> Short int. SMTB (repulsion) + 5 -> Covalent energy SMTB + 6 -> Somme des Q(i)² + ------------------------------------------------------------------------- */ + + // ----------- + bavard = 0; + // ----------- + + /* -------------- N-body forces Calcul --------------- */ + + for (ii = 0; ii < inum; ii++) { +// =============================== + i = ilist[ii]; + itag = tag[i]; + itype = map[type[i]]; + iq = q[i]; + gp = flag_QEq[i]; + + if (gp == 0 && itype > 0) natom += 1.0; + // if (gp == 0 && itype > 0) nmol[gp] += 1.0; + + + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + + // --- For atom i + tmp[gp][6] += iq*iq; + + +// self energy, only on i atom +// --------------------------- + Eself = self(¶ms[itype],iq); + tmp[gp][0] += Eself; + tmp[gp][2] += Eself; + + if (evflag) ev_tally_full (i,0.0,2.0*Eself,0.0,0.0,0.0,0.0); + + +// N-body energy of i +// --------------------- + dq = fabs(params[itype].qform) - fabs(iq); + dqcov = dq*(2.0*ncov/params[itype].sto - dq); + + ecov[i] = - sqrt(sbcov[i]*dqcov + sbmet[i]); + ecovtot += ecov[i]; + tmp[gp][5] += ecov[i]; + + if (evflag) ev_tally_full(i,0.0,2.0*ecov[i],0.0,0.0,0.0,0.0); + + +// Coulombian Interaction +// ----------------------- + evdwl = 2.0*Vself*iq*iq ; + tmp[gp][1] += Vself*iq*iq; + tmp[gp][2] += Vself*iq*iq; + + if (evflag) ev_tally_full (i,0.0,evdwl,0.0,0.0,0.0,0.0); + evdwl = 0.0 ; + + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { +// =============================== + j = jlist[jj]; + jtype = map[type[j]]; + jtag = tag[j]; jq = q[j]; + + +// ....................................................................... + if (itag > jtag) { + if ((itag+jtag) % 2 == 0) continue; + } else if (itag < jtag) { + if ((itag+jtag) % 2 == 1) continue; + } else { + if (x[j][2] < x[i][2]) continue; + if (x[j][2] == ztmp && x[j][1] < ytmp) continue; + if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue; + } +// ....................................................................... + + + // # of interaction + // ---------------- + m = intype[itype][jtype]; + + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + +// --------------------------------- + if (sqrt(rsq) > cutmax) continue; +// --------------------------------- + + + // Coulombian Energy + // ------------------ + evdwl = 0.0 ; fpair = 0.0; + potqeq(i,j,iq,jq,rsq,fpair,eflag,evdwl); + + tmp[gp][1] += evdwl; + tmp[gp][2] += evdwl; + + + // Coulombian Force + // ----------------- + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + + + if (evflag) + ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz); + evdwl = 0.0; fpair = 0.0 ; + + + +// --------------------- + if (m == 0) continue; +// --------------------- + +// ---------------------------------------------- + if ( strcmp(intparams[m].typepot,"buck") == 0 || + strcmp(intparams[m].typepot,"buckPlusAttr") ==0 ) { +// ---------------------------------------------- + + evdwl = 0.0; fpair =0.0; + rep_OO (&intparams[m],rsq,fpair,eflag,evdwl); + ErepOO += evdwl ; + tmp[gp][3] += evdwl; + + + // repulsion is pure two-body, sums up pair repulsive forces + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + + + if (evflag) + ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz); + evdwl = 0.0; fpair = 0.0 ; + + } // ----------------------------------- Rep O-O + + if (strcmp(intparams[m].typepot,"buckPlusAttr") == 0 ) { +// ---------------------------------------------- + + evdwl = 0.0; fpair =0.0; + Attr_OO (&intparams[m],rsq,fpair,eflag,evdwl); + ErepOO += evdwl ; + tmp[gp][3] += evdwl; + + + // repulsion is pure two-body, sums up pair repulsive forces + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + + + if (evflag) + ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz); + evdwl = 0.0; fpair = 0.0 ; + + } // ----------------------------------- Attr O-O + + +// ----------------------------------------------------------------- + if (strcmp(intparams[m].typepot,"second_moment") != 0 ) continue; +// ----------------------------------------------------------------- + + + if (sqrt(rsq) > intparams[m].dc2) continue; +// ------------------------------------------- + +// Repulsion : Energy + force +// ---------------------------- + evdwl = 0.0; fpair = 0.0 ; + repulsive(&intparams[m],rsq,i,j,fpair,eflag,evdwl); + ErepMO += evdwl; + tmp[gp][4] += 2.0*evdwl; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + + + if (evflag) + ev_tally(i,j,nlocal,newton_pair,2.0*evdwl,0.0,fpair,delx,dely,delz); + + evdwl = 0.0 ; fpair = 0.0; +// ----- ----- ----- ----- ----- ----- + +// Attraction : force +// ------------------ + fpair = 0.0; + f_att(&intparams[m], i, j, rsq, fpair) ; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + + if (evflag) + ev_tally(i,j,nlocal,newton_pair,0.0,0.0,fpair,delx,dely,delz); + + + } // --------------------------------- End j + + } // ---------------------------------- End i + + + if (vflag_fdotr) virial_fdotr_compute(); + + + for (i = 0; i < nteam+1; i++) { + MPI_Allreduce(tmp[i],tmpAll[i],7,MPI_DOUBLE,MPI_SUM,world); + } + +// :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: + if (me == 0 && fmod(double(step), Nevery) == 0.0 && strcmp(writeenerg,"true") == 0) { + + ofstream fichierE; + + if (step == 0) { fichierE.open ("Energy_component.txt", ios::out | ios::trunc) ;} + else { fichierE.open ("Energy_component.txt", ios::out | ios::app) ;} + + if (fichierE) fichierE<< setprecision(9) <pair->tail_flag,vflag_fdotr); + printf ("neighbor->includegroup %d\n",neighbor->includegroup); + + + + for (gp=0; gpdestroy(nmol); + memory->destroy(tmp); + memory->destroy(tmpAll); + +} + +/* ---------------------------------------------------------------------- + Partie Electrostatique + ----------------------------------------------------------------------*/ + +double PairSMTBQ::self(Param *param, double qi) +{ + double self_tmp; + double s1=param->chi, s2=param->dj; + + self_tmp = qi*(s1+0.5*qi*s2); + + return self_tmp; +} + +/* ---------------------------------------------------------------------- */ + +double PairSMTBQ::qfo_self(Param *param, double qi) +{ + double self_d; + double s1 = param->chi; + double s2 = param->dj; + + self_d = 0.0 ; + self_d = s1+qi*s2; + + return self_d; +} + +/* ---------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- */ + +void PairSMTBQ::tabqeq() +{ + int i,j,k,m,verbose; + int nntype; + double rc,s,r; + double alf; + + int ii; + double za,zb,ra,rb,gam,dgam,dza,dzb, + d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2,na,nb; + double aCoeff,bCoeff,rcoupe,nang; + + int n = atom->ntypes; + int nlocal = atom->nlocal; + int nghost = atom->nghost; + nmax = atom->nmax; + + verbose = 1; + verbose = 0; + + nntype = int((n+1)*n/2); + + rc = cutmax ; + alf = 0.3 ; + // alf = 0.2 ; + + + if (verbose) printf ("kmax %d, ds %f, nmax %d\n",kmax,ds,nmax); + if (verbose) printf ("nlocal = %d, nghost = %d\n",nlocal,nghost); + if (verbose) printf ("nntypes %d, kmax %d, rc %f, n %d\n",nntype,kmax,rc,n); + + // allocate arrays + + memory->create(coultype,n,n,"pair:intype"); + memory->create(potqn,kmax+5,"pair:potqn"); + memory->create(dpotqn,kmax+5,"pair:dpotqn"); + memory->create(fafb,kmax+5,nntype,"pair:fafb"); + memory->create(dfafb,kmax+5,nntype,"pair:dfafb"); + memory->create(fafbOxOxSurf,kmax+5,"pair:fafbOxOxSurf"); + memory->create(dfafbOxOxSurf,kmax+5,"pair:dfafbOxOxSurf"); + memory->create(fafbTiOxSurf,kmax+5,"pair:fafbTiOxSurf"); + memory->create(dfafbTiOxSurf,kmax+5,"pair:dfafbTiOxSurf"); + + memory->create(fafbOxOxBB,kmax+5,"pair:fafbOxOxBB"); + memory->create(dfafbOxOxBB,kmax+5,"pair:dfafbOxOxBB"); + memory->create(fafbTiOxBB,kmax+5,"pair:fafbTiOxB"); + memory->create(dfafbTiOxBB,kmax+5,"pair:dfafbTiOxBB"); + + + memory->create(ecov,nmax,"pair:ecov"); + memory->create(potmad,nmax,"pair:potmad"); + memory->create(potself,nmax,"pair:potself"); + memory->create(potcov,nmax,"pair:potcov"); + memory->create(sbcov,nmax,"pair:sbcov"); + memory->create(coord,nmax,"pair:coord"); + memory->create(sbmet,nmax,"pair:sbmet"); + memory->create(chimet,nmax,"pair:chimet"); + + // memory->create(nvsm,nmax,"pair:nvsm"); + // memory->create(vsm,nmax,nmax,"pair:vsm"); + memory->create(flag_QEq,nmax,"pair:flag_QEq"); + + memory->create(qf,nmax,"pair:qf"); + memory->create(q1,nmax,"pair:q1"); + memory->create(q2,nmax,"pair:q2"); + memory->create(tab_comm,nmax,"pair:tab_comm"); + + memory->create(fct,31,"pair:fct"); + + // set interaction number: 0-0=0, 1-1=1, 0-1=1-0=2 + + m = 0; k = n; + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + if (j == i) { + coultype[i][j] = m; + m += 1; + } else if (j != i && j > i) { + coultype[i][j] = k; + k += 1; + } else if (j != i && j < i) { + coultype[i][j] = coultype[j][i]; + } + if (verbose) printf ("i %d, j %d, coultype %d\n",i,j,coultype[i][j]); + } + } + + // -------- Tabqn -------- + + // ------------------- + // Ouverture du fichier + // ofstream fichier("tabqeq.txt", ios::out | ios::trunc) ; + // ------------------- + + double pi,mu; + pi = 4.0*atan(1.0); + + mu = erfc(alf*rc)/rc ; + + //if (fichier) fichier <<" r - potqn " <rcoupe) nang = rcoupe - rc ; + bCoeff = (2*dij+ddij*nang)/(dij*nang); + aCoeff = dij*exp(-bCoeff*rc) /pow(nang,2); + } + if (r > rc) {dij = aCoeff *pow((r- rc-nang),2) *exp(bCoeff*r); + ddij = aCoeff*(r- rc-nang) *(2+bCoeff*(r-rc-nang))*exp(bCoeff*r); + } + + + if (r > (rc+nang)) {dij = 0.0 ; ddij = 0.0;} + + fafb[k][m] = potqn[k] - dij ; + if (k == 1) fafb[0][m] = fafb[k][m] ; + + dfafb[k][m] = dpotqn[k] - ddij/r ; + } + + // Make the table fafbOxOxSurf + rc = cutmax; + if(strcmp(params[i].nom,"O")==0 || strcmp(params[j].nom,"O")==0){ + if(strcmp(params[i].nom,"O")==0) { + ra = ROxSurf; + za = (2.0*params[i].ne + 1.0)/(4.0*ra);} + if(strcmp(params[j].nom,"O")==0) { + rb = ROxSurf; + zb = (2.0*params[j].ne + 1.0)/(4.0*rb); } + + + ii = 0 ; nang =cang= 5.0 ; + // -------------------------- + for (k = 0; k < kmax+5; k++) + // -------------------------- + { + gam = dgam = dza = dzb = d2zaa = d2zab = + d2zbb = d2zra = d2zrb = d2gamr2 = 0.0 ; + dij = 0.0 ; + + s = double(k)*ds ; r = sqrt(s) ; + if (k==0) r=10e-30; + + gammas(na,nb,za,zb,r,gam,dgam,dza,dzb, + d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2) ; + + // --- Jij + + dij = 14.4 * (1.0/r - double(gam)); + ddij = 14.4 * (-1.0/(r*r) - double(dgam)) ; + + if (dij < 0.01 && ii==0) + { + ii=2; + if (ii==2) if (verbose) printf ("rc : %f\n",r); + rc = r ; ii=1 ; + if ((rc+nang)>rcoupe) nang = rcoupe - rc ; + bCoeff = (2*dij+ddij*nang)/(dij*nang); + aCoeff = dij*exp(-bCoeff*rc) /pow(nang,2); + } + if (r > rc) {dij = aCoeff *pow((r- rc-nang),2) *exp(bCoeff*r); + ddij = aCoeff*(r- rc-nang) *(2+bCoeff*(r-rc-nang))*exp(bCoeff*r); + } + + + if (r > (rc+nang)) {dij = 0.0 ; ddij = 0.0;} + + if(strcmp(params[i].nom,"O")==0 && strcmp(params[j].nom,"O")==0){ + fafbOxOxSurf[k] = potqn[k] - dij ; + if (k == 1) fafbOxOxSurf[0] = fafbOxOxSurf[k] ; + + dfafbOxOxSurf[k] = dpotqn[k] - ddij/r ; + } + else { fafbTiOxSurf[k] = potqn[k] - dij ; + if (k == 1) fafbTiOxSurf[0] = fafbTiOxSurf[k] ; + + dfafbTiOxSurf[k] = dpotqn[k] - ddij/r ;} + + } + + + } //for k + //end of make the table fafbOxOxSurf + + // Makes the table fafbOxOxBB + rc = cutmax; + if(strcmp(params[i].nom,"O")==0 || strcmp(params[j].nom,"O")==0){ + if(strcmp(params[i].nom,"O")==0) { + ra = ROxBB; + za = (2.0*params[i].ne + 1.0)/(4.0*ra);} + if(strcmp(params[j].nom,"O")==0) { + rb = ROxBB; + zb = (2.0*params[j].ne + 1.0)/(4.0*rb); } + + + ii = 0 ; nang =cang= 5.0 ; + // -------------------------- + for (k = 0; k < kmax+5; k++) + // -------------------------- + { + gam = dgam = dza = dzb = d2zaa = d2zab = + d2zbb = d2zra = d2zrb = d2gamr2 = 0.0 ; + dij = 0.0 ; + + s = double(k)*ds ; r = sqrt(s) ; + if (k==0) r=10e-30; + + gammas(na,nb,za,zb,r,gam,dgam,dza,dzb, + d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2) ; + + // --- Jij + + dij = 14.4 * (1.0/r - double(gam)); + ddij = 14.4 * (-1.0/(r*r) - double(dgam)) ; + + if (dij < 0.01 && ii==0) { + ii=2; + if (ii==2) if (verbose) printf ("rc : %f\n",r); + rc = r ; ii=1 ; + if ((rc+nang)>rcoupe) nang = rcoupe - rc ; + bCoeff = (2*dij+ddij*nang)/(dij*nang); + aCoeff = dij*exp(-bCoeff*rc) /pow(nang,2); + } + if (r > rc) { + dij = aCoeff *pow((r- rc-nang),2) *exp(bCoeff*r); + ddij = aCoeff*(r- rc-nang) *(2+bCoeff*(r-rc-nang))*exp(bCoeff*r); + } + + + if (r > (rc+nang)) {dij = 0.0 ; ddij = 0.0;} + + if(strcmp(params[i].nom,"O")==0 && strcmp(params[j].nom,"O")==0){ + fafbOxOxBB[k] = potqn[k] - dij ; + if (k == 1) fafbOxOxBB[0] = fafbOxOxBB[k] ; + dfafbOxOxBB[k] = dpotqn[k] - ddij/r ; } + else { fafbTiOxBB[k] = potqn[k] - dij ; + if (k == 1) fafbTiOxBB[0] = fafbTiOxBB[k] ; + dfafbTiOxBB[k] = dpotqn[k] - ddij/r ; + } + } + + + + } //for k + //end of make the table fafbOxOxBB + + + + } + } //for i,j + + //if (fichier) fichier.close() ; + +} + +/* ---------------------------------------------------------------------*/ + +void PairSMTBQ::potqeq(int i, int j, double qi, double qj, double rsq, + double &fforce, int eflag, double &eng) +{ + + /* =================================================================== + Coulombian energy calcul between i and j atoms + with fafb table make in sm_table(). + fafb[i][j] : i is the table's step (r) + j is the interaction's # (in intype[itype][jtype]) + dfafb is derivate energy (force) + ==================================================================== */ + + int itype,jtype,l,m; + double r,t1,t2,sds,xi,engBulk,engSurf,fforceBulk,fforceSurf,dcoordloc,dcoupureloc; + double engBB,fforceBB, dIntfcoup2loc,iCoord,jCoord,iIntfCoup2,jIntfCoup2; + + int *type = atom->type; + // int n = atom->ntypes; + + itype = map[type[i]]; + jtype = map[type[j]]; + m = coultype[itype][jtype]; + + r = rsq; + sds = r/ds ; l = int(sds) ; + xi = sds - double(l) ; + + + iCoord=coord[i]; + jCoord=coord[j]; + iIntfCoup2= Intfcoup2(iCoord,coordOxBulk,0.15); + jIntfCoup2= Intfcoup2(jCoord,coordOxBulk,0.15); + + // ---- Energies Interpolation + + t1 = fafb[l][m] + (fafb[l+1][m] - fafb[l][m])*xi; + t2 = fafb[l+1][m] + (fafb[l+2][m] - fafb[l+1][m])*(xi-1.0); + + engBulk = qi*qj*(t1 + (t2 - t1)*xi/2.0); + eng=engBulk; + + + // ---- Forces Interpolation + + t1 = dfafb[l][m] + (dfafb[l+1][m] - dfafb[l][m])*xi; + t2 = dfafb[l+1][m] + (dfafb[l+2][m] - dfafb[l+1][m])*(xi-1); + + + fforce = - qi*qj*(t1 + (t2 - t1)*xi/2.0) ; + + + if(strcmp(params[itype].nom,"O")==0 || strcmp(params[jtype].nom,"O")==0){ + + if(strcmp(params[itype].nom,"O")==0 && strcmp(params[jtype].nom,"O")==0){ + // between two oxygens + + t1 = fafbOxOxSurf[l] + (fafbOxOxSurf[l+1] - fafbOxOxSurf[l])*xi; + t2 = fafbOxOxSurf[l+1] + (fafbOxOxSurf[l+2] - fafbOxOxSurf[l+1])*(xi-1.0); + engSurf = qi*qj*(t1 + (t2 - t1)*xi/2.0); + + t1 = fafbOxOxBB[l] + (fafbOxOxBB[l+1] - fafbOxOxBB[l])*xi; + t2 = fafbOxOxBB[l+1] + (fafbOxOxBB[l+2] - fafbOxOxBB[l+1])*(xi-1.0); + engBB = qi*qj*(t1 + (t2 - t1)*xi/2.0); + + eng= engBulk + (iCoord+jCoord-2*coordOxBulk)/(2*(coordOxBB-coordOxBulk)) *(engBB-engBulk) + + (iIntfCoup2+jIntfCoup2)*((engBulk-engSurf)/(2*(coordOxBulk-coordOxSurf)) + - (engBB-engBulk)/(2*(coordOxBB-coordOxBulk))) ; + + + // ---- Interpolation des forces + + fforceBulk=fforce; + t1 = dfafbOxOxSurf[l] + (dfafbOxOxSurf[l+1] - dfafbOxOxSurf[l])*xi; + t2 = dfafbOxOxSurf[l+1] + (dfafbOxOxSurf[l+2] - dfafbOxOxSurf[l+1])*(xi-1); + fforceSurf = - qi*qj*(t1 + (t2 - t1)*xi/2.0) ; + + t1 = dfafbOxOxBB[l] + (dfafbOxOxBB[l+1] - dfafbOxOxBB[l])*xi; + t2 = dfafbOxOxBB[l+1] + (dfafbOxOxBB[l+2] - dfafbOxOxBB[l+1])*(xi-1); + fforceBB = - qi*qj*(t1 + (t2 - t1)*xi/2.0) ; + + fforce= fforceBulk + (iCoord+jCoord-2*coordOxBulk)/(2*(coordOxBB-coordOxBulk))*(fforceBB-fforceBulk) + + (iIntfCoup2+jIntfCoup2)*((fforceBulk-fforceSurf)/(2*(coordOxBulk-coordOxSurf)) + - (fforceBB-fforceBulk)/(2*(coordOxBB-coordOxBulk))) ; + + } + else{ // between metal and oxygen + + t1 = fafbTiOxSurf[l] + (fafbTiOxSurf[l+1] - fafbTiOxSurf[l])*xi; + t2 = fafbTiOxSurf[l+1] + (fafbTiOxSurf[l+2] - fafbTiOxSurf[l+1])*(xi-1.0); + engSurf = qi*qj*(t1 + (t2 - t1)*xi/2.0); + t1 = fafbTiOxBB[l] + (fafbTiOxBB[l+1] - fafbTiOxBB[l])*xi; + t2 = fafbTiOxBB[l+1] + (fafbTiOxBB[l+2] - fafbTiOxBB[l+1])*(xi-1.0); + engBB = qi*qj*(t1 + (t2 - t1)*xi/2.0); + + if(strcmp(params[jtype].nom,"O")==0) //the atom j is an oxygen + { iIntfCoup2=jIntfCoup2; + iCoord=jCoord; } + + eng = engBulk + (engBulk-engSurf)/(coordOxBulk-coordOxSurf) * iIntfCoup2 + + (engBB-engBulk)/(coordOxBB-coordOxBulk) * (iCoord-coordOxBulk-iIntfCoup2); + + + // ---- Forces Interpolation + + fforceBulk=fforce; + t1 = dfafbTiOxSurf[l] + (dfafbTiOxSurf[l+1] - dfafbTiOxSurf[l])*xi; + t2 = dfafbTiOxSurf[l+1] + (dfafbTiOxSurf[l+2] - dfafbTiOxSurf[l+1])*(xi-1); + fforceSurf = - qi*qj*(t1 + (t2 - t1)*xi/2.0) ; + + t1 = dfafbTiOxBB[l] + (dfafbTiOxBB[l+1] - dfafbTiOxBB[l])*xi; + t2 = dfafbTiOxBB[l+1] + (dfafbTiOxBB[l+2] - dfafbTiOxBB[l+1])*(xi-1); + fforceBB = - qi*qj*(t1 + (t2 - t1)*xi/2.0) ; + + dcoordloc = fcoupured(sqrt(r),r1Coord,r2Coord) ; + + + dcoupureloc = fcoupured(iCoord,coordOxSurf,coordOxBulk) ; + dIntfcoup2loc= fcoup2(iCoord,coordOxBulk,0.15)*dcoupureloc ; + fforce = fforceBulk + 1/(coordOxBulk-coordOxSurf) * ((fforceBulk-fforceSurf)* iIntfCoup2 + - (engBulk-engSurf) *dIntfcoup2loc) + + 1/(coordOxBB-coordOxBulk) * ((fforceBB-fforceBulk)*(iCoord-coordOxBulk- iIntfCoup2) + - (engBB-engBulk) *(dcoordloc-dIntfcoup2loc)); + + + } + + + + } + + +} + +/* -------------------------------------------------------------------- */ + +void PairSMTBQ::pot_ES (int i, int j, double rsq, double &eng) +{ + + /* =================================================================== + Coulombian potentiel energy calcul between i and j atoms + with fafb table make in sm_table(). + fafb[i][j] : i is the table's step (r) + j is the interaction's # (in intype[itype][jtype]) + dfafb is derivate energy (force) + ==================================================================== */ + + int itype,jtype,l,m; + double r,t1,t2,sds,xi,engBulk,engSurf,dcoordloc,dcoupureloc; + double engBB, dIntfcoup2loc,iCoord,jCoord,iIntfCoup2,jIntfCoup2; + + int *type = atom->type; + // int n = atom->ntypes; + + itype = map[type[i]]; + jtype = map[type[j]]; + m = coultype[itype][jtype]; + + r = rsq; + sds = r/ds ; l = int(sds) ; + xi = sds - double(l) ; + + + iCoord=coord[i]; + jCoord=coord[j]; + iIntfCoup2= Intfcoup2(iCoord,coordOxBulk,0.15); + jIntfCoup2= Intfcoup2(jCoord,coordOxBulk,0.15); + + // ---- Energies Interpolation + + t1 = fafb[l][m] + (fafb[l+1][m] - fafb[l][m])*xi; + t2 = fafb[l+1][m] + (fafb[l+2][m] - fafb[l+1][m])*(xi-1.0); + + + eng = (t1 + (t2 - t1)*xi/2.0); + engBulk=eng; + + + if(itype==0 || jtype==0){ + + if(itype==0 && jtype==0){ // between two oxygens + + t1 = fafbOxOxSurf[l] + (fafbOxOxSurf[l+1] - fafbOxOxSurf[l])*xi; + t2 = fafbOxOxSurf[l+1] + (fafbOxOxSurf[l+2] - fafbOxOxSurf[l+1])*(xi-1.0); + engSurf = (t1 + (t2 - t1)*xi/2.0); + + t1 = fafbOxOxBB[l] + (fafbOxOxBB[l+1] - fafbOxOxBB[l])*xi; + t2 = fafbOxOxBB[l+1] + (fafbOxOxBB[l+2] - fafbOxOxBB[l+1])*(xi-1.0); + engBB = (t1 + (t2 - t1)*xi/2.0); + + eng= engBulk + (iCoord+jCoord-2*coordOxBulk)/(2*(coordOxBB-coordOxBulk))*(engBB-engBulk) + + (iIntfCoup2+jIntfCoup2)*((engBulk-engSurf)/(2*(coordOxBulk-coordOxSurf)) + - (engBB-engBulk)/(2*(coordOxBB-coordOxBulk))) ; + + } else { // between metal and oxygen + + t1 = fafbTiOxSurf[l] + (fafbTiOxSurf[l+1] - fafbTiOxSurf[l])*xi; + t2 = fafbTiOxSurf[l+1] + (fafbTiOxSurf[l+2] - fafbTiOxSurf[l+1])*(xi-1.0); + engSurf = (t1 + (t2 - t1)*xi/2.0); + + t1 = fafbTiOxBB[l] + (fafbTiOxBB[l+1] - fafbTiOxBB[l])*xi; + t2 = fafbTiOxBB[l+1] + (fafbTiOxBB[l+2] - fafbTiOxBB[l+1])*(xi-1.0); + engBB = (t1 + (t2 - t1)*xi/2.0); + + if (jtype==0) { //the atom j is an oxygen + iIntfCoup2=jIntfCoup2; + iCoord=jCoord; + } + + eng = engBulk + (engBulk-engSurf)/(coordOxBulk-coordOxSurf)*iIntfCoup2 + + (engBB-engBulk)/(coordOxBB-coordOxBulk) * (iCoord-coordOxBulk-iIntfCoup2); + + + } + + + + } + + +} + +/* -------------------------------------------------------------------- */ + +void PairSMTBQ::pot_ES2 (int i, int j, double rsq, double &pot) +{ + int l,m,itype,jtype; + double sds,xi,t1,t2,r; + + int *type = atom->type; + + + if (sqrt(rsq) > cutmax) return ; + + itype = map[type[i]]; + jtype = map[type[j]]; + m = coultype[itype][jtype]; + + r = rsq ; + sds = r/ds ; l = int(sds) ; + xi = sds - double(l) ; + + // ---- Energies Interpolation + + t1 = fafb[l][m] + (fafb[l+1][m] - fafb[l][m])*xi; + t2 = fafb[l+1][m] + (fafb[l+2][m] - fafb[l+1][m])*(xi-1.0); + + pot = (t1 + (t2 - t1)*xi/2.0) ; + +} + +/* -------------------------------------------------------------------- + Oxygen-Oxygen Interaction + -------------------------------------------------------------------- */ + +void PairSMTBQ::rep_OO(Intparam *intparam, double rsq, double &fforce, + int eflag, double &eng) +{ + double r,tmp_exp,tmp; + double A = intparam->abuck ; + double rho = intparam->rhobuck ; + + r = sqrt(rsq); + tmp = - r/rho ; + tmp_exp = exp( tmp ); + + eng = A * tmp_exp ; + + fforce = A/rho * tmp_exp / r ; //( - ) + +} + + +void PairSMTBQ::Attr_OO(Intparam *intparam, double rsq, double &fforce, + int eflag, double &eng) +{ + double r,tmp_exp,tmp; + double aOO = intparam->aOO ; + double bOO = intparam->bOO ; + double r1OO = intparam->r1OO ; + double r2OO = intparam->r2OO ; + + r = sqrt(rsq); + tmp_exp= exp( bOO* r); + eng = aOO * tmp_exp* fcoupure(r,r1OO,r2OO); + + fforce = - (aOO*bOO * tmp_exp * fcoupure(r,r1OO,r2OO)+ aOO*tmp_exp *fcoupured(r,r1OO,r2OO))/ r ; //( - ) + +} + + +/* ---------------------------------------------------------------------- + covalente Interaction + ----------------------------------------------------------------------*/ + + +void PairSMTBQ::tabsm() +{ + int k,m; + double s,r,tmpb,tmpr,fcv,fcdv; + + memory->create(tabsmb,kmax,maxintsm+1,"pair:tabsmb"); + memory->create(tabsmr,kmax,maxintsm+1,"pair:tabsmr"); + memory->create(dtabsmb,kmax,maxintsm+1,"pair:dtabsmb"); + memory->create(dtabsmr,kmax,maxintsm+1,"pair:dtabsmr"); + + + for (m = 0; m <= maxintparam; m++) { + + if (intparams[m].intsm == 0) continue; + + double rc1 = intparams[m].dc1; + double rc2 = intparams[m].dc2; + double A = intparams[m].a; + double p = intparams[m].p; + double Ksi = intparams[m].ksi; + double q = intparams[m].q; + double rzero = intparams[m].r0; + int sm = intparams[m].intsm; + + + for (k=0; k < kmax; k++) + { + s = double(k)*ds ; r = sqrt(s); + if (k==0) r=10e-30; + tmpb = exp( -2.0*q*(r/rzero - 1.0)); + tmpr = exp( -p*(r/rzero - 1.0)); + + if (r <= rc1) + { + + // -- Energy + tabsmb[k][sm] = Ksi*Ksi * tmpb ; + tabsmr[k][sm] = A * tmpr ; + + // -- Force + /* dtabsmb ne correspond pas vraiment a une force puisqu'il y a le /r + (on a donc une unite force/distance). Le programme multiplie ensuite + (dans le PairSMTBQ::compute ) dtabsmb par la projection du vecteur r + sur un axe x (ou y ou z) pour determiner la composante de la force selon + cette direction. Donc tout est ok au final. */ + + dtabsmb[k][sm] = - 2.0 *Ksi*Ksi* q/rzero * tmpb /r; + dtabsmr[k][sm] = - A * p/rzero * tmpr/r ; + + } // if + + else if (r > rc1 && r <= rc2) + { + + // -- Energie + fcv = fcoupure(r,intparams[sm].dc1,intparams[sm].dc2); + tabsmb[k][sm] = fcv* Ksi*Ksi * tmpb ; + tabsmr[k][sm] = fcv* A * tmpr ; + + // -- Force + /* dtabsmb ne correspond pas vraiment a une force puisqu'il y a le /r + (on a donc une unite force/distance). Le programme multiplie ensuite + (dans le PairSMTBQ::compute ) d tabsmb par la projection du vecteur + r sur un axe x (ou y ou z) pour determiner la composante de la force + selon cette direction. Donc tout est ok au final. */ + + fcdv = fcoupured(r,intparams[sm].dc1,intparams[sm].dc2); + dtabsmb[k][sm] = (fcv*( - 2.0 *Ksi*Ksi* q/rzero * tmpb )+fcdv* Ksi*Ksi * tmpb )/r ; + dtabsmr[k][sm] = (fcv*( - A * p/rzero * tmpr )+fcdv*A * tmpr )/r ; + + } + + else + { + + // -- Energie + tabsmb[k][sm] = 0.0; + tabsmr[k][sm] = 0.0; + + // -- Force + dtabsmb[k][sm] = 0.0; + dtabsmr[k][sm] = 0.0; + + } + + + + } // for kmax + + + } // for maxintparam + +} + + + + + +/* -------------------------------------------------------------- */ + +void PairSMTBQ::repulsive(Intparam *intparam, double rsq, int i, int j, + double &fforce, int eflag, double &eng) +{ + + /* ================================================ + rsq : square of ij distance + fforce : repulsion force + eng : repulsion energy + eflag : Si oui ou non on calcule l'energie + =================================================*/ + + int l; + double r,sds,xi,t1,t2,dt1,dt2,sweet,iq,jq; + + double rrcs = intparam->dc2; + int sm = intparam->intsm; + + // printf ("On rentre dans repulsive\n"); + + + r = rsq; + if (sqrt(r) > rrcs) return ; + + sds = r/ds ; l = int(sds) ; + xi = sds - double(l) ; + + t1 = tabsmr[l][sm] + (tabsmr[l+1][sm] - tabsmr[l][sm])*xi ; + t2 = tabsmr[l+1][sm] + (tabsmr[l+2][sm] - tabsmr[l+1][sm])*(xi-1.0) ; + + dt1 = dtabsmr[l][sm] + (dtabsmr[l+1][sm] - dtabsmr[l][sm])*xi ; + dt2 = dtabsmr[l+1][sm] + (dtabsmr[l+2][sm] - dtabsmr[l+1][sm])*(xi-1.0) ; + + if (strcmp(intparam->mode,"oxide") == 0) + { + fforce = - 2.0*(dt1 + (dt2 - dt1)*xi/2.0); + eng = (t1 + (t2 - t1)*xi/2.0) ; + } + else if (strcmp(intparam->mode,"metal") == 0) + { + sweet = 1.0; + fforce = - 2.0*(dt1 + (dt2 - dt1)*xi/2.0) * sweet ; + eng = (t1 + (t2 - t1)*xi/2.0) * sweet ; + } + +} + + +/* --------------------------------------------------------------------------------- */ + + +void PairSMTBQ::attractive(Intparam *intparam, double rsq, + int eflag, int i, double iq, int j, double jq) +{ + int itype,l; + double r,t1,t2,xi,sds; + double dqcov,sweet,dq,mu; + + double rrcs = intparam->dc2; + int *type = atom->type; + int sm = intparam->intsm; + + itype = map[type[i]]; + + r = rsq; + if (sqrt(r) > rrcs) return ; + + + sds = r/ds ; l = int(sds) ; + xi = sds - double(l) ; + + t1 = tabsmb[l][sm] + (tabsmb[l+1][sm] - tabsmb[l][sm])*xi ; + t2 = tabsmb[l+1][sm] + (tabsmb[l+2][sm] - tabsmb[l+1][sm])*(xi-1.0) ; + + + + if (strcmp(intparam->mode,"oxide") == 0) { + mu = 0.5*(sqrt(params[1].sto) + sqrt(params[0].sto)); + +// dq = fabs(params[itype].qform) - fabs(iq); +// dqcov = dq*(2.0*ncov/params[itype].sto - dq); + + sbcov[i] += (t1 + (t2 - t1)*xi/2.0) *params[itype].sto*mu*mu; + +// if (i < 10) printf ("i %d, iq %f sbcov %f \n",i,iq,sbcov[i]); + + if (sqrt(r)mode,"metal") == 0) { + sweet = 1.0; + sbmet[i] += (t1 + (t2 - t1)*xi/2.0) * sweet ; + } + +} + +/* ---------------------------------------------------------------------- */ + +void PairSMTBQ::f_att(Intparam *intparam, int i, int j,double rsq, double &fforce) +{ + int itype,jtype,l; + int *type = atom->type; + + double r,sds,xi,dt1,dt2,dq,dqcovi,dqcovj; + double fcov_ij,fcov_ji,sweet,iq,jq,mu; + + int sm = intparam->intsm; + double *q = atom->q; + + itype = map[type[i]]; + jtype = map[type[j]]; + iq = q[i] ; jq = q[j]; + + r = rsq; + + sds = r/ds ; l = int(sds) ; + xi = sds - double(l) ; + + dt1 = dtabsmb[l][sm] + (dtabsmb[l+1][sm] - dtabsmb[l][sm])*xi ; + dt2 = dtabsmb[l+1][sm] + (dtabsmb[l+2][sm] - dtabsmb[l+1][sm])*(xi-1.0) ; + + dq = fabs(params[itype].qform) - fabs(iq); + dqcovi = dq*(2.0*ncov/params[itype].sto - dq); + + dq = fabs(params[jtype].qform) - fabs(jq); + dqcovj = dq*(2.0*ncov/params[jtype].sto - dq); + + if (strcmp(intparam->mode,"oxide") == 0) { +//------------------------------------------ + mu = 0.5*(sqrt(params[1].sto) + sqrt(params[0].sto)); + fcov_ij = (dt1 + (dt2 - dt1)*xi/2.0) * dqcovi *params[itype].sto*mu*mu; + fcov_ji = (dt1 + (dt2 - dt1)*xi/2.0) * dqcovj *params[jtype].sto*mu*mu; + + fforce = 0.5 * ( fcov_ij/sqrt(sbcov[i]*dqcovi + sbmet[i]) + + fcov_ji/sqrt(sbcov[j]*dqcovj + sbmet[j]) ) ; + } + + else if (strcmp(intparam->mode,"metal") == 0) { +//----------------------------------------------- + sweet = 1.0; + fcov_ij = (dt1 + (dt2 - dt1)*xi/2.0) * sweet ; + + fforce = 0.5 * fcov_ij*( 1.0/sqrt(sbcov[i]*dqcovi + sbmet[i]) + + 1.0/sqrt(sbcov[j]*dqcovj + sbmet[j]) ) ; + } + +} + +/* ---------------------------------------------------------------------- */ + +void PairSMTBQ::pot_COV(Param *param, int i, double &qforce) +{ + double iq,dq,DQ,sign; + + double *q = atom->q; + double qform = param->qform; + double sto = param->sto; + + sign = qform / fabs(qform); + iq = q[i]; + + dq = fabs(qform) - fabs(iq); + DQ = dq*(2.0*ncov/sto - dq); + + if (fabs(iq) < 1.0e-7 || fabs(sbcov[i]) < 1.0e-7) { + qforce = 0.0; } + else { + qforce = sign*sbcov[i]/sqrt(sbcov[i]*DQ + sbmet[i])*(ncov/sto - dq) ; + } + +} + +/* ---------------------------------------------------------------------- */ + +double PairSMTBQ::potmet(Intparam *intparam, double rsq, + int i, double iq, int j, double jq) +{ + int l,itype,jtype; + int *type = atom->type; + double chi,sds,xi,t1,t2,r,dsweet,dq,dqcovi,dqcovj; + + int sm = intparam->intsm; + itype = map[type[i]]; + jtype = map[type[j]]; + + r = rsq; + sds = r/ds ; l = int(sds) ; + xi = sds - double(l) ; + + t1 = tabsmb[l][sm] + (tabsmb[l+1][sm] - tabsmb[l][sm])*xi ; + t2 = tabsmb[l+1][sm] + (tabsmb[l+2][sm] - tabsmb[l+1][sm])*(xi-1.0) ; + + dq = fabs(params[itype].qform) - fabs(iq); + dqcovi = dq*(2.0*ncov/params[itype].sto - dq); + + dq = fabs(params[jtype].qform) - fabs(jq); + dqcovj = dq*(2.0*ncov/params[jtype].sto - dq); + + dsweet = 0.0; + chi = (t1 + (t2 - t1)*xi/2.0) * dsweet *( 1.0/(2.0*sqrt(sbcov[i]*dqcovi+sbmet[i])) + + 1.0/(2.0*sqrt(sbcov[j]*dqcovj+sbmet[j])) ); + + return chi; +} + + +/* ---------------------------------------------------------------------- + Cutting Function + ----------------------------------------------------------------------*/ + + +/* -------------------------------------------------------------------- */ + +double PairSMTBQ::fcoupure(double r, double rep_dc1, double rep_dc2) +{ + double ddc,a3,a4,a5,x; + + if (r rep_dc2) + {return 0;} + else + { + + ddc = rep_dc2 - rep_dc1; + x = r - rep_dc2; + + a3 = -10/(ddc*ddc*ddc); + a4 = -15/(ddc*ddc*ddc*ddc); + a5 = -6/(ddc*ddc*ddc*ddc*ddc); + + return x*x*x*(a3 + x*(a4 + x*a5));} +} + +/* ---------------------------------------------------------------------- + Derivate of cutting function + ----------------------------------------------------------------------*/ + + +/* ----------------------------------------------------------------------- */ + +double PairSMTBQ::fcoupured(double r, double rep_dc1, double rep_dc2) +{ + + double ddc,a3,a4,a5,x; + + if ( r>rep_dc1 && r x+delta) + {return 0;} + else + { + dc = c - x-delta; + return dc*dc*(3*delta+dc)/(4*delta*delta*delta); + } +} + +/* ---------------------------------------------------------------------- + Primitive of cutting function for derive (force) + ----------------------------------------------------------------------*/ + + +/* -------------------------------------------------------------------- */ + +double PairSMTBQ::Primfcoup2(double c, double x, double delta) +{ + + return (c*(c*c*c - 4* c*c* x - 4* (x - 2 *delta) * (x+delta)*(x+delta) + + 6* c *(x*x - delta*delta)))/(16* delta*delta*delta); + +} + + +/* ---------------------------------------------------------------------- + Integral of cutting function for derive (force) between x and c + ----------------------------------------------------------------------*/ + + +/* -------------------------------------------------------------------- */ + +double PairSMTBQ::Intfcoup2(double c, double x, double delta) +{ + + if (c x+delta) + {return Primfcoup2(x+delta,x,delta) - Primfcoup2(x,x,delta) ;} + else + { + return Primfcoup2(c,x,delta) - Primfcoup2(x,x,delta) ;} +} + + +/* --------------------------------------------------------------------- + Energy derivation respect charge Q + --------------------------------------------------------------------- */ + +void PairSMTBQ::QForce_charge(int loop) +{ + int i,j,ii,jj,jnum; + int itype,jtype,m,gp; + double xtmp,ytmp,ztmp,evdwlCoul,fpairCoul; + double rsq,delr[3],chi_ij; + int *ilist,*jlist,*numneigh,**firstneigh; + double iq,jq,fqi,fqj,fqij,fqij2,fqjj; + int eflag; + + + double **x = atom->x; + double *q = atom->q; + int *type = atom->type; + int step = update->ntimestep; + + int inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + int nlocal = atom->nlocal; + + + // loop over full neighbor list of my atoms + + fqi = fqj = fqij = fqij2 = fqjj = 0.0; + + + // ================== + if (loop == 0) { + // ================== + + + + for (ii = 0; ii < inum; ii ++) { + //-------------------------------- + i = ilist[ii]; + itype = map[type[i]]; + + gp = flag_QEq[i]; + + sbcov[i] =coord[i]= sbmet[i] = 0.0; + + itype = map[type[i]]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + iq = q[i]; + + + + + // two-body interactions + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { +// ------------------------------- + j = jlist[jj]; + j &= NEIGHMASK; + + jtype = map[type[j]]; + jq = q[j]; + + m = intype[itype][jtype]; + if (intparams[m].intsm == 0) continue ; + + + delr[0] = x[j][0] - xtmp; + delr[1] = x[j][1] - ytmp; + delr[2] = x[j][2] - ztmp; + rsq = vec3_dot(delr,delr); + + +// Covalente charge forces - sbcov initialization +// ------------------------------------------------ + if (sqrt(rsq) > intparams[m].dc2) continue; + + attractive (&intparams[m],rsq,eflag,i,iq,j,jq); + + + } // ---------------------------------------------- for jj + + + } // -------------------------------------------- ii + + // =============================================== + // Communicates the tables *sbcov and *sbmet + // to calculate the N-body forces + // ================================================ + + forward (sbcov) ; reverse (sbcov); + forward (coord) ; reverse (coord); + forward (sbmet) ; reverse (sbmet); + + + if (nteam == 0) return; //no oxide + if (Qstep == 0 || fmod(double(step), double(Qstep)) != 0.0) return; + + // ======================= + } // End of If(loop) + // ======================= + + + // =============================================== + + for (ii=0; ii cutmax) continue; + + // 1/r charge forces + // -------------------- + fqij = 0.0; +// pot_ES2 (i,j,rsq,fqij2); + pot_ES (i,j,rsq,fqij); + + potmad[i] += jq*fqij ; + + + } // ------ jj + + fqi = 0.0; + pot_COV (¶ms[itype],i,fqi) ; + potcov[i] = fqi ; + + + } // ------- ii + + +} + +/* ---------------------------------------------------------------------- */ + +void PairSMTBQ::Charge() +{ + int i,ii,iloop,itype,gp,m; + int *ilist; + double heatpq,qmass,dtq,dtq2,qtot,qtotll; + double t_init,t_end,dt; + + double *Transf,*TransfAll; + + double *q = atom->q; + double **x = atom->x; + int *type = atom->type; + int step = update->ntimestep; + + int inum = list->inum; + ilist = list->ilist; + + + if (me == 0) t_init = MPI_Wtime(); + if (step == 0) cluster = 0; + + // --------------------------- + // Mise en place des groupes + // --------------------------- + + if (strcmp(QEqMode,"BulkFromSlab") == 0) + groupBulkFromSlab_QEq(); + else if (strcmp(QEqMode,"QEqAll") == 0) + groupQEqAll_QEq(); + else if (strcmp(QEqMode,"QEqAllParallel") == 0) + groupQEqAllParallel_QEq(); + else if (strcmp(QEqMode,"Surface") == 0) + groupSurface_QEq(); + + + + if (nteam+1 != cluster) { + memory->destroy(nQEqall); + memory->destroy(nQEqaall); + memory->destroy(nQEqcall); + + cluster = nteam+1; + memory->create(nQEqall,nteam+1,"pair:nQEq"); + memory->create(nQEqaall,nteam+1,"pair:nQEqa"); + memory->create(nQEqcall,nteam+1,"pair:nQEqc"); + } + // --------------------------- + + + double enegtotall[nteam+1],enegchkall[nteam+1],enegmaxall[nteam+1],qtota[nteam+1],qtotc[nteam+1]; + double qtotcll[nteam+1],qtotall[nteam+1]; + double sigmaa[nteam+1],sigmac[nteam+1],sigmaall[nteam+1],sigmacll[nteam+1]; + int end[nteam+1], nQEq[nteam+1],nQEqc[nteam+1],nQEqa[nteam+1]; + + + iloop = 0; + + + heatpq = 0.07; + qmass = 0.000548580; + dtq = 0.0006; // 0.0006 + dtq2 = 0.5*dtq*dtq/qmass; + + double enegchk[nteam+1]; + double enegtot[nteam+1]; + double enegmax[nteam+1]; + + + + for (i=0; intimestep == 0 && (strcmp(QInitMode,"true") == 0) ) { + //Carefull here it won't be fine if there are more than 2 species!!! + QOxInit=max(QOxInit, -0.98* params[1].qform *nQEqcall[gp]/nQEqaall[gp]) ; + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; itype = map[type[i]]; + gp = flag_QEq[i]; + +// if (gp == 0) continue; + + if (itype == 0) q[i] = QOxInit ; + if (itype > 0) q[i] = -QOxInit * nQEqaall[gp]/nQEqcall[gp]; + } + } + + if (nteam == 0 || Qstep == 0) return; + if (fmod(double(step), double(Qstep)) != 0.0) return; + // -------------------------------------- + + // ---- + + // ---- + + + if (me == 0 && strcmp(Bavard,"false") != 0) { + for (gp = 0; gp < nteam+1; gp++) { + printf (" ++++ Groupe %d - Nox %d Ncat %d\n",gp,nQEqaall[gp],nQEqcall[gp]); + if (nQEqcall[gp] !=0 && nQEqaall[gp] !=0 ) + printf (" neutralite des charges %f\n qtotc %f qtota %f\n", + qtotll,qtotcll[gp]/nQEqcall[gp],qtotall[gp]/nQEqaall[gp]); + printf (" ---------------------------- \n");} + } + + // ======================= Tab transfert ================== + // Transf[gp] = enegtot[gp] + // Transf[gp+cluster] = Qtotc[gp] + // Transf[gp+2cluster] = Qtota[gp] + // Transf[3cluster] = Qtot + // ------------------------------------------------------- + memory->create(Transf,3*cluster+1,"pair:Tranf"); + memory->create(TransfAll,3*cluster+1,"pair:TranfAll"); + // ======================================================== + + + // -------------------------------------------- + for (iloop = 0; iloop < loopmax; iloop ++ ) { + // -------------------------------------------- + + qtot = qtotll = Transf[3*cluster] = 0.0 ; + for (gp=0; gpdestroy(Transf); + memory->destroy(TransfAll); + +} + +/* ---------------------------------------------------------------------- */ + +void PairSMTBQ::groupBulkFromSlab_QEq() +{ int ii,i; + double **x=atom->x; + int *ilist; + double ztmp; + int inum = list->inum; + ilist = list->ilist; + + for (ii = 0; ii < inum; ii++) + { + i = ilist[ii]; + ztmp = x[i][2]; + if (ztmp>zlim1QEq && ztmp< zlim2QEq) + flag_QEq[i]=1; + else + flag_QEq[i]=0; + + nteam=1; + + } + +} + +// ---------------------------------------------- + +void PairSMTBQ::groupQEqAll_QEq() +{ int ii,i; + int *ilist; + int inum = list->inum; + ilist = list->ilist; + + nteam=1; + + for (ii = 0; ii < inum; ii++) + { + i= ilist[ii]; + flag_QEq[i]=1; + } + +} + +// ---------------------------------------------- + +void PairSMTBQ::groupSurface_QEq() +{ int ii,i; + double **x=atom->x; + int *ilist; + double ztmp; + int inum = list->inum; + ilist = list->ilist; + + for (ii = 0; ii < inum; ii++) + { + i = ilist[ii]; + ztmp = x[i][2]; + if (ztmp>zlim1QEq) + flag_QEq[i]=1; + else + flag_QEq[i]=0; + + nteam=1; + + } + +} + + +void PairSMTBQ::groupQEqAllParallel_QEq() +{ + int ii,i,jj,j,kk,k,itype,jtype,ktype,jnum,m,gp,zz,z,kgp; + int iproc,team_elt[10][nproc],team_QEq[10][nproc][5]; + int *ilist,*jlist,*numneigh,**firstneigh,ngp,igp,nboite; + double delr[3],xtmp,ytmp,ztmp,rsq; + int **flag_gp, *nelt, **tab_gp; + int QEq,QEqall[nproc]; + + double **x = atom->x; + int *type = atom->type; + int inum = list->inum; + int nlocal = atom->nlocal; + int nghost = atom->nghost; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + + // +++++++++++++++++++++++++++++++++++++++++++++++++ + // On declare et initialise nos p'tits tableaux + // +++++++++++++++++++++++++++++++++++++++++++++++++ + + nboite = nlocal + nghost; + int **tabtemp,**Alltabtemp, *gptmp, *Allgptmp; + + memory->create(tabtemp,10*nproc+10,nproc,"pair:tabtemp"); + memory->create(Alltabtemp,10*nproc+10,nproc,"pair:Alltabtemp"); + memory->create(gptmp,10*nproc+10,"pair:gptmp"); + memory->create(Allgptmp,10*nproc+10,"pair:Allgptmp"); + + memory->create(flag_gp,nproc,nboite,"pair:flag_gp"); + memory->create(nelt,nboite,"pair:nelt"); + memory->create(tab_gp,10,nboite,"pair:flag_gp"); + + + for (i = 0; i < nlocal+nghost ; i++) { flag_QEq[i] = 0; } + for (i = 0; i < 10*nproc; i++) { + gptmp[i] = 0; Allgptmp[i] = 0; + for (j=0;jdestroy(tabtemp); + memory->destroy(Alltabtemp); + memory->destroy(gptmp); + memory->destroy(Allgptmp); + memory->destroy(flag_gp); + memory->destroy(tab_gp); + memory->destroy(nelt); + + return; + } + // ::::::::::::::::::::::::::::::::::::::::::::::::::::::: + + + for (m = 0; m < nproc; m++) { + for (i = 0; i < nboite; i++) { flag_gp[m][i] = 0; } + } + + // OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO + // It includes oxygens entering the QEq scheme O + // OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO + + + ngp = igp = 0; nelt[ngp] = 0; + + // On prend un oxygène + // printf ("[me %d] On prend un oxygene\n",me); + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii] ; itype = map[type[i]]; + if (itype != 0 || flag_QEq[i] == 0) continue; + + m = 0; + + if (ngp != 0 && flag_gp[me][i] == ngp) continue; + + + // Grouping Initialisation + // ----------------------------- + if (flag_gp[me][i] == 0) { + ngp += 1; nelt[ngp] = 0; + tab_gp[ngp][nelt[ngp]] = i; + flag_gp[me][i] = ngp; + nelt[ngp] += 1; + } + // ------------------------------- + + + // Loop on the groups + // ---------------------- + for (kk = 0; kk < nelt[ngp]; kk++) + { + k = tab_gp[ngp][kk]; + ktype = map[type[k]]; + // printf ("[me %d] kk - gp %d elemt %d : atom %d(%d)\n",me,ngp,kk,k,ktype); + if (k >= nlocal) continue; + + xtmp = x[k][0]; + ytmp = x[k][1]; + ztmp = x[k][2]; + + // Loop on the oxygen's neighbor of the group + // --------------------------------------------- + jlist = firstneigh[k]; + jnum = numneigh[k]; + for (j = 0; j < nboite; j++ ) + { + jtype = map[type[j]]; + if (jtype == ktype) continue; + m = intype[itype][jtype]; + + if (jtype == 0 && flag_QEq[j] == 0) continue; + + + if (flag_gp[me][j] == ngp) continue; + + delr[0] = x[j][0] - xtmp; + delr[1] = x[j][1] - ytmp; + delr[2] = x[j][2] - ztmp; + rsq = vec3_dot(delr,delr); + + // ------------------------------------- + if (sqrt(rsq) <= cutmax) { + + flag_QEq[j] = 1; //Entre dans le schema QEq + + // :::::::::::::::::::: Meeting of two group in the same proc ::::::::::::::::::::: + + if (flag_gp[me][j] != 0 && flag_gp[me][j] != ngp && nelt[flag_gp[me][j]] != 0) { + printf("[me %d] (atom %d) %d [elt %d] rencontre un nouveau groupe %d [elt %d] (atom %d)\n", + me,k,ngp,nelt[ngp],flag_gp[me][j],nelt[flag_gp[me][j]],j); + + // On met a jours les tableaux + // ----------------------------- + igp = flag_gp[me][j]; + z = min(igp,ngp); + + if (z == igp) { igp = z; } + else if (z == ngp) { + ngp = igp ; igp = z; + flag_gp[me][j] = ngp; + } + + for (zz = 0; zz < nelt[ngp]; zz++) { + z = tab_gp[ngp][zz]; + tab_gp[igp][nelt[igp]] = z; + nelt[igp] += 1; + flag_gp[me][z] = igp; + tab_gp[ngp][zz] = 0; + } + + nelt[ngp] = 0; + for (z = nlocal; z < nboite; z++) { + if (flag_gp[me][z] == ngp) flag_gp[me][z] = igp; + } + + m = 1; kk = 0; + ngp = igp; + break; + } + // :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: + + flag_gp[me][j] = ngp; + if (j < nlocal) + { + tab_gp[ngp][nelt[ngp]] = j; + nelt[ngp] += 1; + } + } + } // for j + } // for k + } // for ii + + // OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO + // Groups communication + // OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO + for (i = 0; i < nproc; i++) { + forward_int(flag_gp[i]); reverse_int(flag_gp[i]); + } + // --- + + + // ======================================================= + // Loop on the cation to make them joined in the oxygen's + // group which it interacts + // ======================================================= + igp = 0; + for (ii = 0; ii < inum; ii++) + { + i = ilist[ii] ; itype = map[type[i]]; + if (itype == 0) continue; + + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + for (jj = 0; jj < jnum; jj++ ) + { + j = jlist[jj] ; jtype = map[type[j]]; + if (jtype != 0) continue; + + m = 0; + for (iproc = 0; iproc < nproc; iproc++) { + if (flag_gp[iproc][j] != 0) m = flag_gp[iproc][j]; + } + if (m == 0) continue; + + delr[0] = x[j][0] - xtmp; + delr[1] = x[j][1] - ytmp; + delr[2] = x[j][2] - ztmp; + rsq = vec3_dot(delr,delr); + + // ---------------------------------------- + if (sqrt(rsq) <= cutmax) { + // if (sqrt(rsq) <= intparams[m].dc2) { + // ---------------------------------------- + + flag_QEq[i] = 1; igp = flag_gp[me][j]; + + if (flag_gp[me][i] == 0) flag_gp[me][i] = igp; + + if (flag_gp[me][i] != igp && igp != 0) { + printf ("[me %d] Cation i %d gp %d [nelt %d] rencontre j %d(%d)du groupe %d [nelt %d]\n", + me,i,flag_gp[me][i],nelt[flag_gp[me][i]],j,jtype,igp,nelt[igp]); + + igp = min(flag_gp[me][i],flag_gp[me][j]); + if (igp == flag_gp[me][i]) { kgp = flag_gp[me][j]; } + else { kgp = flag_gp[me][i]; } + + for (k = 0; k < nelt[kgp]; k++) { + z = tab_gp[kgp][k]; + tab_gp[igp][nelt[igp]] = z; + nelt[igp] += 1; + flag_gp[me][z] = igp; + tab_gp[kgp][k] = 0; + } + nelt[kgp] = 0; + + for (k = 0; k < nboite; k++) { + if (flag_gp[me][k] == kgp) flag_gp[me][k] = igp; + } + + } + m = 0; + for (k = 0; k < nelt[igp]; k++) { + if (tab_gp[igp][k] == i) m = 1; + } + + if (i >= nlocal || m == 1 ) continue; + // printf ("[me %d] igp %d - nelt %d atom %d\n",me,igp,nelt[igp],i); + tab_gp[igp][nelt[igp]] = i; + nelt[igp] += 1; + break; + } + + } // voisin j + + } // atom i + + /* ================================================== + Group Communication between proc for unification + ================================================== */ + for (i = 0; i < nproc; i++) { + forward_int(flag_gp[i]); reverse_int(flag_gp[i]); + } + + // =============== End of COMM ================= + + + for (i = 0; i < nboite; i++) { + + m = 10*me + flag_gp[me][i]; + if (m == 10*me) continue; // Pas de groupe zero + gptmp[m] = 1; + for (k = 0; k < nproc; k++) { + + if (k == me) continue; + if (tabtemp[m][k] != 0) continue; + + if (flag_gp[k][i] != 0) { + tabtemp[m][k] = 10*k + flag_gp[k][i]; + } + } + + } + + for (k = 0; k < 10*nproc; k++) { + MPI_Allreduce(tabtemp[k],Alltabtemp[k],nproc,MPI_INT,MPI_SUM,world); } + MPI_Allreduce(gptmp,Allgptmp,10*nproc,MPI_INT,MPI_SUM,world); + + nteam = 0; iproc = 0; + for (igp = 0; igp < 10*nproc; igp++) { + if (Allgptmp[igp] == 0) continue; + iproc = int(double(igp)/10.0); + ngp = igp - 10*iproc; + if (nteam == 0) { + + nteam += 1; + team_elt[nteam][iproc] = 0; + team_QEq[nteam][iproc][team_elt[nteam][iproc]] = ngp; + team_elt[nteam][iproc] += 1; + } else { + m = 0; + for (i = 1; i < nteam+1; i++) { + for (k = 0; k < team_elt[i][iproc]; k++) { + if (ngp == team_QEq[i][iproc][k]) m = 1; + } } + if (m == 1) continue; + // create a new team!! + // --------------------------- + if (m == 0) { + nteam += 1; + team_elt[nteam][iproc] = 0; + team_QEq[nteam][iproc][team_elt[nteam][iproc]] = ngp; + team_elt[nteam][iproc] += 1; + } + } + // ------- + // On a mis une graine dans le groupe et nous allons + // remplir se groupe en questionnant le "tabtemp[igp][iproc]=jgp" + // + for (kk = 0; kk < nproc; kk++) { + for (k = 0; k < team_elt[nteam][kk]; k++) { + + // On prend le gp le k ieme element de la team nteam sur le proc iproc + // ngp = 0; + ngp = team_QEq[nteam][kk][k]; + kgp = 10*kk + ngp; + + // On regarde sur les autre proc si ce gp ne pointe pas vers un autre. + for (i = 0; i < nproc; i++) { + if (i == kk) continue; + if (Alltabtemp[kgp][i] == 0) continue; + + if (Alltabtemp[kgp][i] != 0) ngp = Alltabtemp[kgp][i]; + ngp = ngp - 10*i; + + // Est ce que ce groupe est nouveau? + m = 0; + for (j = 0; j < team_elt[nteam][i]; j++) { + if (team_QEq[nteam][i][j] == ngp) m = 1; + } + + if (m == 0) { + iproc = i; k = 0; + team_QEq[nteam][i][team_elt[nteam][i]] = ngp ; + team_elt[nteam][i] += 1; + } + } // regard sur les autre proc + + } // On rempli de proche en proche + } // boucle kk sur les proc + } + + // Finalement on met le numero de la team en indice du flag_QEq, c mieu! + // --------------------------------------------------------------------- + + for (ii = 0; ii < inum; ii++) + { + i = ilist[ii]; m = 0; itype = map[type[i]]; + if (flag_QEq[i] == 0) continue; + + gp = flag_gp[me][i]; + for (j = 1; j <= nteam; j++) { + for (k = 0; k < team_elt[j][me]; k++) { + if (gp == team_QEq[j][me][k]) { + flag_QEq[i] = j; m = 1; + break; + } + } + if (m == 1) break; + } + } + + memory->destroy(tabtemp); + memory->destroy(Alltabtemp); + memory->destroy(gptmp); + memory->destroy(Allgptmp); + memory->destroy(flag_gp); + memory->destroy(tab_gp); + memory->destroy(nelt); + +} + +/* ---------------------------------------------------------------------- */ + +void PairSMTBQ::Init_charge(int *nQEq, int *nQEqa, int *nQEqc) +{ + int ii,i,gp,itype; + int *ilist,test[nteam],init[nteam]; + double bound,tot,totll; + + int inum = list->inum; + int *type = atom->type; + double *q = atom->q; + ilist = list->ilist; + + if (nteam == 0) return; + + if (me == 0) printf (" ======== Init_charge ======== \n"); + for (gp = 0; gp < cluster; gp++) { + test[gp] = 0; init[gp] = 0; + } + + + // On fait un test sur les charges pour voir sont + // elles sont dans le domaine delimiter par DeltaQ + // ------------------------------------------------- + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; itype = map[type[i]]; + gp = flag_QEq[i]; + + if (gp != 0 && itype == 0) { + bound = fabs(2.0*ncov/params[itype].sto - fabs(params[itype].qform)) ; + if (bound == fabs(params[itype].qform)) continue; + if (fabs(q[i]) < bound) test[gp] = 1; + } + } + + MPI_Allreduce(test,init,nteam+1,MPI_INT,MPI_SUM,world); + + // On fait que sur les atomes hybrides!!! + // ---------------------------------------- + + tot = totll = 0.0; + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; itype = map[type[i]]; + gp = flag_QEq[i]; + + if (gp != 0 && init[gp] != 0) { + if (itype == 0) q[i] = -1.96; + if (itype != 0) q[i] = 1.96 * double(nQEqaall[gp]) / double(nQEqcall[gp]); + } + tot += q[i]; + } + MPI_Allreduce(&tot,&totll,1,MPI_INT,MPI_SUM,world); + if (me == 0) printf (" === Fin de init_charge qtot %20.15f ====\n",totll); + +} +/* ---------------------------------------------------------------------- + * COMMUNICATION + * ---------------------------------------------------------------------- */ + +int PairSMTBQ::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) +{ + int i,j,m; + + m = 0; + for (i = 0; i < n; i ++) { + j = list[i]; + buf[m++] = tab_comm[j]; +// if (j < 3) printf ("[%d] %d pfc %d %d buf_send = %f \n",me,n,i,m-1,buf[m-1]); + } + return 1; +} + +/* ---------------------------------------------------------------------- */ + +void PairSMTBQ::unpack_forward_comm(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n ; + for (i = first; i < last; i++) { + tab_comm[i] = buf[m++]; +// if (inlocal; + int nghost = atom->nghost; + + for (i=0; iforward_comm_pair(this); + + for (i=0; inlocal; + int nghost = atom->nghost; + + for (i=0; ireverse_comm_pair(this); + + for (i=0; inlocal; + int nghost = atom->nghost; + + for (i=0; iforward_comm_pair(this); + + for (i=0; i 0.1) tab[i] = int(tab_comm[i]) ; } +} + +/* ---------------------------------------------------------------------- */ + +void PairSMTBQ::reverse_int(int *tab) +{ + int i; + int nlocal = atom->nlocal; + int nghost = atom->nghost; + + for (i=0; ireverse_comm_pair(this); + + for (i=0; i 0.1) tab[i] = int(tab_comm[i]); } +} + +/* ---------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- */ + +double PairSMTBQ::memory_usage() +{ + double bytes = maxeatom * sizeof(double); + bytes += maxvatom*6 * sizeof(double); + bytes += nmax * sizeof(int); + bytes += MAXNEIGH * nmax * sizeof(int); + return bytes; +} + +/* ---------------------------------------------------------------------- */ + +void PairSMTBQ::add_pages(int howmany) +{ + int toppage = maxpage; + maxpage += howmany*PGDELTA; + + pages = (int **) + memory->srealloc(pages,maxpage*sizeof(int *),"pair:pages"); + for (int i = toppage; i < maxpage; i++) + memory->create(pages[i],pgsize,"pair:pages[i]"); +} + +/* ---------------------------------------------------------------------- */ + + +int PairSMTBQ::Tokenize( char* s, char*** tok ) +{ + char test[MAXLINE]; + const char *sep = "' "; + char *mot; + int count=0; + mot = NULL; + + + strncpy( test, s, MAXLINE ); + + for( mot = strtok(test, sep); mot; mot = strtok(NULL, sep) ) { + strncpy( (*tok)[count], mot, MAXLINE ); + count++; + } + + return count; +} + + + +void PairSMTBQ::CheckEnergyVSForce() +{ + double drL,iq,jq,rsq,evdwlCoul,fpairCoul,eflag,ErepR,frepR,fpair,evdwl; + int i,j,iiiMax,iii,iCoord; + int itype,jtype,l,m; + double r,t1,t2,sds,xi,engSurf,fforceSurf; + double eng,fforce,engBB,fforceBB; + + double za,zb,gam,dgam,dza,dzb, + d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2,na,nb; + int *type = atom->type; + char *NameFile; + + + i=0; + j=1; + map[type[i]]=0; //ox + itype=map[type[i]]; + iq=-1; + + + map[type[j]]=0; //ox + jtype=map[type[j]]; + jq=-1; + coord[i]=coordOxBulk; + coord[j]=coordOxBulk; + m = intype[itype][jtype]; + + + na = params[itype].ne ; + nb = params[jtype].ne ; + za = params[itype].dzeta ; + zb = params[jtype].dzeta ; + + + // Ouverture du fichier + + for (iCoord=1;iCoord<5; iCoord++) + { + + if (iCoord==1) + {coord[i]=2.2; + coord[j]=2.1; + NameFile="energyandForceOxOxUnderCoord.txt"; + } + if (iCoord==2) + {coord[i]=coordOxBulk; + coord[j]=coordOxBulk; + NameFile="energyandForceOxOxCoordBulk.txt"; + } + if (iCoord==3) + {coord[i]=3.8; + coord[j]=4; + NameFile="energyandForceOxOxOverCoord.txt"; + } + if (iCoord==4) + {coord[i]=2.2; + coord[j]=3.5; + NameFile="energyandForceOxOxUnderOverCoord.txt"; + } + + + ofstream fichierOxOx(NameFile, ios::out | ios::trunc) ; + + drL=0.0001; + iiiMax=int((cutmax-1.2)/drL); + for (iii=1; iii< iiiMax ; iii++){ + r=1.2+drL*iii; + rsq=r*r; + evdwlCoul = 0.0 ; fpairCoul = 0.0; + potqeq(i,j,iq,jq,rsq,fpairCoul,eflag,evdwlCoul); + fpairCoul=fpairCoul*r; + + rep_OO (&intparams[m],rsq,fpair,eflag,evdwl); + ErepR = evdwl; + frepR= fpair*r; + + gam = dgam = dza = dzb = d2zaa = d2zab = + d2zbb = d2zra = d2zrb = d2gamr2 = 0.0 ; + + +// gammas_(na,nb,za,zb,r,gam,dgam,dza,dzb, +// d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2) ; + gammas(na,nb,za,zb,r,gam,dgam,dza,dzb, + d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2) ; + + + sds = rsq/ds ; l = int(sds) ; + xi = sds - double(l) ; + + + t1 = fafb[l][m] + (fafb[l+1][m] - fafb[l][m])*xi; + t2 = fafb[l+1][m] + (fafb[l+2][m] - fafb[l+1][m])*(xi-1.0); + eng = iq*jq*(t1 + (t2 - t1)*xi/2.0); + + t1 = dfafb[l][m] + (dfafb[l+1][m] - dfafb[l][m])*xi; + t2 = dfafb[l+1][m] + (dfafb[l+2][m] - dfafb[l+1][m])*(xi-1); + fforce = - iq*jq*(t1 + (t2 - t1)*xi/2.0)*r ; + + + t1 = fafbOxOxSurf[l] + (fafbOxOxSurf[l+1] - fafbOxOxSurf[l])*xi; + t2 = fafbOxOxSurf[l+1] + (fafbOxOxSurf[l+2] - fafbOxOxSurf[l+1])*(xi-1.0); + engSurf = iq*jq*(t1 + (t2 - t1)*xi/2.0); + + t1 = fafbOxOxBB[l] + (fafbOxOxBB[l+1] - fafbOxOxBB[l])*xi; + t2 = fafbOxOxBB[l+1] + (fafbOxOxBB[l+2] - fafbOxOxBB[l+1])*(xi-1.0); + engBB = iq*jq*(t1 + (t2 - t1)*xi/2.0); + + t1 = dfafbOxOxSurf[l] + (dfafbOxOxSurf[l+1] - dfafbOxOxSurf[l])*xi; + t2 = dfafbOxOxSurf[l+1] + (dfafbOxOxSurf[l+2] - dfafbOxOxSurf[l+1])*(xi-1); + fforceSurf = - iq*jq*(t1 + (t2 - t1)*xi/2.0)*r ; + + t1 = dfafbOxOxBB[l] + (dfafbOxOxBB[l+1] - dfafbOxOxBB[l])*xi; + t2 = dfafbOxOxBB[l+1] + (dfafbOxOxBB[l+2] - dfafbOxOxBB[l+1])*(xi-1); + fforceBB = - iq*jq*(t1 + (t2 - t1)*xi/2.0)*r ; + + if (fichierOxOx) { fichierOxOx<< setprecision (9) <= 1; i--) { + rtrm=rtrm*halfr; + drtrm=drtrm*halfr; + ztrm=ztrm*2.0*zb; + ctrm=ztrm/factorial(nb2-i); + + css(ss,na2-1,nb2-i,z2ra,z2rb,r,deriv,dzeta1,dzeta2, + d2zeta11,d2zeta12,d2zeta22,d2zeta1r,d2zeta2r,deriv2); + + trm1=float(i)*ctrm; + trm2=trm1*rtrm; + gam=gam-trm2*ss; + trm3=trm1*float(na2+nb2-i)*drtrm; + dgam=dgam-trm2*deriv-0.5*trm3*ss; + d2gamr2=d2gamr2-trm2*deriv2-trm3*deriv-0.5*trm3*float(na2+nb2-i-1)*ss/r; + dza=dza-trm2*dzeta1; + dzb=dzb-(trm2/zb)*((float(nb2-i))*ss+zb*dzeta2); + d2zaa=d2zaa-trm2*d2zeta11; + d2zab=d2zab-(trm2/zb)*((float(nb2-i))*dzeta1+zb*d2zeta12); + d2zbb=d2zbb-(trm2/zb)*(2.0*(float(nb2-i))*dzeta2+zb*d2zeta22 + + (float((nb2-i-1)*(nb2-i))*ss/zb)); + d2zra=d2zra-trm2*d2zeta1r-0.5*trm3*dzeta1; + d2zrb=d2zrb-(trm2/zb)*((float(nb2-i))*deriv+zb*d2zeta2r) - + 0.5*(trm3/zb)*((float(nb2-i))*ss+zb*dzeta2); + } + +// Multiply by coefficients + + trm3=pow(2.0*za,na2+1)/factorial(na2); + gam=gam*trm3; + dgam=dgam*trm3; + rfct1=((float(na2+1))/za); + rgam1=rfct1*gam; + dza=dza*trm3; + rdza1=2.0*rfct1*dza; + dza=dza+rgam1; + dzb=dzb*trm3; + rgam2=rgam1*float(na2)/za; + d2zaa=d2zaa*trm3+rgam2+rdza1; + d2zab=d2zab*trm3+rfct1*dzb; + d2zbb=d2zbb*trm3; + d2zra=d2zra*trm3+rfct1*dgam; + d2zrb=d2zrb*trm3; + d2gamr2=d2gamr2*trm3; + return; + + } +/* -------------------------------------------------------------------------------- + Css + -------------------------------------------------------------------------------- */ +void PairSMTBQ::css(double &s, double nn1, double nn2, double alpha, double beta, double r, + double &deriv, double &dzeta1, double &dzeta2, double &d2zeta11, double &d2zeta12, + double &d2zeta22, double &d2zeta1r, double &d2zeta2r, double &deriv2) +{ +// implicit real (a-h,o-z) +// common /fctrl/ fct(30) // A RAJOUTER DANS Pair_SMTBQ.h +/* ------------------------------------------------------------------ + Modified integral calculation routine for Slater orbitals + including derivatives. This version is for S orbitals only. + + dzeta1 and dzeta2 are the first derivatives with respect to zetas + and d2zeta11/d2zeta12/d2zeta22 are the second. + d2zeta1r and d2zeta2r are the mixed zeta/r second derivatives + deriv2 is the second derivative with respect to r + + Julian Gale, Imperial College, December 1997 + ------------------------------------------------------------------- */ + int i,i1,nni1; //ulim + double ulim,n1,n2,p,pt,x,k,dpdz1,dpdz2,dptdz1,dptdz2,dpdr,dptdr,d2pdz1r, + d2pdz2r,d2ptdz1r,d2ptdz2r,zeta1,zeta2,sumzeta,difzeta,coff; + + double da1[30],da2[30],db1[30],db2[30]; + double d2a11[30],d2a12[30],d2a22[30],dar[30]; + double d2b11[30],d2b12[30],d2b22[30],dbr[30]; + double d2a1r[30],d2a2r[30],d2b1r[30],d2b2r[30]; + double d2ar2[30],d2br2[30]; + + double *a,*b; + memory->create(a,31,"pair:a"); + memory->create(b,31,"pair:a"); + + +// Set up factorials - stored as factorial(n) in location(n+1) + + for (i = 1; i <= 30; i++) { + fct[i]=factorial(i-1); + } + dzeta1=0.0; + dzeta2=0.0; + d2zeta11=0.0; + d2zeta12=0.0; + d2zeta22=0.0; + d2zeta1r=0.0; + d2zeta2r=0.0; + deriv=0.0; + deriv2=0.0; + n1=nn1; + n2=nn2; + p =(alpha + beta)*0.5; + pt=(alpha - beta)*0.5; + x = 0.0; + zeta1=alpha/r; + zeta2=beta/r; + sumzeta=zeta1+zeta2; + difzeta=zeta1-zeta2; + +// Partial derivative terms for zeta derivatives + + dpdz1=r; + dpdz2=r; + dptdz1=r; + dptdz2=-r; + dpdr=0.5*sumzeta; + dptdr=0.5*difzeta; + d2pdz1r=1.0; + d2pdz2r=1.0; + d2ptdz1r=1.0; + d2ptdz2r=-1.0; + +// Reverse quantum numbers if necessary - +// also change the sign of difzeta to match +// change in sign of pt + + if (n2 < n1) { + k = n1; + n1= n2; + n2= k; + pt=-pt; + difzeta=-difzeta; + dptdr=-dptdr; + dptdz1=-dptdz1; + dptdz2=-dptdz2; + d2ptdz1r=-d2ptdz1r; + d2ptdz2r=-d2ptdz2r; + } + +// Trap for enormously long distances which would cause +// caintgs or cbintgs to crash with an overflow + + if (p > 86.0 || pt > 86.0) { + s=0.0; + return; + } +//*************************** +// Find a and b integrals * +//*************************** + caintgs(p,n1+n2+3,a); + cbintgs(pt,n1+n2+3,b); + +// Convert derivatives with respect to p and pt +// into derivatives with respect to zeta1 and +// zeta2 + + ulim=n1+n2+1; + for (i = 1; i <= int(ulim); i++) { + da1[i]=-a[i+1]*dpdz1; + da2[i]=-a[i+1]*dpdz2; + db1[i]=-b[i+1]*dptdz1; + db2[i]=-b[i+1]*dptdz2; + d2a11[i]=a[i+2]*dpdz1*dpdz1; + d2a12[i]=a[i+2]*dpdz1*dpdz2; + d2a22[i]=a[i+2]*dpdz2*dpdz2; + d2b11[i]=b[i+2]*dptdz1*dptdz1; + d2b12[i]=b[i+2]*dptdz1*dptdz2; + d2b22[i]=b[i+2]*dptdz2*dptdz2; + dar[i]=-a[i+1]*dpdr; + dbr[i]=-b[i+1]*dptdr; + d2a1r[i]=a[i+2]*dpdz1*dpdr-a[i+1]*d2pdz1r; + d2a2r[i]=a[i+2]*dpdz2*dpdr-a[i+1]*d2pdz2r; + d2b1r[i]=b[i+2]*dptdz1*dptdr-b[i+1]*d2ptdz1r; + d2b2r[i]=b[i+2]*dptdz2*dptdr-b[i+1]*d2ptdz2r; + d2ar2[i]=a[i+2]*dpdr*dpdr; + d2br2[i]=b[i+2]*dptdr*dptdr; + } + +// Begin section used for overlap integrals involving s functions + + for (i1 = 1; i1 <= int(ulim); i1++) { + nni1=n1+n2-i1+2; + coff=coeffs(n1,n2,i1-1); + deriv=deriv+coff*(dar[i1]*b[nni1]+a[i1]*dbr[nni1]); + x=x+coff*a[i1]*b[nni1]; + dzeta1=dzeta1+coff*(da1[i1]*b[nni1]+a[i1]*db1[nni1]); + dzeta2=dzeta2+coff*(da2[i1]*b[nni1]+a[i1]*db2[nni1]); + d2zeta11=d2zeta11+coff*(d2a11[i1]*b[nni1]+a[i1]*d2b11[nni1]+ + 2.0*da1[i1]*db1[nni1]); + d2zeta12=d2zeta12+coff*(d2a12[i1]*b[nni1]+a[i1]*d2b12[nni1]+ + da1[i1]*db2[nni1]+da2[i1]*db1[nni1]); + d2zeta22=d2zeta22+coff*(d2a22[i1]*b[nni1]+a[i1]*d2b22[nni1]+ + 2.0*da2[i1]*db2[nni1]); + d2zeta1r=d2zeta1r+coff*(d2a1r[i1]*b[nni1]+dar[i1]*db1[nni1]+ + da1[i1]*dbr[nni1]+a[i1]*d2b1r[nni1]); + d2zeta2r=d2zeta2r+coff*(d2a2r[i1]*b[nni1]+dar[i1]*db2[nni1]+ + da2[i1]*dbr[nni1]+a[i1]*d2b2r[nni1]); + deriv2=deriv2+coff*(d2ar2[i1]*b[nni1]+a[i1]*d2br2[nni1]+ + 2.0*dar[i1]*dbr[nni1]); + } + s=x*0.5; + deriv=0.5*deriv; + deriv2=0.5*deriv2; + dzeta1=0.5*dzeta1; + dzeta2=0.5*dzeta2; + d2zeta11=0.5*d2zeta11; + d2zeta12=0.5*d2zeta12; + d2zeta22=0.5*d2zeta22; + d2zeta1r=0.5*d2zeta1r; + d2zeta2r=0.5*d2zeta2r; + + memory->destroy(a); + memory->destroy(b); + + return; +} +/* ------------------------------------------------------------------------------- + coeffs + ------------------------------------------------------------------------------- */ + double PairSMTBQ::coeffs(int na, int nb, int k) + { + // implicit real (a-h,o-z) + // common /fctrl/ fct(30) + + int il,lie,je,ia,i,j,ie,l; + double coeffs; + +// Statement function +// binm(n,i)=fct(n+1)/(fct(n-i+1)*fct(i+1)); + + coeffs=0.0; + l=na+nb-k; + ie=min(l,na)+1; + je=min(l,nb); + ia=l-je+1; + for (il = ia; il <= ie; il++) { + i=il-1; + j=l-i; // D'ou vient le i + coeffs=coeffs + binm(na,i)*binm(nb,j)*pow(-1.,j); + } + return coeffs; + } + +// ============================================ + +double PairSMTBQ::binm(int n, int i) +{ + return fct[n+1]/(fct[n-i+1]*fct[i+1]); +} + +/* --------------------------------------------------------------------------------- + Caintgs + -------------------------------------------------------------------------------- */ + void PairSMTBQ::caintgs (double x, int k, double *a) + { +// implicit real (a-h,o-z) +// dimension a(30) + int i; + double cste,rx; + + cste=exp(-x); + rx=1.0/x; + a[1]=cste*rx; + for (i = 1; i <= k; i++) { + a[i+1]=(a[i]*float(i)+cste)*rx; + } + return; + } +/* ----------------------------------------------------------------------------------- + Cbintgs + ----------------------------------------------------------------------------------- */ +void PairSMTBQ::cbintgs( double x, int k, double *b) +{ +// implicit real (a-h,o-z) +/* ******************************************************************* +! Fills array of b-integrals. note that b(i) is b(i-1) in the +! usual notation +! for x.gt.3 exponential formula is used +! for 2.lt.x.le.3 and k.le.10 exponential formula is used +! for 2.lt.x.le.3 and k.gt.10 15 term series is used +! for 1.lt.x .e.2 and k.le.7 exponential formula is used +! for 1.lt.x.le.2 and k.gt.7 12 term series is used +! for .5.lt.x.le.1 and k.le.5 exponential formula is used +! for .5.lt.x.le.1 and k.gt.5 7 term series is used +! for x.le..5 6 term series is used +!******************************************************************* */ +// dimension b(30) +// common /fctrl/ fct(30) + + int i0,m,last,i; + double absx,expx,expmx,ytrm,y,rx; + + i0=0; + absx=fabs(x); + + if (absx > 3.0) goto g120; + if (absx > 2.0) goto g20; + if (absx > 1.0) goto g50; + if (absx > 0.5) goto g80; + if (absx > 1.0e-8) goto g110; + goto g170; + g110: last=6; + goto g140; + g80: if (k <= 5) goto g120; + last=7; + goto g140; + g50: if (k <= 7) goto g120; + last=12; + goto g140; + g20: if (k <= 10) goto g120; + last=15; + goto g140; + + g120: expx=exp(x); + expmx=1./expx; + rx=1.0/x; + b[1]=(expx-expmx)*rx; + for (i = 1; i <= k ; i++) { + b[i+1]=(float(i)*b[i]+ pow(-1.0,i)*expx-expmx)*rx; + } + goto g190; +// +// Series to calculate b(i) +// + g140: for (i = i0; i <= k ; i++) { + y=0.; + for (m = i0; m <= last; m++) { + ytrm = pow(-x,m-1)*(1. - pow(-1.,m+i+1))/(fct[m+1]*float(m+i+1)); + y = y + ytrm*(-x); + } + b[i+1] = y; + } + goto g190; +// +// x extremely small +// + g170: for (i = i0; i <= k; i++) { + b[i+1] = (1.-pow(-1.,i+1))/float(i+1); + } + g190: + return; + } +/* ------------------------------------------------------------------------------------ + Factorial + ------------------------------------------------------------------------------------ */ +double PairSMTBQ::factorial(double n) +{ +// implicit real(a-h,o-z) + double rn,factorial; + int i; + +// +// Calculates the factorial of an integer n +// + rn = n; + if (n <= 1.) { + factorial=1.0; + return factorial; + } + factorial=1.0; + for (i = 2; i <= int(n); i++) { + factorial = factorial*float(i); + } + return factorial; +} + + +/* ============================== This is the END... ================================== */ diff --git a/src/USER-SMTBQ/pair_smtbq.h b/src/USER-SMTBQ/pair_smtbq.h new file mode 100644 index 0000000000..2a1dc3bb8a --- /dev/null +++ b/src/USER-SMTBQ/pair_smtbq.h @@ -0,0 +1,197 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(smtbq,PairSMTBQ) + +#else + +#ifndef LMP_PAIR_SMTBQ_H +#define LMP_PAIR_SMTBQ_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairSMTBQ : public Pair { + public: + PairSMTBQ(class LAMMPS *); + virtual ~PairSMTBQ(); + virtual void compute(int, int); + + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + double memory_usage(); + + +protected: + struct Param { + double sto,n0,ne,chi,dj; + double R,dzeta; //Rayon slater + double cutsq; + double qform, masse; // Charge formelle + char *nom; + }; + + struct Intparam { + double a,p,ksi,q,r0,dc1,dc2; + double abuck,rhobuck,neig_cut,aOO,bOO,r1OO,r2OO; + char *typepot,*mode; + int intsm; + }; + + double rmin,dr,ds; // table parameter + int kmax; + int Qstep; // Frenquence of charge resolution + double precision; // acurate of convergence + int loopmax; // max of interation + + double cutmax; // max cutoff for all elements + int nelements; // # of unique elements + char **elements; // names of unique elements + char *QEqMode; // name of QEqMode + char *Bavard; // Verbose parameter + char *writepot; // write or not the electronegativity component + char *writeenerg; // write or not the energy component + char *QInitMode; // mode of initialization of charges + double zlim1QEq; // z limit for QEq equilibration + double zlim2QEq; // z limit for QEq equilibration + double QOxInit; // Initial charge for oxygen atoms (if the charge is not specified) + int *map; // mapping from atom types to elements + int nparams; // # of stored parameter sets + int maxparam; // max # of parameter sets + int maxintparam; // max # of interaction sets + int maxintsm; // max # of interaction SM + double r1Coord,r2Coord; + Param *params; // parameter set for an I atom + Intparam *intparams; // parameter set for an I interaction + + int nmax,*nQEqall,*nQEqaall,*nQEqcall; + double *qf,*q1,*q2,Nevery,Neverypot; + +// Coulombian interaction + double *esm, **fafb, **dfafb, *fafbOxOxSurf, *dfafbOxOxSurf, *fafbTiOxSurf,*dfafbTiOxSurf; + double *potqn, *dpotqn, Vself, *Zsm,*coord, *fafbOxOxBB, *dfafbOxOxBB,*fafbTiOxBB, *dfafbTiOxBB ; + int **intype, **coultype; + int *NCo; + double coordOxBulk,coordOxSurf,ROxSurf,coordOxBB,ROxBB; + +// Covalent interaction + double *ecov, *potmad, *potself, *potcov, *chimet; + double **tabsmb,**dtabsmb, **tabsmr, **dtabsmr, *sbcov, *sbmet; + double ncov; + +// Neighbor Table + int nteam,cluster,*hybrid; + int *nvsm, **vsm, *flag_QEq; + +// Parallelisation + int me, nproc; + double *tab_comm; + +// GAMMAS function + double *fct; + +// HERE its routines +// ===================================== + void allocate(); + virtual void read_file(char *); + + void tabsm(); + void tabqeq(); + + void potqeq(int, int, double, double, double, + double &, int, double &); + void pot_ES (int, int, double, double &); + void pot_ES2 (int, int, double, double &); + + double self(Param *, double); + double qfo_self(Param *, double); + + virtual void repulsive(Intparam *, double, int, int, double &, int, double &); + virtual void rep_OO (Intparam *, double, double &, int, double &); + virtual void Attr_OO (Intparam *, double, double &, int, double &); + virtual void attractive(Intparam *, double, int, int, double, int, double ); + void f_att(Intparam *, int, int, double, double &) ; + void pot_COV(Param *, int, double &); + double potmet(Intparam *, double, int, double, int, double); + + double fcoupure(double, double, double); + double fcoupured(double, double, double); + + double fcoup2(double, double, double); + double Intfcoup2(double, double, double); + double Primfcoup2(double, double, double); + + void groupBulkFromSlab_QEq(); + void groupQEqAllParallel_QEq(); + void groupQEqAll_QEq(); + void groupSurface_QEq(); + void QForce_charge(int); + void Charge(); + void Init_charge(int*, int*, int*); + void CheckEnergyVSForce(); + +// =========================================== +// Communication pack + int pack_forward_comm (int, int*, double*, int, int*); + void unpack_forward_comm (int, int, double*); + int pack_reverse_comm (int, int, double*); + void unpack_reverse_comm (int, int*, double*); + void forward (double*); void reverse (double*); + void forward_int (int*); void reverse_int (int*); + + int Tokenize( char* , char*** ); + + inline double vec3_dot(const double x[3], const double y[3]) const { + return x[0]*y[0] + x[1]*y[1] + x[2]*y[2]; + } + + template const T& min ( const T& a, const T& b ) { + return !(b Date: Thu, 22 Oct 2015 23:03:43 +0000 Subject: [PATCH 11/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14173 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/USER-OMP/respa_omp.cpp | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/src/USER-OMP/respa_omp.cpp b/src/USER-OMP/respa_omp.cpp index f5603adf92..e3e425a77f 100644 --- a/src/USER-OMP/respa_omp.cpp +++ b/src/USER-OMP/respa_omp.cpp @@ -74,17 +74,6 @@ void RespaOMP::setup() fprintf(screen," Unit style : %s\n", update->unit_style); fprintf(screen," Current step : " BIGINT_FORMAT "\n", update->ntimestep); fprintf(screen," OuterTime step: %g\n", update->dt); - if (update->max_wall > 0) { - char outtime[128]; - double totalclock = update->max_wall; - int seconds = fmod(totalclock,60.0); - totalclock = (totalclock - seconds) / 60.0; - int minutes = fmod(totalclock,60.0); - int hours = (totalclock - minutes) / 60.0; - sprintf(outtime," Max walltime: " - "%d:%02d:%02d\n", hours, minutes, seconds); - fputs(outtime,screen); - } } update->setupflag = 1; From f8d13ac85323f098a2d8f67fa6b6d48420a989f8 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 22 Oct 2015 23:36:53 +0000 Subject: [PATCH 12/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14174 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- examples/USER/mgpt/Ta6.8x.mgpt.README | 57 + examples/USER/mgpt/Ta6.8x.mgpt.parmin | 2 + examples/USER/mgpt/Ta6.8x.mgpt.potin | 11253 ++++++++++++++++++++++++ examples/USER/mgpt/in.bcc0 | 68 + examples/USER/mgpt/in.vac0-bcc | 76 + examples/USER/mgpt/in.vacmin-bcc | 71 + examples/USER/mgpt/log.bcc0 | 53 + examples/USER/mgpt/log.lammps | 78 + examples/USER/mgpt/log.vac0-bcc | 55 + examples/USER/mgpt/log.vacmin-bcc | 78 + 10 files changed, 11791 insertions(+) create mode 100644 examples/USER/mgpt/Ta6.8x.mgpt.README create mode 100644 examples/USER/mgpt/Ta6.8x.mgpt.parmin create mode 100644 examples/USER/mgpt/Ta6.8x.mgpt.potin create mode 100644 examples/USER/mgpt/in.bcc0 create mode 100644 examples/USER/mgpt/in.vac0-bcc create mode 100644 examples/USER/mgpt/in.vacmin-bcc create mode 100644 examples/USER/mgpt/log.bcc0 create mode 100644 examples/USER/mgpt/log.lammps create mode 100644 examples/USER/mgpt/log.vac0-bcc create mode 100644 examples/USER/mgpt/log.vacmin-bcc diff --git a/examples/USER/mgpt/Ta6.8x.mgpt.README b/examples/USER/mgpt/Ta6.8x.mgpt.README new file mode 100644 index 0000000000..5b26939ee2 --- /dev/null +++ b/examples/USER/mgpt/Ta6.8x.mgpt.README @@ -0,0 +1,57 @@ +MGPT multi-ion potentials: Ta6.8x (Ta, version 6.8x) + +Author: John A. Moriarty + +Potential data files: Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin + +Volume mesh for potential data, with x = (vol/vol0)**(1/3): + + + x vol/vol0 vol(au) rws(au) dens(g/cc) dens/dens0 + + 1.080 1.260 153.181 3.31924 13.237 0.794 + 1.070 1.225 148.965 3.28851 13.612 0.816 + 1.060 1.191 144.828 3.25777 14.001 0.840 + 1.050 1.158 140.767 3.22704 14.405 0.864 + 1.040 1.125 136.783 3.19631 14.824 0.889 + 1.030 1.093 132.876 3.16557 15.260 0.915 + 1.020 1.061 129.043 3.13484 15.714 0.942 + 1.010 1.030 125.285 3.10410 16.185 0.971 + 1.000 1.000 121.600 3.07337 16.675 1.000 + 0.990 0.970 117.988 3.04264 17.186 1.031 + 0.980 0.941 114.449 3.01190 17.717 1.062 + 0.970 0.913 110.981 2.98117 18.271 1.096 + 0.960 0.885 107.584 2.95044 18.848 1.130 + 0.950 0.857 104.257 2.91970 19.449 1.166 + 0.940 0.831 100.999 2.88897 20.077 1.204 + 0.930 0.804 97.810 2.85824 20.731 1.243 + 0.920 0.779 94.688 2.82750 21.415 1.284 + 0.910 0.754 91.634 2.79677 22.128 1.327 + 0.900 0.729 88.646 2.76603 22.874 1.372 + 0.890 0.705 85.724 2.73530 23.654 1.419 + 0.880 0.681 82.867 2.70457 24.470 1.467 + 0.870 0.659 80.074 2.67383 25.323 1.519 + 0.860 0.636 77.344 2.64310 26.217 1.572 + 0.850 0.614 74.678 2.61237 27.153 1.628 + 0.840 0.593 72.073 2.58163 28.134 1.687 + 0.830 0.572 69.529 2.55090 29.164 1.749 + 0.820 0.551 67.046 2.52016 30.244 1.814 + 0.810 0.531 64.623 2.48943 31.378 1.882 + 0.800 0.512 62.259 2.45870 32.569 1.953 + +Corresponding T = 0 bcc pressure range: -30 GPa to 422 GPa + + +General references to MGPT potentials: + + J. A. Moriarty, Phys. Rev. B 42, 1609 (1990) and 49, 12431 (1994). + + J. A. Moriarty, L. X. Benedict, J. N. Glosli, R. Q. Hood, D. A. Orlikowski, M. V. Patel, + P. Soderlind, F. H. Streitz, M. Tang, and L. H. Yang, J. Mater. Res. 21, 563 (2006). + + +Specific references to Ta6.8x potentials: + + J. A. Moriarty and J. B. Haskins, Phys. Rev. B 90, 054113 (2014). + + J. B. Haskins, J. A. Moriarty, and R. Q. Hood, Phys. Rev. B 86, 224104 (2012). diff --git a/examples/USER/mgpt/Ta6.8x.mgpt.parmin b/examples/USER/mgpt/Ta6.8x.mgpt.parmin new file mode 100644 index 0000000000..39517f112b --- /dev/null +++ b/examples/USER/mgpt/Ta6.8x.mgpt.parmin @@ -0,0 +1,2 @@ + 0.80 1.08 0.01 121.60 + 6.00 -4.00 1.00 0.00 2 diff --git a/examples/USER/mgpt/Ta6.8x.mgpt.potin b/examples/USER/mgpt/Ta6.8x.mgpt.potin new file mode 100644 index 0000000000..9c014000a4 --- /dev/null +++ b/examples/USER/mgpt/Ta6.8x.mgpt.potin @@ -0,0 +1,11253 @@ +# DATE: 2015-07-30 CONTRIBUTOR: John Moriarty moriarty2@llnl.gov CITATION: see Ta6.8x.mgpt.README in potentials directory + ta 0 4 0.00000 + 2.00000E+00 1.53181E+02 3.31924E+00 1.80948E+02 + 2.15000E+00 7.50000E+01 2.75000E+00 4.25000E+00 + 3.80000E+00 1.00000E-05 -3.65805E-01 -2.92162E-03 -2.44225E-01 + 3.11534E-04 3.79378E-02 -4.86257E-03 1.69740E-03 3.51980E-03 + -2.94905E+01 9.66935E-01 1.08166E+01 6.76695E+00 1.99299E-01 + 2.00000E+00 2.10000E+01 5.00000E-02 + 2.00 2.213039E+01 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eos in bulk bcc structure + +echo screen + +units electron +atom_style atomic + +# Atomic volume for MGPT potential in a.u. +variable atomic_vol equal 121.6 + +# Derive lattice constant from volume +variable lattice_constant equal (${atomic_vol}*2.0)^(1.0/3.0) + +# Create bcc lattice with 5x5x5 unit cells (250 atoms) +lattice bcc ${lattice_constant} +region box block 0 5 0 5 0 5 +create_box 1 box +create_atoms 1 box + +# Define potential for use in simulation +pair_style mgpt + +# Set parameters for potential: +# parameter files atomic volume +#pair_coeff * * parmin potin ${atomic_vol} +pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol} + +# Create velocities at 0 K +velocity all create 0.0 87287 + +# Set neighbor list parameters +neighbor 0.1 bin +neigh_modify every 1 delay 0 check yes + +# Set up microcanonical integrator +fix 1 all nve + +# Dump coordinates to file every 50 timesteps +dump id all atom 50 dump.bcc0 + +# Output thermodynamical data every 10 timesteps +thermo 10 + +# Set output quantities and output format +thermo_style custom step vol temp pe etotal press + +## Example: Output floating point number with 5 digits exponential notation. +#thermo_modify format float %15.5e + +# Run 0 timesteps +run 0 + +# Convert energy to rydbergs and pressure to gpa + +variable natoms equal "count(all)" +variable voltot equal "vol" +variable atvol equal "v_voltot/v_natoms" +variable etot equal "2.0*pe" +variable etotry equal "v_etot/v_natoms" +variable ptot equal "press" +variable ptotgpa equal "v_ptot/1.0e+09" + +print "number of atoms = ${natoms}" +print "atomic volume (a.u.) = ${atvol}" +print "total energy (ry/atom) = ${etotry}" +print "pressure (gpa) = ${ptotgpa}" +print "${natoms} ${atvol} ${etot} ${ptotgpa}" +print "${atvol} ${etotry} ${ptotgpa}" diff --git a/examples/USER/mgpt/in.vac0-bcc b/examples/USER/mgpt/in.vac0-bcc new file mode 100644 index 0000000000..529506ab64 --- /dev/null +++ b/examples/USER/mgpt/in.vac0-bcc @@ -0,0 +1,76 @@ +# script for mgpt t=0 eos with unrelaxed vacancy in bcc lattice: +# input for unrelaxed vacancy formation energy at constant atomic volume + +echo screen + +units electron +atom_style atomic + +# Atomic volume for MGPT potential in a.u. +variable atomic_vol equal 121.6 + +# Derive effective lattice volume from atomic volume for 249-site cell +variable lat_vol equal ${atomic_vol}*249/250 + +# Derive lattice constant from lattice volume +variable lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0) + +# Create bcc lattice with 5x5x5 unit cells (250 atoms) +lattice bcc ${lattice_constant} +region box block 0 5 0 5 0 5 +create_box 1 box +create_atoms 1 box + +# Remove central atom from bcc lattice to create vacancy +region vacancy sphere 2.5 2.5 2.5 0.1 units lattice +delete_atoms region vacancy + +# Define potential for use in simulation +pair_style mgpt + +# Set parameters for potential: +# parameter files atomic volume +#pair_coeff * * parmin potin ${atomic_vol} +pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol} + +# Create velocities at 0 K +velocity all create 0.0 87287 + +# Set neighbor list parameters +neighbor 0.1 bin +neigh_modify every 1 delay 0 check yes + +# Set up microcanonical integrator +fix 1 all nve + +# Dump coordinates to file every 50 timesteps +dump id all atom 50 dump.vac0-bcc + +# Output thermodynamical data every 10 timesteps +thermo 10 + +# Set output quantities and output format +thermo_style custom step vol temp pe etotal press + +## Example: Output floating point number with 5 digits exponential notation. +#thermo_modify format float %15.5e + +# Run 0 timesteps +run 0 + +# Convert energy to rydbergs and pressure to gpa + +variable natoms equal "count(all)" +variable voltot equal "vol" +variable atvol equal "v_voltot/v_natoms" +variable etot equal "2.0*pe" +variable etotry equal "v_etot/v_natoms" +variable ptot equal "press" +variable ptotgpa equal "v_ptot/1.0e+09" + +print "number of atoms = ${natoms}" +print "atomic volume (a.u.) = ${atvol}" +print "total energy (ry/atom) = ${etotry}" +print "pressure (gpa) = ${ptotgpa}" +print "${natoms} ${atvol} ${etot} ${ptotgpa}" +print "${atvol} ${etotry} ${ptotgpa}" diff --git a/examples/USER/mgpt/in.vacmin-bcc b/examples/USER/mgpt/in.vacmin-bcc new file mode 100644 index 0000000000..85fc72ff63 --- /dev/null +++ b/examples/USER/mgpt/in.vacmin-bcc @@ -0,0 +1,71 @@ +# script for mgpt t=0 eos with relaxed vacancy in bcc structure: +# input for relaxed vacancy formation energy at constant pressure + +echo screen + +units electron +atom_style atomic + +# Atomic volume for MGPT potential +variable atomic_vol equal 121.863 + +# Derive effective lattice volume from atomic volume for 249-site cell +variable lat_vol equal ${atomic_vol}*249/250 + +# Derive lattice constant from lattice volume +variable lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0) + +# Create bcc lattice with 5x5x5 unit cells (250 atoms) +lattice bcc ${lattice_constant} +region box block 0 5 0 5 0 5 +create_box 1 box +create_atoms 1 box + +# Remove central atom from bcc lattice to create vacancy +region vacancy sphere 2.5 2.5 2.5 0.1 units lattice +delete_atoms region vacancy + +# Define potential for use in simulation +pair_style mgpt + +# Set parameters for potential: +# parameter files atomic volume +#pair_coeff * * parmin potin ${atomic_vol} +pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol} + +# Set neighbor list parameters +neighbor 0.1 bin +neigh_modify every 1 delay 0 check yes + +# Dump coordinates to file every 50 timesteps +dump id all atom 50 dump.vacmin-bcc + +# Output thermodynamical data every 10 timesteps +thermo 10 + +# Set output quantities and output format +thermo_style custom step vol temp pe etotal press + +## Example: Output floating point number with 5 digits exponential notation. +#thermo_modify format float %15.5e + +# minimize total energy +min_style cg +minimize 1.0e-10 1.0e-10 5000 10000 + +# Convert energy to rydbergs and pressure to gpa + +variable natoms equal "count(all)" +variable voltot equal "vol" +variable atvol equal "v_voltot/v_natoms" +variable etot equal "2.0*pe" +variable etotry equal "v_etot/v_natoms" +variable ptot equal "press" +variable ptotgpa equal "v_ptot/1.0e+09" + +print "number of atoms = ${natoms}" +print "atomic volume (a.u.) = ${atvol}" +print "total energy (ry/atom) = ${etotry}" +print "pressure (gpa) = ${ptotgpa}" +print "${natoms} ${atvol} ${etot} ${ptotgpa}" +print "${atvol} ${etotry} ${ptotgpa}" diff --git a/examples/USER/mgpt/log.bcc0 b/examples/USER/mgpt/log.bcc0 new file mode 100644 index 0000000000..4e4df5da4f --- /dev/null +++ b/examples/USER/mgpt/log.bcc0 @@ -0,0 +1,53 @@ +LAMMPS (23 Oct 2015) +# script for mgpt t=0 eos in bulk bcc structure + +echo screen +Lattice spacing in x,y,z = 6.24196 6.24196 6.24196 +Created orthogonal box = (0 0 0) to (31.2098 31.2098 31.2098) + 1 by 1 by 1 MPI processor grid +Created 250 atoms +Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30 +Neighbor list info ... + 2 neighbor list requests + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13.1618 + ghost atom cutoff = 13.1618 + binsize = 6.58091 -> bins = 5 5 5 +Memory usage per processor = 3.54482 Mbytes +Step Volume Temp PotEng TotEng Press + 0 30400 0 -74.412503 -74.412503 -1.1594626e+09 +Loop time of 1.90735e-06 on 1 procs for 0 steps with 250 atoms + +0.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.907e-06 | | |100.00 + +Nlocal: 250 ave 250 max 250 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1479 ave 1479 max 1479 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8000 ave 8000 max 8000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 16000 ave 16000 max 16000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 16000 +Ave neighs/atom = 64 +Neighbor list builds = 0 +Dangerous builds = 0 +number of atoms = 250 +atomic volume (a.u.) = 121.6 +total energy (ry/atom) = -0.59530002488734 +pressure (gpa) = -1.15946260887556 +250 121.6 -148.825006221835 -1.15946260887556 +121.6 -0.59530002488734 -1.15946260887556 +Total wall time: 0:00:00 diff --git a/examples/USER/mgpt/log.lammps b/examples/USER/mgpt/log.lammps new file mode 100644 index 0000000000..9485c36e47 --- /dev/null +++ b/examples/USER/mgpt/log.lammps @@ -0,0 +1,78 @@ +LAMMPS (23 Oct 2015) +# script for mgpt t=0 eos with relaxed vacancy in bcc structure: +# input for relaxed vacancy formation energy at constant pressure + +echo screen +Lattice spacing in x,y,z = 6.23812 6.23812 6.23812 +Created orthogonal box = (0 0 0) to (31.1906 31.1906 31.1906) + 1 by 1 by 1 MPI processor grid +Created 250 atoms +Deleted 1 atoms, new total = 249 +Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30 +Neighbor list info ... + 2 neighbor list requests + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13.1712 + ghost atom cutoff = 13.1712 + binsize = 6.58562 -> bins = 5 5 5 +Memory usage per processor = 4.66978 Mbytes +Step Volume Temp PotEng TotEng Press + 0 30343.887 0 -73.994511 -73.994511 -1.0504398e+09 + 10 30343.887 0 -74.002332 -74.002332 -1.107516e+09 + 20 30343.887 0 -74.00485 -74.00485 -1.1316373e+09 + 30 30343.887 0 -74.005762 -74.005762 -1.143304e+09 + 40 30343.887 0 -74.006116 -74.006116 -1.149395e+09 + 50 30343.887 0 -74.006262 -74.006262 -1.1527914e+09 + 60 30343.887 0 -74.006323 -74.006323 -1.1547677e+09 + 70 30343.887 0 -74.00635 -74.00635 -1.1559529e+09 + 80 30343.887 0 -74.006361 -74.006361 -1.1566763e+09 + 90 30343.887 0 -74.006366 -74.006366 -1.1571256e+09 + 100 30343.887 0 -74.006369 -74.006369 -1.1574093e+09 + 110 30343.887 0 -74.00637 -74.00637 -1.1575908e+09 + 120 30343.887 0 -74.00637 -74.00637 -1.1577083e+09 + 130 30343.887 0 -74.00637 -74.00637 -1.1577849e+09 + 139 30343.887 0 -74.006371 -74.006371 -1.1578311e+09 +Loop time of 4.33109 on 1 procs for 139 steps with 249 atoms + +92.4% CPU use with 1 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -73.9945109564 -74.0063705487 -74.0063705557 + Force two-norm initial, final = 0.0366227 8.09081e-05 + Force max component initial, final = 0.00730948 8.05242e-06 + Final line search alpha, max atom move = 1 8.05242e-06 + Iterations, force evaluations = 139 139 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.3064 | 4.3064 | 4.3064 | 0.0 | 99.43 +Neigh | 0.019113 | 0.019113 | 0.019113 | 0.0 | 0.44 +Comm | 0.0017624 | 0.0017624 | 0.0017624 | 0.0 | 0.04 +Output | 0.00084376 | 0.00084376 | 0.00084376 | 0.0 | 0.02 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.00297 | | | 0.07 + +Nlocal: 249 ave 249 max 249 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1479 ave 1479 max 1479 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7936 ave 7936 max 7936 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 15872 ave 15872 max 15872 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15872 +Ave neighs/atom = 63.743 +Neighbor list builds = 4 +Dangerous builds = 0 +number of atoms = 249 +atomic volume (a.u.) = 121.863 +total energy (ry/atom) = -0.594428679162064 +pressure (gpa) = -1.15783109519801 +249 121.863 -148.012741111354 -1.15783109519801 +121.863 -0.594428679162064 -1.15783109519801 +Total wall time: 0:00:04 diff --git a/examples/USER/mgpt/log.vac0-bcc b/examples/USER/mgpt/log.vac0-bcc new file mode 100644 index 0000000000..63880de450 --- /dev/null +++ b/examples/USER/mgpt/log.vac0-bcc @@ -0,0 +1,55 @@ +LAMMPS (23 Oct 2015) +# script for mgpt t=0 eos with unrelaxed vacancy in bcc lattice: +# input for unrelaxed vacancy formation energy at constant atomic volume + +echo screen +Lattice spacing in x,y,z = 6.23363 6.23363 6.23363 +Created orthogonal box = (0 0 0) to (31.1681 31.1681 31.1681) + 1 by 1 by 1 MPI processor grid +Created 250 atoms +Deleted 1 atoms, new total = 249 +Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30 +Neighbor list info ... + 2 neighbor list requests + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13.1618 + ghost atom cutoff = 13.1618 + binsize = 6.58091 -> bins = 5 5 5 +Memory usage per processor = 3.54478 Mbytes +Step Volume Temp PotEng TotEng Press + 0 30278.4 0 -73.996387 -73.996387 -6.3426731e+08 +Loop time of 1.90735e-06 on 1 procs for 0 steps with 249 atoms + +0.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.907e-06 | | |100.00 + +Nlocal: 249 ave 249 max 249 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1479 ave 1479 max 1479 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7936 ave 7936 max 7936 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 15872 ave 15872 max 15872 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15872 +Ave neighs/atom = 63.743 +Neighbor list builds = 0 +Dangerous builds = 0 +number of atoms = 249 +atomic volume (a.u.) = 121.6 +total energy (ry/atom) = -0.594348488796036 +pressure (gpa) = -0.634267307139601 +249 121.6 -147.992773710213 -0.634267307139601 +121.6 -0.594348488796036 -0.634267307139601 +Total wall time: 0:00:00 diff --git a/examples/USER/mgpt/log.vacmin-bcc b/examples/USER/mgpt/log.vacmin-bcc new file mode 100644 index 0000000000..876b34eb1e --- /dev/null +++ b/examples/USER/mgpt/log.vacmin-bcc @@ -0,0 +1,78 @@ +LAMMPS (23 Oct 2015) +# script for mgpt t=0 eos with relaxed vacancy in bcc structure: +# input for relaxed vacancy formation energy at constant pressure + +echo screen +Lattice spacing in x,y,z = 6.23812 6.23812 6.23812 +Created orthogonal box = (0 0 0) to (31.1906 31.1906 31.1906) + 1 by 1 by 1 MPI processor grid +Created 250 atoms +Deleted 1 atoms, new total = 249 +Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30 +Neighbor list info ... + 2 neighbor list requests + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13.1712 + ghost atom cutoff = 13.1712 + binsize = 6.58562 -> bins = 5 5 5 +Memory usage per processor = 4.66978 Mbytes +Step Volume Temp PotEng TotEng Press + 0 30343.887 0 -73.994511 -73.994511 -1.0504398e+09 + 10 30343.887 0 -74.002332 -74.002332 -1.107516e+09 + 20 30343.887 0 -74.00485 -74.00485 -1.1316373e+09 + 30 30343.887 0 -74.005762 -74.005762 -1.143304e+09 + 40 30343.887 0 -74.006116 -74.006116 -1.149395e+09 + 50 30343.887 0 -74.006262 -74.006262 -1.1527914e+09 + 60 30343.887 0 -74.006323 -74.006323 -1.1547677e+09 + 70 30343.887 0 -74.00635 -74.00635 -1.1559529e+09 + 80 30343.887 0 -74.006361 -74.006361 -1.1566763e+09 + 90 30343.887 0 -74.006366 -74.006366 -1.1571256e+09 + 100 30343.887 0 -74.006369 -74.006369 -1.1574093e+09 + 110 30343.887 0 -74.00637 -74.00637 -1.1575908e+09 + 120 30343.887 0 -74.00637 -74.00637 -1.1577083e+09 + 130 30343.887 0 -74.00637 -74.00637 -1.1577849e+09 + 139 30343.887 0 -74.006371 -74.006371 -1.1578311e+09 +Loop time of 4.22107 on 1 procs for 139 steps with 249 atoms + +92.1% CPU use with 1 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -73.9945109564 -74.0063705487 -74.0063705557 + Force two-norm initial, final = 0.0366227 8.09081e-05 + Force max component initial, final = 0.00730948 8.05242e-06 + Final line search alpha, max atom move = 1 8.05242e-06 + Iterations, force evaluations = 139 139 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.1973 | 4.1973 | 4.1973 | 0.0 | 99.44 +Neigh | 0.018799 | 0.018799 | 0.018799 | 0.0 | 0.45 +Comm | 0.0017059 | 0.0017059 | 0.0017059 | 0.0 | 0.04 +Output | 0.00080252 | 0.00080252 | 0.00080252 | 0.0 | 0.02 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.002477 | | | 0.06 + +Nlocal: 249 ave 249 max 249 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1479 ave 1479 max 1479 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7936 ave 7936 max 7936 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 15872 ave 15872 max 15872 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15872 +Ave neighs/atom = 63.743 +Neighbor list builds = 4 +Dangerous builds = 0 +number of atoms = 249 +atomic volume (a.u.) = 121.863 +total energy (ry/atom) = -0.594428679162064 +pressure (gpa) = -1.15783109519801 +249 121.863 -148.012741111354 -1.15783109519801 +121.863 -0.594428679162064 -1.15783109519801 +Total wall time: 0:00:04 From d815b390baf127bee961ff2747a579df1db0e87c Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 22 Oct 2015 23:39:46 +0000 Subject: [PATCH 13/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14175 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/Makefile | 2 +- src/USER-MGPT/README | 33 + src/USER-MGPT/mgpt_bgmul_7.c.h | 181 ++ src/USER-MGPT/mgpt_linalg.cpp | 203 ++ src/USER-MGPT/mgpt_linalg.h | 69 + src/USER-MGPT/mgpt_mmul3_538.c.h | 295 ++ src/USER-MGPT/mgpt_mmul3_748.c.h | 508 ++++ src/USER-MGPT/mgpt_mmul3d_526.c.h | 443 +++ src/USER-MGPT/mgpt_mmul3d_744.c.h | 1116 +++++++ src/USER-MGPT/mgpt_mmul_bg_552.c.h | 358 +++ src/USER-MGPT/mgpt_mmul_bg_722.c.h | 1075 +++++++ src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h | 236 ++ src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h | 332 +++ src/USER-MGPT/mgpt_readpot.cpp | 566 ++++ src/USER-MGPT/mgpt_readpot.h | 418 +++ src/USER-MGPT/mgpt_splinetab.cpp | 125 + src/USER-MGPT/mgpt_splinetab.h | 62 + src/USER-MGPT/mgpt_ttr_5022.c.h | 202 ++ src/USER-MGPT/mgpt_ttr_5042.c.h | 150 + src/USER-MGPT/mgpt_ttr_5123.c.h | 245 ++ src/USER-MGPT/mgpt_ttr_5141.c.h | 142 + src/USER-MGPT/mgpt_ttr_7022.c.h | 345 +++ src/USER-MGPT/mgpt_ttr_7042.c.h | 194 ++ src/USER-MGPT/mgpt_ttr_7123.c.h | 349 +++ src/USER-MGPT/mgpt_ttr_7141.c.h | 174 ++ src/USER-MGPT/pair_mgpt.cpp | 2927 +++++++++++++++++++ src/USER-MGPT/pair_mgpt.h | 718 +++++ 27 files changed, 11467 insertions(+), 1 deletion(-) create mode 100644 src/USER-MGPT/README create mode 100644 src/USER-MGPT/mgpt_bgmul_7.c.h create mode 100644 src/USER-MGPT/mgpt_linalg.cpp create mode 100644 src/USER-MGPT/mgpt_linalg.h create mode 100644 src/USER-MGPT/mgpt_mmul3_538.c.h create mode 100644 src/USER-MGPT/mgpt_mmul3_748.c.h create mode 100644 src/USER-MGPT/mgpt_mmul3d_526.c.h create mode 100644 src/USER-MGPT/mgpt_mmul3d_744.c.h create mode 100644 src/USER-MGPT/mgpt_mmul_bg_552.c.h create mode 100644 src/USER-MGPT/mgpt_mmul_bg_722.c.h create mode 100644 src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h create mode 100644 src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h create mode 100644 src/USER-MGPT/mgpt_readpot.cpp create mode 100644 src/USER-MGPT/mgpt_readpot.h create mode 100644 src/USER-MGPT/mgpt_splinetab.cpp create mode 100644 src/USER-MGPT/mgpt_splinetab.h create mode 100644 src/USER-MGPT/mgpt_ttr_5022.c.h create mode 100644 src/USER-MGPT/mgpt_ttr_5042.c.h create mode 100644 src/USER-MGPT/mgpt_ttr_5123.c.h create mode 100644 src/USER-MGPT/mgpt_ttr_5141.c.h create mode 100644 src/USER-MGPT/mgpt_ttr_7022.c.h create mode 100644 src/USER-MGPT/mgpt_ttr_7042.c.h create mode 100644 src/USER-MGPT/mgpt_ttr_7123.c.h create mode 100644 src/USER-MGPT/mgpt_ttr_7141.c.h create mode 100644 src/USER-MGPT/pair_mgpt.cpp create mode 100644 src/USER-MGPT/pair_mgpt.h diff --git a/src/Makefile b/src/Makefile index 25184d998f..93277f6078 100755 --- a/src/Makefile +++ b/src/Makefile @@ -48,7 +48,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole fld gpu \ PACKUSER = user-atc user-awpmd user-cg-cmm user-colvars user-cuda \ user-diffraction user-drude user-eff user-fep user-h5md \ - user-intel user-lb \ + user-intel user-lb user-mgpt \ user-misc user-molfile user-omp user-phonon user-qmmm user-qtb \ user-quip user-reaxc user-smd user-smtbq user-sph user-tally diff --git a/src/USER-MGPT/README b/src/USER-MGPT/README new file mode 100644 index 0000000000..09c7b7c336 --- /dev/null +++ b/src/USER-MGPT/README @@ -0,0 +1,33 @@ +This package contains a fast implementation for LAMMPS of quantum-based +MGPT multi-ion potentials. The MGPT or model GPT method derives from +first-principles DFT-based generalized pseudopotential theory (GPT) +through a series of systematic approximations valid for mid-period +transition metals with nearly half-filled d bands. The MGPT method +was originally developed by John Moriarty at Lawrence Livermore +National Lab (LLNL). + +In the general matrix representation of MGPT, which can also be applied +to f-band actinide metals, the multi-ion potentials are evaluated on the +fly during a simulation through d- or f-state matrix multiplication, and +the forces that move the ions are determined analytically. The mgpt +pair style in this package calculates forces and energies using an +optimized matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. + +See the doc page for the mgpt pair style for full details on using +this package in LAMMPS. In particular, the user should note that the +MGPT potentials are explicitly volume dependent, requiring special +attention in their application. Useful example scripts are given +in the "examples/mgpt" directory. These scripts show the necessary +steps to perform constant-volume calculations and simulations. It +is strongly recommended that the user work through and understand +these examples before proceeding to more complex simulations. + +Specific MGPT potential data for the transition metals tantalum +(Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials), and +vanadium (V6.1 potentials) are contained in the LAMMPS "potentials" +directory. It is expected that MGPT potentials for additional +materials will be added over time. + +The persons who created the USER-MGPT package are Tomas Oppelstrup +(oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov) +Contact them directly if you have any questions. diff --git a/src/USER-MGPT/mgpt_bgmul_7.c.h b/src/USER-MGPT/mgpt_bgmul_7.c.h new file mode 100644 index 0000000000..d4e87c9fe6 --- /dev/null +++ b/src/USER-MGPT/mgpt_bgmul_7.c.h @@ -0,0 +1,181 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + + +//#define TESTING + +#ifdef TESTING + +typedef struct { + double x,y; +} pair; + + +#define CPLX pair + +#define __creal my_creal +#define __cimag my_cimag +#define __lfpd my_lfpd +#define __stfpd my_stfpd +#define __fxsmul my_fxsmul +#define __fxcpmadd my_fxcpmadd + +#else + +#define CPLX double _Complex + +#endif + +static double my_creal(CPLX x) { + return ((double *) &x)[0]; +} +static double my_cimag(CPLX x) { + return ((double *) &x)[1]; +} +static CPLX my_lfpd(const double *p) { + return ((CPLX *) p)[0]; +} +static void my_stfpd(double *p,CPLX x) { + ((CPLX *) p)[0] = x; +} +static CPLX my_fxsmul(CPLX x,double a) { + double y[2]; + y[0] = a * my_creal(x); + y[1] = a * my_cimag(x); + return ((CPLX *) y)[0]; +} +static CPLX my_fxcpmadd(CPLX t,CPLX x,double a) { + double y[2]; + y[0] = my_creal(t) + a * my_creal(x); + y[1] = my_cimag(t) + a * my_cimag(x); + return ((CPLX *) y)[0]; +} + +void bgmul_7(double (* restrict Ain)[8],double (* restrict Bin)[8],double (* restrict Cin)[8]) { + +CPLX C1,C2,C3,C4,C5,C6,C7; +CPLX A1_01,A1_23,A1_45,A1_67; +CPLX A2_23,A2_45,A2_67; +CPLX A3_23,A3_45,A3_67; +CPLX A4_45,A4_67; +CPLX A5_45,A5_67; +CPLX A6_67; +CPLX A7_67; +CPLX Bkj; + + double (* restrict A)[8] = &Ain[-1]; + double (* restrict B)[8] = &Bin[-1]; + double (* restrict C)[8] = &Cin[-1]; + + +int j; +A1_01 = __lfpd(&A[1][0]); A1_23 = __lfpd(&A[1][2]); A1_45 = __lfpd(&A[1][4]); A1_67 = __lfpd(&A[1][6]); + A2_23 = __lfpd(&A[2][2]); A2_45 = __lfpd(&A[2][4]); A2_67 = __lfpd(&A[2][6]); + A3_23 = __lfpd(&A[3][2]); A3_45 = __lfpd(&A[3][4]); A3_67 = __lfpd(&A[3][6]); + A4_45 = __lfpd(&A[4][4]); A4_67 = __lfpd(&A[4][6]); + A5_45 = __lfpd(&A[5][4]); A5_67 = __lfpd(&A[5][6]); + A6_67 = __lfpd(&A[6][6]); + A7_67 = __lfpd(&A[7][6]); + +for(j = 0; j<7; j+=2) { + /* k = 1 */ + Bkj = __lfpd(&B[1][j]); + + C1 = __fxsmul(Bkj,__cimag(A1_01)); + C2 = __fxsmul(Bkj,__creal(A1_23)); + C3 = __fxsmul(Bkj,__cimag(A1_23)); + C4 = __fxsmul(Bkj,__creal(A1_45)); + C5 = __fxsmul(Bkj,__cimag(A1_45)); + C6 = __fxsmul(Bkj,__creal(A1_67)); + C7 = __fxsmul(Bkj,__cimag(A1_67)); + + /* k = 2 */ + Bkj = __lfpd(&B[2][j]); + + C1 = __fxcpmadd(C1,Bkj,__creal(A1_23)); + C2 = __fxcpmadd(C2,Bkj,__creal(A2_23)); + C3 = __fxcpmadd(C3,Bkj,__cimag(A2_23)); + C4 = __fxcpmadd(C4,Bkj,__creal(A2_45)); + C5 = __fxcpmadd(C5,Bkj,__cimag(A2_45)); + C6 = __fxcpmadd(C6,Bkj,__creal(A2_67)); + C7 = __fxcpmadd(C7,Bkj,__cimag(A2_67)); + + /* k = 3 */ + Bkj = __lfpd(&B[3][j]); + + C1 = __fxcpmadd(C1,Bkj,__cimag(A1_23)); + C2 = __fxcpmadd(C2,Bkj,__cimag(A2_23)); + C3 = __fxcpmadd(C3,Bkj,__cimag(A3_23)); + C4 = __fxcpmadd(C4,Bkj,__creal(A3_45)); + C5 = __fxcpmadd(C5,Bkj,__cimag(A3_45)); + C6 = __fxcpmadd(C6,Bkj,__creal(A3_67)); + C7 = __fxcpmadd(C7,Bkj,__cimag(A3_67)); + + /* k = 4 */ + Bkj = __lfpd(&B[4][j]); + + C1 = __fxcpmadd(C1,Bkj,__creal(A1_45)); + C2 = __fxcpmadd(C2,Bkj,__creal(A2_45)); + C3 = __fxcpmadd(C3,Bkj,__creal(A3_45)); + C4 = __fxcpmadd(C4,Bkj,__creal(A4_45)); + C5 = __fxcpmadd(C5,Bkj,__cimag(A4_45)); + C6 = __fxcpmadd(C6,Bkj,__creal(A4_67)); + C7 = __fxcpmadd(C7,Bkj,__cimag(A4_67)); + + /* k = 5 */ + Bkj = __lfpd(&B[5][j]); + + C1 = __fxcpmadd(C1,Bkj,__cimag(A1_45)); + C2 = __fxcpmadd(C2,Bkj,__cimag(A2_45)); + C3 = __fxcpmadd(C3,Bkj,__cimag(A3_45)); + C4 = __fxcpmadd(C4,Bkj,__cimag(A4_45)); + C5 = __fxcpmadd(C5,Bkj,__cimag(A5_45)); + C6 = __fxcpmadd(C6,Bkj,__creal(A5_67)); + C7 = __fxcpmadd(C7,Bkj,__cimag(A5_67)); + + /* k = 6 */ + Bkj = __lfpd(&B[6][j]); + + C1 = __fxcpmadd(C1,Bkj,__creal(A1_67)); + C2 = __fxcpmadd(C2,Bkj,__creal(A2_67)); + C3 = __fxcpmadd(C3,Bkj,__creal(A3_67)); + C4 = __fxcpmadd(C4,Bkj,__creal(A4_67)); + C5 = __fxcpmadd(C5,Bkj,__creal(A5_67)); + C6 = __fxcpmadd(C6,Bkj,__creal(A6_67)); + C7 = __fxcpmadd(C7,Bkj,__cimag(A6_67)); + + /* k = 7 */ + Bkj = __lfpd(&B[7][j]); + + C1 = __fxcpmadd(C1,Bkj,__cimag(A1_67)); + C2 = __fxcpmadd(C2,Bkj,__cimag(A2_67)); + C3 = __fxcpmadd(C3,Bkj,__cimag(A3_67)); + C4 = __fxcpmadd(C4,Bkj,__cimag(A4_67)); + C5 = __fxcpmadd(C5,Bkj,__cimag(A5_67)); + C6 = __fxcpmadd(C6,Bkj,__cimag(A6_67)); + C7 = __fxcpmadd(C7,Bkj,__cimag(A7_67)); + + __stfpd(&C[1][j],C1); + __stfpd(&C[2][j],C2); + __stfpd(&C[3][j],C3); + __stfpd(&C[4][j],C4); + __stfpd(&C[5][j],C5); + __stfpd(&C[6][j],C6); + __stfpd(&C[7][j],C7); +} +} diff --git a/src/USER-MGPT/mgpt_linalg.cpp b/src/USER-MGPT/mgpt_linalg.cpp new file mode 100644 index 0000000000..185b61e1c7 --- /dev/null +++ b/src/USER-MGPT/mgpt_linalg.cpp @@ -0,0 +1,203 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + +#include "mgpt_linalg.h" + +#include +#include +#include +#include + +#define restrict __restrict__ + +#ifdef IBM_BG_SIMD +#include + +/* Double precision 440d (double hummer) matrix multiplication */ +#define const +#include "mgpt_mmul_bg_552.c.h" +#include "mgpt_mmul_bg_722.c.h" +#include "mgpt_bgmul_7.c.h" + +/* Double precision 440d (double hummer) product trace */ +#define real double +#include "mgpt_ttr_5123.c.h" +#include "mgpt_ttr_7123.c.h" +#undef real +#undef const +#endif + + +#ifdef IBM_BGQ_SIMD +/* Double precision QPX matrix multiplication */ +#include "mgpt_mmul_bgq_n5_lda8_2x8.c.h" +#include "mgpt_mmul_bgq_n7_lda8_4x8.c.h" + +/* Double precision QPX product trace */ +#include "mgpt_ttr_5141.c.h" +#include "mgpt_ttr_7141.c.h" +#endif + + +#ifdef x86_SIMD +/* Double precision SSE2 matrix multiplication */ +#include "mgpt_mmul3d_526.c.h" +#include "mgpt_mmul3d_744.c.h" + +/* Single precision SSE2 matrix multiplication */ +#include "mgpt_mmul3_538.c.h" +#include "mgpt_mmul3_748.c.h" + +/* Double precision SSE3 product trace */ +#define real double +#include "mgpt_ttr_5022.c.h" +#include "mgpt_ttr_7022.c.h" +#undef real + +/* Single precision SSE3 product trace */ +#define real float +#include "mgpt_ttr_5042.c.h" +#include "mgpt_ttr_7042.c.h" +#undef real + +#endif + +#if defined(IBM_BG_SIMD) || defined(IBM_BGQ_SIMD) +#define const +#endif +static void transprod_generic(const double * restrict A, + const double * restrict B, + double * restrict C) { + const int lda = 8,n = mgpt_linalg::matrix_size; + int i,j,k; + double s; + for(i = 0; i + +void mmul3_5_8_3x8v4(const float * restrict A, + const float * restrict B, + float * restrict C) { + __m128 + Creg00,Creg04, + Creg10,Creg14, + Creg20,Creg24; + __m128 Areg0,Areg1,Areg2; + __m128 Breg0,Breg4; + __m128 Atmp,Btmp; + + + /* Computing C(0:2,0:5) */ + + Areg0 = _mm_load_ps(&A[0]) ; + Areg1 = _mm_load_ps(&A[8]) ; + Areg2 = _mm_load_ps(&A[16]) ; + + Breg0 = _mm_load_ps(&B[0]) ; + Breg4 = _mm_load_ps(&B[4]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(1,1,1,1)) ; + Creg00 = Breg0 ; + Creg00 = _mm_mul_ps(Creg00,Atmp) ; + Creg04 = Breg4 ; + Creg04 = _mm_mul_ps(Creg04,Atmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(1,1,1,1)) ; + Creg10 = Breg0 ; + Creg10 = _mm_mul_ps(Creg10,Atmp) ; + Creg14 = Breg4 ; + Creg14 = _mm_mul_ps(Creg14,Atmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(1,1,1,1)) ; + Creg20 = Breg0 ; + Creg20 = _mm_mul_ps(Creg20,Atmp) ; + Creg24 = Breg4 ; + Creg24 = _mm_mul_ps(Creg24,Atmp) ; + + + Breg0 = _mm_load_ps(&B[8]) ; + Breg4 = _mm_load_ps(&B[12]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg20 = _mm_add_ps(Creg20,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg24 = _mm_add_ps(Creg24,Btmp) ; + + + Breg0 = _mm_load_ps(&B[16]) ; + Breg4 = _mm_load_ps(&B[20]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg20 = _mm_add_ps(Creg20,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg24 = _mm_add_ps(Creg24,Btmp) ; + + + Areg0 = _mm_load_ps(&A[4]) ; + Areg1 = _mm_load_ps(&A[12]) ; + Areg2 = _mm_load_ps(&A[20]) ; + + Breg0 = _mm_load_ps(&B[24]) ; + Breg4 = _mm_load_ps(&B[28]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(0,0,0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(0,0,0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(0,0,0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg20 = _mm_add_ps(Creg20,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg24 = _mm_add_ps(Creg24,Btmp) ; + + + Breg0 = _mm_load_ps(&B[32]) ; + Breg4 = _mm_load_ps(&B[36]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(1,1,1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(1,1,1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(1,1,1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg20 = _mm_add_ps(Creg20,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg24 = _mm_add_ps(Creg24,Btmp) ; + + + _mm_store_ps(&C[0],Creg00) ; + _mm_store_ps(&C[4],Creg04) ; + _mm_store_ps(&C[8],Creg10) ; + _mm_store_ps(&C[12],Creg14) ; + _mm_store_ps(&C[16],Creg20) ; + _mm_store_ps(&C[20],Creg24) ; + + + /* Computing C(3:4,0:5) */ + + Areg0 = _mm_load_ps(&A[24]) ; + Areg1 = _mm_load_ps(&A[32]) ; + + Breg0 = _mm_load_ps(&B[0]) ; + Breg4 = _mm_load_ps(&B[4]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(1,1,1,1)) ; + Creg00 = Breg0 ; + Creg00 = _mm_mul_ps(Creg00,Atmp) ; + Creg04 = Breg4 ; + Creg04 = _mm_mul_ps(Creg04,Atmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(1,1,1,1)) ; + Creg10 = Breg0 ; + Creg10 = _mm_mul_ps(Creg10,Atmp) ; + Creg14 = Breg4 ; + Creg14 = _mm_mul_ps(Creg14,Atmp) ; + + + Breg0 = _mm_load_ps(&B[8]) ; + Breg4 = _mm_load_ps(&B[12]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + + Breg0 = _mm_load_ps(&B[16]) ; + Breg4 = _mm_load_ps(&B[20]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + + Areg0 = _mm_load_ps(&A[28]) ; + Areg1 = _mm_load_ps(&A[36]) ; + + Breg0 = _mm_load_ps(&B[24]) ; + Breg4 = _mm_load_ps(&B[28]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(0,0,0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(0,0,0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + + Breg0 = _mm_load_ps(&B[32]) ; + Breg4 = _mm_load_ps(&B[36]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(1,1,1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(1,1,1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + + _mm_store_ps(&C[24],Creg00) ; + _mm_store_ps(&C[28],Creg04) ; + _mm_store_ps(&C[32],Creg10) ; + _mm_store_ps(&C[36],Creg14) ; + + +} diff --git a/src/USER-MGPT/mgpt_mmul3_748.c.h b/src/USER-MGPT/mgpt_mmul3_748.c.h new file mode 100644 index 0000000000..298fe753c1 --- /dev/null +++ b/src/USER-MGPT/mgpt_mmul3_748.c.h @@ -0,0 +1,508 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + +#include + +void mmul3_7_8_4x8v4(const float * restrict A, + const float * restrict B, + float * restrict C) { + __m128 + Creg00,Creg04, + Creg10,Creg14, + Creg20,Creg24, + Creg30,Creg34; + __m128 Areg0,Areg1,Areg2,Areg3; + __m128 Breg0,Breg4; + __m128 Atmp,Btmp; + + + /* Computing C(0:3,0:7) */ + + Areg0 = _mm_load_ps(&A[0]) ; + Areg1 = _mm_load_ps(&A[8]) ; + Areg2 = _mm_load_ps(&A[16]) ; + Areg3 = _mm_load_ps(&A[24]) ; + + Breg0 = _mm_load_ps(&B[0]) ; + Breg4 = _mm_load_ps(&B[4]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(1,1,1,1)) ; + Creg00 = Breg0 ; + Creg00 = _mm_mul_ps(Creg00,Atmp) ; + Creg04 = Breg4 ; + Creg04 = _mm_mul_ps(Creg04,Atmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(1,1,1,1)) ; + Creg10 = Breg0 ; + Creg10 = _mm_mul_ps(Creg10,Atmp) ; + Creg14 = Breg4 ; + Creg14 = _mm_mul_ps(Creg14,Atmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(1,1,1,1)) ; + Creg20 = Breg0 ; + Creg20 = _mm_mul_ps(Creg20,Atmp) ; + Creg24 = Breg4 ; + Creg24 = _mm_mul_ps(Creg24,Atmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg3,_MM_SHUFFLE(1,1,1,1)) ; + Creg30 = Breg0 ; + Creg30 = _mm_mul_ps(Creg30,Atmp) ; + Creg34 = Breg4 ; + Creg34 = _mm_mul_ps(Creg34,Atmp) ; + + + Breg0 = _mm_load_ps(&B[8]) ; + Breg4 = _mm_load_ps(&B[12]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg20 = _mm_add_ps(Creg20,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg24 = _mm_add_ps(Creg24,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg3,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg30 = _mm_add_ps(Creg30,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg34 = _mm_add_ps(Creg34,Btmp) ; + + + Breg0 = _mm_load_ps(&B[16]) ; + Breg4 = _mm_load_ps(&B[20]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg20 = _mm_add_ps(Creg20,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg24 = _mm_add_ps(Creg24,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg3,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg30 = _mm_add_ps(Creg30,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg34 = _mm_add_ps(Creg34,Btmp) ; + + + Areg0 = _mm_load_ps(&A[4]) ; + Areg1 = _mm_load_ps(&A[12]) ; + Areg2 = _mm_load_ps(&A[20]) ; + Areg3 = _mm_load_ps(&A[28]) ; + + Breg0 = _mm_load_ps(&B[24]) ; + Breg4 = _mm_load_ps(&B[28]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(0,0,0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(0,0,0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(0,0,0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg20 = _mm_add_ps(Creg20,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg24 = _mm_add_ps(Creg24,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg3,_MM_SHUFFLE(0,0,0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg30 = _mm_add_ps(Creg30,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg34 = _mm_add_ps(Creg34,Btmp) ; + + + Breg0 = _mm_load_ps(&B[32]) ; + Breg4 = _mm_load_ps(&B[36]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(1,1,1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(1,1,1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(1,1,1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg20 = _mm_add_ps(Creg20,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg24 = _mm_add_ps(Creg24,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg3,_MM_SHUFFLE(1,1,1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg30 = _mm_add_ps(Creg30,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg34 = _mm_add_ps(Creg34,Btmp) ; + + + Breg0 = _mm_load_ps(&B[40]) ; + Breg4 = _mm_load_ps(&B[44]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg20 = _mm_add_ps(Creg20,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg24 = _mm_add_ps(Creg24,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg3,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg30 = _mm_add_ps(Creg30,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg34 = _mm_add_ps(Creg34,Btmp) ; + + + Breg0 = _mm_load_ps(&B[48]) ; + Breg4 = _mm_load_ps(&B[52]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg20 = _mm_add_ps(Creg20,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg24 = _mm_add_ps(Creg24,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg3,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg30 = _mm_add_ps(Creg30,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg34 = _mm_add_ps(Creg34,Btmp) ; + + + _mm_store_ps(&C[0],Creg00) ; + _mm_store_ps(&C[4],Creg04) ; + _mm_store_ps(&C[8],Creg10) ; + _mm_store_ps(&C[12],Creg14) ; + _mm_store_ps(&C[16],Creg20) ; + _mm_store_ps(&C[20],Creg24) ; + _mm_store_ps(&C[24],Creg30) ; + _mm_store_ps(&C[28],Creg34) ; + + + /* Computing C(4:6,0:7) */ + + Areg0 = _mm_load_ps(&A[32]) ; + Areg1 = _mm_load_ps(&A[40]) ; + Areg2 = _mm_load_ps(&A[48]) ; + + Breg0 = _mm_load_ps(&B[0]) ; + Breg4 = _mm_load_ps(&B[4]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(1,1,1,1)) ; + Creg00 = Breg0 ; + Creg00 = _mm_mul_ps(Creg00,Atmp) ; + Creg04 = Breg4 ; + Creg04 = _mm_mul_ps(Creg04,Atmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(1,1,1,1)) ; + Creg10 = Breg0 ; + Creg10 = _mm_mul_ps(Creg10,Atmp) ; + Creg14 = Breg4 ; + Creg14 = _mm_mul_ps(Creg14,Atmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(1,1,1,1)) ; + Creg20 = Breg0 ; + Creg20 = _mm_mul_ps(Creg20,Atmp) ; + Creg24 = Breg4 ; + Creg24 = _mm_mul_ps(Creg24,Atmp) ; + + + Breg0 = _mm_load_ps(&B[8]) ; + Breg4 = _mm_load_ps(&B[12]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg20 = _mm_add_ps(Creg20,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg24 = _mm_add_ps(Creg24,Btmp) ; + + + Breg0 = _mm_load_ps(&B[16]) ; + Breg4 = _mm_load_ps(&B[20]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg20 = _mm_add_ps(Creg20,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg24 = _mm_add_ps(Creg24,Btmp) ; + + + Areg0 = _mm_load_ps(&A[36]) ; + Areg1 = _mm_load_ps(&A[44]) ; + Areg2 = _mm_load_ps(&A[52]) ; + + Breg0 = _mm_load_ps(&B[24]) ; + Breg4 = _mm_load_ps(&B[28]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(0,0,0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(0,0,0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(0,0,0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg20 = _mm_add_ps(Creg20,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg24 = _mm_add_ps(Creg24,Btmp) ; + + + Breg0 = _mm_load_ps(&B[32]) ; + Breg4 = _mm_load_ps(&B[36]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(1,1,1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(1,1,1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(1,1,1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg20 = _mm_add_ps(Creg20,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg24 = _mm_add_ps(Creg24,Btmp) ; + + + Breg0 = _mm_load_ps(&B[40]) ; + Breg4 = _mm_load_ps(&B[44]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(2,2,2,2)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg20 = _mm_add_ps(Creg20,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg24 = _mm_add_ps(Creg24,Btmp) ; + + + Breg0 = _mm_load_ps(&B[48]) ; + Breg4 = _mm_load_ps(&B[52]) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg0,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg00 = _mm_add_ps(Creg00,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg04 = _mm_add_ps(Creg04,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg1,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg10 = _mm_add_ps(Creg10,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg14 = _mm_add_ps(Creg14,Btmp) ; + + Atmp = (__m128) _mm_shuffle_epi32((__m128i) Areg2,_MM_SHUFFLE(3,3,3,3)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg20 = _mm_add_ps(Creg20,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_ps(Btmp,Atmp) ; + Creg24 = _mm_add_ps(Creg24,Btmp) ; + + + _mm_store_ps(&C[32],Creg00) ; + _mm_store_ps(&C[36],Creg04) ; + _mm_store_ps(&C[40],Creg10) ; + _mm_store_ps(&C[44],Creg14) ; + _mm_store_ps(&C[48],Creg20) ; + _mm_store_ps(&C[52],Creg24) ; + + +} diff --git a/src/USER-MGPT/mgpt_mmul3d_526.c.h b/src/USER-MGPT/mgpt_mmul3d_526.c.h new file mode 100644 index 0000000000..47a4c26a26 --- /dev/null +++ b/src/USER-MGPT/mgpt_mmul3d_526.c.h @@ -0,0 +1,443 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + +#include + +void mmul3_5_8_2x6v2(const double * restrict A, + const double * restrict B, + double * restrict C) { + __m128d + Creg00,Creg02,Creg04, + Creg10,Creg12,Creg14; + __m128d Areg0,Areg1; + __m128d Breg0,Breg2,Breg4; + __m128d Atmp,Btmp; + + + /* Computing C(0:1,0:5) */ + + Areg0 = _mm_load_pd(&A[0]) ; + Areg1 = _mm_load_pd(&A[8]) ; + + Breg0 = _mm_load_pd(&B[0]) ; + Breg2 = _mm_load_pd(&B[2]) ; + Breg4 = _mm_load_pd(&B[4]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Creg00 = Breg0 ; + Creg00 = _mm_mul_pd(Creg00,Atmp) ; + Creg02 = Breg2 ; + Creg02 = _mm_mul_pd(Creg02,Atmp) ; + Creg04 = Breg4 ; + Creg04 = _mm_mul_pd(Creg04,Atmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Creg10 = Breg0 ; + Creg10 = _mm_mul_pd(Creg10,Atmp) ; + Creg12 = Breg2 ; + Creg12 = _mm_mul_pd(Creg12,Atmp) ; + Creg14 = Breg4 ; + Creg14 = _mm_mul_pd(Creg14,Atmp) ; + + + Areg0 = _mm_load_pd(&A[2]) ; + Areg1 = _mm_load_pd(&A[10]) ; + + Breg0 = _mm_load_pd(&B[8]) ; + Breg2 = _mm_load_pd(&B[10]) ; + Breg4 = _mm_load_pd(&B[12]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg04 = _mm_add_pd(Creg04,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg14 = _mm_add_pd(Creg14,Btmp) ; + + + Breg0 = _mm_load_pd(&B[16]) ; + Breg2 = _mm_load_pd(&B[18]) ; + Breg4 = _mm_load_pd(&B[20]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg04 = _mm_add_pd(Creg04,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg14 = _mm_add_pd(Creg14,Btmp) ; + + + Areg0 = _mm_load_pd(&A[4]) ; + Areg1 = _mm_load_pd(&A[12]) ; + + Breg0 = _mm_load_pd(&B[24]) ; + Breg2 = _mm_load_pd(&B[26]) ; + Breg4 = _mm_load_pd(&B[28]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg04 = _mm_add_pd(Creg04,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg14 = _mm_add_pd(Creg14,Btmp) ; + + + Breg0 = _mm_load_pd(&B[32]) ; + Breg2 = _mm_load_pd(&B[34]) ; + Breg4 = _mm_load_pd(&B[36]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg04 = _mm_add_pd(Creg04,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg14 = _mm_add_pd(Creg14,Btmp) ; + + + _mm_store_pd(&C[0],Creg00) ; + _mm_store_pd(&C[2],Creg02) ; + _mm_store_pd(&C[4],Creg04) ; + _mm_store_pd(&C[8],Creg10) ; + _mm_store_pd(&C[10],Creg12) ; + _mm_store_pd(&C[12],Creg14) ; + + + /* Computing C(2:3,0:5) */ + + Areg0 = _mm_load_pd(&A[16]) ; + Areg1 = _mm_load_pd(&A[24]) ; + + Breg0 = _mm_load_pd(&B[0]) ; + Breg2 = _mm_load_pd(&B[2]) ; + Breg4 = _mm_load_pd(&B[4]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Creg00 = Breg0 ; + Creg00 = _mm_mul_pd(Creg00,Atmp) ; + Creg02 = Breg2 ; + Creg02 = _mm_mul_pd(Creg02,Atmp) ; + Creg04 = Breg4 ; + Creg04 = _mm_mul_pd(Creg04,Atmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Creg10 = Breg0 ; + Creg10 = _mm_mul_pd(Creg10,Atmp) ; + Creg12 = Breg2 ; + Creg12 = _mm_mul_pd(Creg12,Atmp) ; + Creg14 = Breg4 ; + Creg14 = _mm_mul_pd(Creg14,Atmp) ; + + + Areg0 = _mm_load_pd(&A[18]) ; + Areg1 = _mm_load_pd(&A[26]) ; + + Breg0 = _mm_load_pd(&B[8]) ; + Breg2 = _mm_load_pd(&B[10]) ; + Breg4 = _mm_load_pd(&B[12]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg04 = _mm_add_pd(Creg04,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg14 = _mm_add_pd(Creg14,Btmp) ; + + + Breg0 = _mm_load_pd(&B[16]) ; + Breg2 = _mm_load_pd(&B[18]) ; + Breg4 = _mm_load_pd(&B[20]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg04 = _mm_add_pd(Creg04,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg14 = _mm_add_pd(Creg14,Btmp) ; + + + Areg0 = _mm_load_pd(&A[20]) ; + Areg1 = _mm_load_pd(&A[28]) ; + + Breg0 = _mm_load_pd(&B[24]) ; + Breg2 = _mm_load_pd(&B[26]) ; + Breg4 = _mm_load_pd(&B[28]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg04 = _mm_add_pd(Creg04,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg14 = _mm_add_pd(Creg14,Btmp) ; + + + Breg0 = _mm_load_pd(&B[32]) ; + Breg2 = _mm_load_pd(&B[34]) ; + Breg4 = _mm_load_pd(&B[36]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg04 = _mm_add_pd(Creg04,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg14 = _mm_add_pd(Creg14,Btmp) ; + + + _mm_store_pd(&C[16],Creg00) ; + _mm_store_pd(&C[18],Creg02) ; + _mm_store_pd(&C[20],Creg04) ; + _mm_store_pd(&C[24],Creg10) ; + _mm_store_pd(&C[26],Creg12) ; + _mm_store_pd(&C[28],Creg14) ; + + + /* Computing C(4:4,0:5) */ + + Areg0 = _mm_load_pd(&A[32]) ; + + Breg0 = _mm_load_pd(&B[0]) ; + Breg2 = _mm_load_pd(&B[2]) ; + Breg4 = _mm_load_pd(&B[4]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Creg00 = Breg0 ; + Creg00 = _mm_mul_pd(Creg00,Atmp) ; + Creg02 = Breg2 ; + Creg02 = _mm_mul_pd(Creg02,Atmp) ; + Creg04 = Breg4 ; + Creg04 = _mm_mul_pd(Creg04,Atmp) ; + + + Areg0 = _mm_load_pd(&A[34]) ; + + Breg0 = _mm_load_pd(&B[8]) ; + Breg2 = _mm_load_pd(&B[10]) ; + Breg4 = _mm_load_pd(&B[12]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg04 = _mm_add_pd(Creg04,Btmp) ; + + + Breg0 = _mm_load_pd(&B[16]) ; + Breg2 = _mm_load_pd(&B[18]) ; + Breg4 = _mm_load_pd(&B[20]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg04 = _mm_add_pd(Creg04,Btmp) ; + + + Areg0 = _mm_load_pd(&A[36]) ; + + Breg0 = _mm_load_pd(&B[24]) ; + Breg2 = _mm_load_pd(&B[26]) ; + Breg4 = _mm_load_pd(&B[28]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg04 = _mm_add_pd(Creg04,Btmp) ; + + + Breg0 = _mm_load_pd(&B[32]) ; + Breg2 = _mm_load_pd(&B[34]) ; + Breg4 = _mm_load_pd(&B[36]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + Btmp = Breg4 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg04 = _mm_add_pd(Creg04,Btmp) ; + + + _mm_store_pd(&C[32],Creg00) ; + _mm_store_pd(&C[34],Creg02) ; + _mm_store_pd(&C[36],Creg04) ; + + +} diff --git a/src/USER-MGPT/mgpt_mmul3d_744.c.h b/src/USER-MGPT/mgpt_mmul3d_744.c.h new file mode 100644 index 0000000000..0f90438440 --- /dev/null +++ b/src/USER-MGPT/mgpt_mmul3d_744.c.h @@ -0,0 +1,1116 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + +#include + +void mmul3_7_8_4x4v2(const double * restrict A, + const double * restrict B, + double * restrict C) { + __m128d + Creg00,Creg02, + Creg10,Creg12, + Creg20,Creg22, + Creg30,Creg32; + __m128d Areg0,Areg1,Areg2,Areg3; + __m128d Breg0,Breg2; + __m128d Atmp,Btmp; + + + /* Computing C(0:3,0:3) */ + + Areg0 = _mm_load_pd(&A[0]) ; + Areg1 = _mm_load_pd(&A[8]) ; + Areg2 = _mm_load_pd(&A[16]) ; + Areg3 = _mm_load_pd(&A[24]) ; + + Breg0 = _mm_load_pd(&B[0]) ; + Breg2 = _mm_load_pd(&B[2]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Creg00 = Breg0 ; + Creg00 = _mm_mul_pd(Creg00,Atmp) ; + Creg02 = Breg2 ; + Creg02 = _mm_mul_pd(Creg02,Atmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Creg10 = Breg0 ; + Creg10 = _mm_mul_pd(Creg10,Atmp) ; + Creg12 = Breg2 ; + Creg12 = _mm_mul_pd(Creg12,Atmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ; + Creg20 = Breg0 ; + Creg20 = _mm_mul_pd(Creg20,Atmp) ; + Creg22 = Breg2 ; + Creg22 = _mm_mul_pd(Creg22,Atmp) ; + + Atmp = Areg3 ; + Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(1,1)) ; + Creg30 = Breg0 ; + Creg30 = _mm_mul_pd(Creg30,Atmp) ; + Creg32 = Breg2 ; + Creg32 = _mm_mul_pd(Creg32,Atmp) ; + + + Areg0 = _mm_load_pd(&A[2]) ; + Areg1 = _mm_load_pd(&A[10]) ; + Areg2 = _mm_load_pd(&A[18]) ; + Areg3 = _mm_load_pd(&A[26]) ; + + Breg0 = _mm_load_pd(&B[8]) ; + Breg2 = _mm_load_pd(&B[10]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + Atmp = Areg3 ; + Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg30 = _mm_add_pd(Creg30,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg32 = _mm_add_pd(Creg32,Btmp) ; + + + Breg0 = _mm_load_pd(&B[16]) ; + Breg2 = _mm_load_pd(&B[18]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + Atmp = Areg3 ; + Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg30 = _mm_add_pd(Creg30,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg32 = _mm_add_pd(Creg32,Btmp) ; + + + Areg0 = _mm_load_pd(&A[4]) ; + Areg1 = _mm_load_pd(&A[12]) ; + Areg2 = _mm_load_pd(&A[20]) ; + Areg3 = _mm_load_pd(&A[28]) ; + + Breg0 = _mm_load_pd(&B[24]) ; + Breg2 = _mm_load_pd(&B[26]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + Atmp = Areg3 ; + Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg30 = _mm_add_pd(Creg30,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg32 = _mm_add_pd(Creg32,Btmp) ; + + + Breg0 = _mm_load_pd(&B[32]) ; + Breg2 = _mm_load_pd(&B[34]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + Atmp = Areg3 ; + Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg30 = _mm_add_pd(Creg30,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg32 = _mm_add_pd(Creg32,Btmp) ; + + + Areg0 = _mm_load_pd(&A[6]) ; + Areg1 = _mm_load_pd(&A[14]) ; + Areg2 = _mm_load_pd(&A[22]) ; + Areg3 = _mm_load_pd(&A[30]) ; + + Breg0 = _mm_load_pd(&B[40]) ; + Breg2 = _mm_load_pd(&B[42]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + Atmp = Areg3 ; + Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg30 = _mm_add_pd(Creg30,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg32 = _mm_add_pd(Creg32,Btmp) ; + + + Breg0 = _mm_load_pd(&B[48]) ; + Breg2 = _mm_load_pd(&B[50]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + Atmp = Areg3 ; + Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg30 = _mm_add_pd(Creg30,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg32 = _mm_add_pd(Creg32,Btmp) ; + + + _mm_store_pd(&C[0],Creg00) ; + _mm_store_pd(&C[2],Creg02) ; + _mm_store_pd(&C[8],Creg10) ; + _mm_store_pd(&C[10],Creg12) ; + _mm_store_pd(&C[16],Creg20) ; + _mm_store_pd(&C[18],Creg22) ; + _mm_store_pd(&C[24],Creg30) ; + _mm_store_pd(&C[26],Creg32) ; + + + /* Computing C(0:3,4:7) */ + + Areg0 = _mm_load_pd(&A[0]) ; + Areg1 = _mm_load_pd(&A[8]) ; + Areg2 = _mm_load_pd(&A[16]) ; + Areg3 = _mm_load_pd(&A[24]) ; + + Breg0 = _mm_load_pd(&B[4]) ; + Breg2 = _mm_load_pd(&B[6]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Creg00 = Breg0 ; + Creg00 = _mm_mul_pd(Creg00,Atmp) ; + Creg02 = Breg2 ; + Creg02 = _mm_mul_pd(Creg02,Atmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Creg10 = Breg0 ; + Creg10 = _mm_mul_pd(Creg10,Atmp) ; + Creg12 = Breg2 ; + Creg12 = _mm_mul_pd(Creg12,Atmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ; + Creg20 = Breg0 ; + Creg20 = _mm_mul_pd(Creg20,Atmp) ; + Creg22 = Breg2 ; + Creg22 = _mm_mul_pd(Creg22,Atmp) ; + + Atmp = Areg3 ; + Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(1,1)) ; + Creg30 = Breg0 ; + Creg30 = _mm_mul_pd(Creg30,Atmp) ; + Creg32 = Breg2 ; + Creg32 = _mm_mul_pd(Creg32,Atmp) ; + + + Areg0 = _mm_load_pd(&A[2]) ; + Areg1 = _mm_load_pd(&A[10]) ; + Areg2 = _mm_load_pd(&A[18]) ; + Areg3 = _mm_load_pd(&A[26]) ; + + Breg0 = _mm_load_pd(&B[12]) ; + Breg2 = _mm_load_pd(&B[14]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + Atmp = Areg3 ; + Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg30 = _mm_add_pd(Creg30,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg32 = _mm_add_pd(Creg32,Btmp) ; + + + Breg0 = _mm_load_pd(&B[20]) ; + Breg2 = _mm_load_pd(&B[22]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + Atmp = Areg3 ; + Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg30 = _mm_add_pd(Creg30,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg32 = _mm_add_pd(Creg32,Btmp) ; + + + Areg0 = _mm_load_pd(&A[4]) ; + Areg1 = _mm_load_pd(&A[12]) ; + Areg2 = _mm_load_pd(&A[20]) ; + Areg3 = _mm_load_pd(&A[28]) ; + + Breg0 = _mm_load_pd(&B[28]) ; + Breg2 = _mm_load_pd(&B[30]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + Atmp = Areg3 ; + Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg30 = _mm_add_pd(Creg30,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg32 = _mm_add_pd(Creg32,Btmp) ; + + + Breg0 = _mm_load_pd(&B[36]) ; + Breg2 = _mm_load_pd(&B[38]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + Atmp = Areg3 ; + Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg30 = _mm_add_pd(Creg30,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg32 = _mm_add_pd(Creg32,Btmp) ; + + + Areg0 = _mm_load_pd(&A[6]) ; + Areg1 = _mm_load_pd(&A[14]) ; + Areg2 = _mm_load_pd(&A[22]) ; + Areg3 = _mm_load_pd(&A[30]) ; + + Breg0 = _mm_load_pd(&B[44]) ; + Breg2 = _mm_load_pd(&B[46]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + Atmp = Areg3 ; + Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg30 = _mm_add_pd(Creg30,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg32 = _mm_add_pd(Creg32,Btmp) ; + + + Breg0 = _mm_load_pd(&B[52]) ; + Breg2 = _mm_load_pd(&B[54]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + Atmp = Areg3 ; + Atmp = _mm_shuffle_pd(Atmp,Areg3,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg30 = _mm_add_pd(Creg30,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg32 = _mm_add_pd(Creg32,Btmp) ; + + + _mm_store_pd(&C[4],Creg00) ; + _mm_store_pd(&C[6],Creg02) ; + _mm_store_pd(&C[12],Creg10) ; + _mm_store_pd(&C[14],Creg12) ; + _mm_store_pd(&C[20],Creg20) ; + _mm_store_pd(&C[22],Creg22) ; + _mm_store_pd(&C[28],Creg30) ; + _mm_store_pd(&C[30],Creg32) ; + + + /* Computing C(4:6,0:3) */ + + Areg0 = _mm_load_pd(&A[32]) ; + Areg1 = _mm_load_pd(&A[40]) ; + Areg2 = _mm_load_pd(&A[48]) ; + + Breg0 = _mm_load_pd(&B[0]) ; + Breg2 = _mm_load_pd(&B[2]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Creg00 = Breg0 ; + Creg00 = _mm_mul_pd(Creg00,Atmp) ; + Creg02 = Breg2 ; + Creg02 = _mm_mul_pd(Creg02,Atmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Creg10 = Breg0 ; + Creg10 = _mm_mul_pd(Creg10,Atmp) ; + Creg12 = Breg2 ; + Creg12 = _mm_mul_pd(Creg12,Atmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ; + Creg20 = Breg0 ; + Creg20 = _mm_mul_pd(Creg20,Atmp) ; + Creg22 = Breg2 ; + Creg22 = _mm_mul_pd(Creg22,Atmp) ; + + + Areg0 = _mm_load_pd(&A[34]) ; + Areg1 = _mm_load_pd(&A[42]) ; + Areg2 = _mm_load_pd(&A[50]) ; + + Breg0 = _mm_load_pd(&B[8]) ; + Breg2 = _mm_load_pd(&B[10]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + + Breg0 = _mm_load_pd(&B[16]) ; + Breg2 = _mm_load_pd(&B[18]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + + Areg0 = _mm_load_pd(&A[36]) ; + Areg1 = _mm_load_pd(&A[44]) ; + Areg2 = _mm_load_pd(&A[52]) ; + + Breg0 = _mm_load_pd(&B[24]) ; + Breg2 = _mm_load_pd(&B[26]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + + Breg0 = _mm_load_pd(&B[32]) ; + Breg2 = _mm_load_pd(&B[34]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + + Areg0 = _mm_load_pd(&A[38]) ; + Areg1 = _mm_load_pd(&A[46]) ; + Areg2 = _mm_load_pd(&A[54]) ; + + Breg0 = _mm_load_pd(&B[40]) ; + Breg2 = _mm_load_pd(&B[42]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + + Breg0 = _mm_load_pd(&B[48]) ; + Breg2 = _mm_load_pd(&B[50]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + + _mm_store_pd(&C[32],Creg00) ; + _mm_store_pd(&C[34],Creg02) ; + _mm_store_pd(&C[40],Creg10) ; + _mm_store_pd(&C[42],Creg12) ; + _mm_store_pd(&C[48],Creg20) ; + _mm_store_pd(&C[50],Creg22) ; + + + /* Computing C(4:6,4:7) */ + + Areg0 = _mm_load_pd(&A[32]) ; + Areg1 = _mm_load_pd(&A[40]) ; + Areg2 = _mm_load_pd(&A[48]) ; + + Breg0 = _mm_load_pd(&B[4]) ; + Breg2 = _mm_load_pd(&B[6]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Creg00 = Breg0 ; + Creg00 = _mm_mul_pd(Creg00,Atmp) ; + Creg02 = Breg2 ; + Creg02 = _mm_mul_pd(Creg02,Atmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Creg10 = Breg0 ; + Creg10 = _mm_mul_pd(Creg10,Atmp) ; + Creg12 = Breg2 ; + Creg12 = _mm_mul_pd(Creg12,Atmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ; + Creg20 = Breg0 ; + Creg20 = _mm_mul_pd(Creg20,Atmp) ; + Creg22 = Breg2 ; + Creg22 = _mm_mul_pd(Creg22,Atmp) ; + + + Areg0 = _mm_load_pd(&A[34]) ; + Areg1 = _mm_load_pd(&A[42]) ; + Areg2 = _mm_load_pd(&A[50]) ; + + Breg0 = _mm_load_pd(&B[12]) ; + Breg2 = _mm_load_pd(&B[14]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + + Breg0 = _mm_load_pd(&B[20]) ; + Breg2 = _mm_load_pd(&B[22]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + + Areg0 = _mm_load_pd(&A[36]) ; + Areg1 = _mm_load_pd(&A[44]) ; + Areg2 = _mm_load_pd(&A[52]) ; + + Breg0 = _mm_load_pd(&B[28]) ; + Breg2 = _mm_load_pd(&B[30]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + + Breg0 = _mm_load_pd(&B[36]) ; + Breg2 = _mm_load_pd(&B[38]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + + Areg0 = _mm_load_pd(&A[38]) ; + Areg1 = _mm_load_pd(&A[46]) ; + Areg2 = _mm_load_pd(&A[54]) ; + + Breg0 = _mm_load_pd(&B[44]) ; + Breg2 = _mm_load_pd(&B[46]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(0,0)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + + Breg0 = _mm_load_pd(&B[52]) ; + Breg2 = _mm_load_pd(&B[54]) ; + + Atmp = Areg0 ; + Atmp = _mm_shuffle_pd(Atmp,Areg0,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg00 = _mm_add_pd(Creg00,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg02 = _mm_add_pd(Creg02,Btmp) ; + + Atmp = Areg1 ; + Atmp = _mm_shuffle_pd(Atmp,Areg1,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg10 = _mm_add_pd(Creg10,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg12 = _mm_add_pd(Creg12,Btmp) ; + + Atmp = Areg2 ; + Atmp = _mm_shuffle_pd(Atmp,Areg2,_MM_SHUFFLE2(1,1)) ; + Btmp = Breg0 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg20 = _mm_add_pd(Creg20,Btmp) ; + Btmp = Breg2 ; + Btmp = _mm_mul_pd(Btmp,Atmp) ; + Creg22 = _mm_add_pd(Creg22,Btmp) ; + + + _mm_store_pd(&C[36],Creg00) ; + _mm_store_pd(&C[38],Creg02) ; + _mm_store_pd(&C[44],Creg10) ; + _mm_store_pd(&C[46],Creg12) ; + _mm_store_pd(&C[52],Creg20) ; + _mm_store_pd(&C[54],Creg22) ; + + +} diff --git a/src/USER-MGPT/mgpt_mmul_bg_552.c.h b/src/USER-MGPT/mgpt_mmul_bg_552.c.h new file mode 100644 index 0000000000..16c6e9e4a8 --- /dev/null +++ b/src/USER-MGPT/mgpt_mmul_bg_552.c.h @@ -0,0 +1,358 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + + +/* #define TESTING */ + +#ifdef TESTING + +typedef struct { + double x,y; +} pair; + + +#define CPLX pair + +static double my_creal(CPLX x) { + return ((double *) &x)[0]; +} +static double my_cimag(CPLX x) { + return ((double *) &x)[1]; +} +static CPLX my_lfpd(const double *p) { + return ((CPLX *) p)[0]; +} +static void my_stfpd(double *p,CPLX x) { + ((CPLX *) p)[0] = x; +} +static CPLX my_fxsmul(CPLX x,double a) { + double y[2]; + y[0] = a * my_creal(x); + y[1] = a * my_cimag(x); + return ((CPLX *) y)[0]; +} +static CPLX my_fxcpmadd(CPLX t,CPLX x,double a) { + double y[2]; + y[0] = my_creal(t) + a * my_creal(x); + y[1] = my_cimag(t) + a * my_cimag(x); + return ((CPLX *) y)[0]; +} + +#define __creal my_creal +#define __cimag my_cimag +#define __lfpd my_lfpd +#define __stfpd my_stfpd +#define __fxsmul my_fxsmul +#define __fxcpmadd my_fxcpmadd + +#else + +#define CPLX double _Complex + +#endif + +void mmul_bg_5_8_5x2v2(const double * restrict A, + const double * restrict B, + double * restrict C) { + CPLX + Creg00, + Creg10, + Creg20, + Creg30, + Creg40; + CPLX Areg0,Areg1,Areg2,Areg3,Areg4; + CPLX Breg0; + + + /* Computing C(0:4,0:1) */ + + Areg0 = __lfpd(&A[0]) ; + Areg1 = __lfpd(&A[8]) ; + Areg2 = __lfpd(&A[16]) ; + Areg3 = __lfpd(&A[24]) ; + Areg4 = __lfpd(&A[32]) ; + + Breg0 = __lfpd(&B[0]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ; + + Creg20 = __fxsmul(Breg0,__cimag(Areg2)) ; + + Creg30 = __fxsmul(Breg0,__cimag(Areg3)) ; + + Creg40 = __fxsmul(Breg0,__cimag(Areg4)) ; + + + Areg0 = __lfpd(&A[2]) ; + Areg1 = __lfpd(&A[10]) ; + Areg2 = __lfpd(&A[18]) ; + Areg3 = __lfpd(&A[26]) ; + Areg4 = __lfpd(&A[34]) ; + + Breg0 = __lfpd(&B[8]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + Creg20 = __fxcpmadd(Creg20,Breg0,__creal(Areg2)) ; + + Creg30 = __fxcpmadd(Creg30,Breg0,__creal(Areg3)) ; + + Creg40 = __fxcpmadd(Creg40,Breg0,__creal(Areg4)) ; + + + Breg0 = __lfpd(&B[16]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + Creg20 = __fxcpmadd(Creg20,Breg0,__cimag(Areg2)) ; + + Creg30 = __fxcpmadd(Creg30,Breg0,__cimag(Areg3)) ; + + Creg40 = __fxcpmadd(Creg40,Breg0,__cimag(Areg4)) ; + + + Areg0 = __lfpd(&A[4]) ; + Areg1 = __lfpd(&A[12]) ; + Areg2 = __lfpd(&A[20]) ; + Areg3 = __lfpd(&A[28]) ; + Areg4 = __lfpd(&A[36]) ; + + Breg0 = __lfpd(&B[24]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + Creg20 = __fxcpmadd(Creg20,Breg0,__creal(Areg2)) ; + + Creg30 = __fxcpmadd(Creg30,Breg0,__creal(Areg3)) ; + + Creg40 = __fxcpmadd(Creg40,Breg0,__creal(Areg4)) ; + + + Breg0 = __lfpd(&B[32]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + Creg20 = __fxcpmadd(Creg20,Breg0,__cimag(Areg2)) ; + + Creg30 = __fxcpmadd(Creg30,Breg0,__cimag(Areg3)) ; + + Creg40 = __fxcpmadd(Creg40,Breg0,__cimag(Areg4)) ; + + + __stfpd(&C[0],Creg00) ; + __stfpd(&C[8],Creg10) ; + __stfpd(&C[16],Creg20) ; + __stfpd(&C[24],Creg30) ; + __stfpd(&C[32],Creg40) ; + + + /* Computing C(0:4,2:3) */ + + Areg0 = __lfpd(&A[0]) ; + Areg1 = __lfpd(&A[8]) ; + Areg2 = __lfpd(&A[16]) ; + Areg3 = __lfpd(&A[24]) ; + Areg4 = __lfpd(&A[32]) ; + + Breg0 = __lfpd(&B[2]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ; + + Creg20 = __fxsmul(Breg0,__cimag(Areg2)) ; + + Creg30 = __fxsmul(Breg0,__cimag(Areg3)) ; + + Creg40 = __fxsmul(Breg0,__cimag(Areg4)) ; + + + Areg0 = __lfpd(&A[2]) ; + Areg1 = __lfpd(&A[10]) ; + Areg2 = __lfpd(&A[18]) ; + Areg3 = __lfpd(&A[26]) ; + Areg4 = __lfpd(&A[34]) ; + + Breg0 = __lfpd(&B[10]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + Creg20 = __fxcpmadd(Creg20,Breg0,__creal(Areg2)) ; + + Creg30 = __fxcpmadd(Creg30,Breg0,__creal(Areg3)) ; + + Creg40 = __fxcpmadd(Creg40,Breg0,__creal(Areg4)) ; + + + Breg0 = __lfpd(&B[18]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + Creg20 = __fxcpmadd(Creg20,Breg0,__cimag(Areg2)) ; + + Creg30 = __fxcpmadd(Creg30,Breg0,__cimag(Areg3)) ; + + Creg40 = __fxcpmadd(Creg40,Breg0,__cimag(Areg4)) ; + + + Areg0 = __lfpd(&A[4]) ; + Areg1 = __lfpd(&A[12]) ; + Areg2 = __lfpd(&A[20]) ; + Areg3 = __lfpd(&A[28]) ; + Areg4 = __lfpd(&A[36]) ; + + Breg0 = __lfpd(&B[26]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + Creg20 = __fxcpmadd(Creg20,Breg0,__creal(Areg2)) ; + + Creg30 = __fxcpmadd(Creg30,Breg0,__creal(Areg3)) ; + + Creg40 = __fxcpmadd(Creg40,Breg0,__creal(Areg4)) ; + + + Breg0 = __lfpd(&B[34]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + Creg20 = __fxcpmadd(Creg20,Breg0,__cimag(Areg2)) ; + + Creg30 = __fxcpmadd(Creg30,Breg0,__cimag(Areg3)) ; + + Creg40 = __fxcpmadd(Creg40,Breg0,__cimag(Areg4)) ; + + + __stfpd(&C[2],Creg00) ; + __stfpd(&C[10],Creg10) ; + __stfpd(&C[18],Creg20) ; + __stfpd(&C[26],Creg30) ; + __stfpd(&C[34],Creg40) ; + + + /* Computing C(0:4,4:5) */ + + Areg0 = __lfpd(&A[0]) ; + Areg1 = __lfpd(&A[8]) ; + Areg2 = __lfpd(&A[16]) ; + Areg3 = __lfpd(&A[24]) ; + Areg4 = __lfpd(&A[32]) ; + + Breg0 = __lfpd(&B[4]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ; + + Creg20 = __fxsmul(Breg0,__cimag(Areg2)) ; + + Creg30 = __fxsmul(Breg0,__cimag(Areg3)) ; + + Creg40 = __fxsmul(Breg0,__cimag(Areg4)) ; + + + Areg0 = __lfpd(&A[2]) ; + Areg1 = __lfpd(&A[10]) ; + Areg2 = __lfpd(&A[18]) ; + Areg3 = __lfpd(&A[26]) ; + Areg4 = __lfpd(&A[34]) ; + + Breg0 = __lfpd(&B[12]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + Creg20 = __fxcpmadd(Creg20,Breg0,__creal(Areg2)) ; + + Creg30 = __fxcpmadd(Creg30,Breg0,__creal(Areg3)) ; + + Creg40 = __fxcpmadd(Creg40,Breg0,__creal(Areg4)) ; + + + Breg0 = __lfpd(&B[20]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + Creg20 = __fxcpmadd(Creg20,Breg0,__cimag(Areg2)) ; + + Creg30 = __fxcpmadd(Creg30,Breg0,__cimag(Areg3)) ; + + Creg40 = __fxcpmadd(Creg40,Breg0,__cimag(Areg4)) ; + + + Areg0 = __lfpd(&A[4]) ; + Areg1 = __lfpd(&A[12]) ; + Areg2 = __lfpd(&A[20]) ; + Areg3 = __lfpd(&A[28]) ; + Areg4 = __lfpd(&A[36]) ; + + Breg0 = __lfpd(&B[28]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + Creg20 = __fxcpmadd(Creg20,Breg0,__creal(Areg2)) ; + + Creg30 = __fxcpmadd(Creg30,Breg0,__creal(Areg3)) ; + + Creg40 = __fxcpmadd(Creg40,Breg0,__creal(Areg4)) ; + + + Breg0 = __lfpd(&B[36]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + Creg20 = __fxcpmadd(Creg20,Breg0,__cimag(Areg2)) ; + + Creg30 = __fxcpmadd(Creg30,Breg0,__cimag(Areg3)) ; + + Creg40 = __fxcpmadd(Creg40,Breg0,__cimag(Areg4)) ; + + + __stfpd(&C[4],Creg00) ; + __stfpd(&C[12],Creg10) ; + __stfpd(&C[20],Creg20) ; + __stfpd(&C[28],Creg30) ; + __stfpd(&C[36],Creg40) ; + + +} diff --git a/src/USER-MGPT/mgpt_mmul_bg_722.c.h b/src/USER-MGPT/mgpt_mmul_bg_722.c.h new file mode 100644 index 0000000000..e9821436e3 --- /dev/null +++ b/src/USER-MGPT/mgpt_mmul_bg_722.c.h @@ -0,0 +1,1075 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + + +/* #define TESTING */ + +#ifdef TESTING + +typedef struct { + double x,y; +} pair; + + +#define CPLX pair + +static double my_creal(CPLX x) { + return ((double *) &x)[0]; +} +static double my_cimag(CPLX x) { + return ((double *) &x)[1]; +} +static CPLX my_lfpd(const double *p) { + return ((CPLX *) p)[0]; +} +static void my_stfpd(double *p,CPLX x) { + ((CPLX *) p)[0] = x; +} +static CPLX my_fxsmul(CPLX x,double a) { + double y[2]; + y[0] = a * my_creal(x); + y[1] = a * my_cimag(x); + return ((CPLX *) y)[0]; +} +static CPLX my_fxcpmadd(CPLX t,CPLX x,double a) { + double y[2]; + y[0] = my_creal(t) + a * my_creal(x); + y[1] = my_cimag(t) + a * my_cimag(x); + return ((CPLX *) y)[0]; +} + +#define __creal my_creal +#define __cimag my_cimag +#define __lfpd my_lfpd +#define __stfpd my_stfpd +#define __fxsmul my_fxsmul +#define __fxcpmadd my_fxcpmadd + +#else + +#define CPLX double _Complex + +#endif + +void mmul_bg_7_8_2x2v2(const double * restrict A, + const double * restrict B, + double * restrict C) { + CPLX + Creg00, + Creg10; + CPLX Areg0,Areg1; + CPLX Breg0; + + + /* Computing C(0:1,0:1) */ + + Areg0 = __lfpd(&A[0]) ; + Areg1 = __lfpd(&A[8]) ; + + Breg0 = __lfpd(&B[0]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[2]) ; + Areg1 = __lfpd(&A[10]) ; + + Breg0 = __lfpd(&B[8]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[16]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[4]) ; + Areg1 = __lfpd(&A[12]) ; + + Breg0 = __lfpd(&B[24]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[32]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[6]) ; + Areg1 = __lfpd(&A[14]) ; + + Breg0 = __lfpd(&B[40]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[48]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + __stfpd(&C[0],Creg00) ; + __stfpd(&C[8],Creg10) ; + + + /* Computing C(0:1,2:3) */ + + Areg0 = __lfpd(&A[0]) ; + Areg1 = __lfpd(&A[8]) ; + + Breg0 = __lfpd(&B[2]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[2]) ; + Areg1 = __lfpd(&A[10]) ; + + Breg0 = __lfpd(&B[10]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[18]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[4]) ; + Areg1 = __lfpd(&A[12]) ; + + Breg0 = __lfpd(&B[26]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[34]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[6]) ; + Areg1 = __lfpd(&A[14]) ; + + Breg0 = __lfpd(&B[42]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[50]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + __stfpd(&C[2],Creg00) ; + __stfpd(&C[10],Creg10) ; + + + /* Computing C(0:1,4:5) */ + + Areg0 = __lfpd(&A[0]) ; + Areg1 = __lfpd(&A[8]) ; + + Breg0 = __lfpd(&B[4]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[2]) ; + Areg1 = __lfpd(&A[10]) ; + + Breg0 = __lfpd(&B[12]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[20]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[4]) ; + Areg1 = __lfpd(&A[12]) ; + + Breg0 = __lfpd(&B[28]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[36]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[6]) ; + Areg1 = __lfpd(&A[14]) ; + + Breg0 = __lfpd(&B[44]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[52]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + __stfpd(&C[4],Creg00) ; + __stfpd(&C[12],Creg10) ; + + + /* Computing C(0:1,6:7) */ + + Areg0 = __lfpd(&A[0]) ; + Areg1 = __lfpd(&A[8]) ; + + Breg0 = __lfpd(&B[6]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[2]) ; + Areg1 = __lfpd(&A[10]) ; + + Breg0 = __lfpd(&B[14]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[22]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[4]) ; + Areg1 = __lfpd(&A[12]) ; + + Breg0 = __lfpd(&B[30]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[38]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[6]) ; + Areg1 = __lfpd(&A[14]) ; + + Breg0 = __lfpd(&B[46]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[54]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + __stfpd(&C[6],Creg00) ; + __stfpd(&C[14],Creg10) ; + + + /* Computing C(2:3,0:1) */ + + Areg0 = __lfpd(&A[16]) ; + Areg1 = __lfpd(&A[24]) ; + + Breg0 = __lfpd(&B[0]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[18]) ; + Areg1 = __lfpd(&A[26]) ; + + Breg0 = __lfpd(&B[8]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[16]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[20]) ; + Areg1 = __lfpd(&A[28]) ; + + Breg0 = __lfpd(&B[24]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[32]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[22]) ; + Areg1 = __lfpd(&A[30]) ; + + Breg0 = __lfpd(&B[40]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[48]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + __stfpd(&C[16],Creg00) ; + __stfpd(&C[24],Creg10) ; + + + /* Computing C(2:3,2:3) */ + + Areg0 = __lfpd(&A[16]) ; + Areg1 = __lfpd(&A[24]) ; + + Breg0 = __lfpd(&B[2]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[18]) ; + Areg1 = __lfpd(&A[26]) ; + + Breg0 = __lfpd(&B[10]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[18]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[20]) ; + Areg1 = __lfpd(&A[28]) ; + + Breg0 = __lfpd(&B[26]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[34]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[22]) ; + Areg1 = __lfpd(&A[30]) ; + + Breg0 = __lfpd(&B[42]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[50]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + __stfpd(&C[18],Creg00) ; + __stfpd(&C[26],Creg10) ; + + + /* Computing C(2:3,4:5) */ + + Areg0 = __lfpd(&A[16]) ; + Areg1 = __lfpd(&A[24]) ; + + Breg0 = __lfpd(&B[4]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[18]) ; + Areg1 = __lfpd(&A[26]) ; + + Breg0 = __lfpd(&B[12]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[20]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[20]) ; + Areg1 = __lfpd(&A[28]) ; + + Breg0 = __lfpd(&B[28]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[36]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[22]) ; + Areg1 = __lfpd(&A[30]) ; + + Breg0 = __lfpd(&B[44]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[52]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + __stfpd(&C[20],Creg00) ; + __stfpd(&C[28],Creg10) ; + + + /* Computing C(2:3,6:7) */ + + Areg0 = __lfpd(&A[16]) ; + Areg1 = __lfpd(&A[24]) ; + + Breg0 = __lfpd(&B[6]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[18]) ; + Areg1 = __lfpd(&A[26]) ; + + Breg0 = __lfpd(&B[14]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[22]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[20]) ; + Areg1 = __lfpd(&A[28]) ; + + Breg0 = __lfpd(&B[30]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[38]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[22]) ; + Areg1 = __lfpd(&A[30]) ; + + Breg0 = __lfpd(&B[46]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[54]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + __stfpd(&C[22],Creg00) ; + __stfpd(&C[30],Creg10) ; + + + /* Computing C(4:5,0:1) */ + + Areg0 = __lfpd(&A[32]) ; + Areg1 = __lfpd(&A[40]) ; + + Breg0 = __lfpd(&B[0]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[34]) ; + Areg1 = __lfpd(&A[42]) ; + + Breg0 = __lfpd(&B[8]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[16]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[36]) ; + Areg1 = __lfpd(&A[44]) ; + + Breg0 = __lfpd(&B[24]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[32]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[38]) ; + Areg1 = __lfpd(&A[46]) ; + + Breg0 = __lfpd(&B[40]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[48]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + __stfpd(&C[32],Creg00) ; + __stfpd(&C[40],Creg10) ; + + + /* Computing C(4:5,2:3) */ + + Areg0 = __lfpd(&A[32]) ; + Areg1 = __lfpd(&A[40]) ; + + Breg0 = __lfpd(&B[2]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[34]) ; + Areg1 = __lfpd(&A[42]) ; + + Breg0 = __lfpd(&B[10]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[18]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[36]) ; + Areg1 = __lfpd(&A[44]) ; + + Breg0 = __lfpd(&B[26]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[34]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[38]) ; + Areg1 = __lfpd(&A[46]) ; + + Breg0 = __lfpd(&B[42]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[50]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + __stfpd(&C[34],Creg00) ; + __stfpd(&C[42],Creg10) ; + + + /* Computing C(4:5,4:5) */ + + Areg0 = __lfpd(&A[32]) ; + Areg1 = __lfpd(&A[40]) ; + + Breg0 = __lfpd(&B[4]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[34]) ; + Areg1 = __lfpd(&A[42]) ; + + Breg0 = __lfpd(&B[12]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[20]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[36]) ; + Areg1 = __lfpd(&A[44]) ; + + Breg0 = __lfpd(&B[28]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[36]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[38]) ; + Areg1 = __lfpd(&A[46]) ; + + Breg0 = __lfpd(&B[44]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[52]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + __stfpd(&C[36],Creg00) ; + __stfpd(&C[44],Creg10) ; + + + /* Computing C(4:5,6:7) */ + + Areg0 = __lfpd(&A[32]) ; + Areg1 = __lfpd(&A[40]) ; + + Breg0 = __lfpd(&B[6]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + Creg10 = __fxsmul(Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[34]) ; + Areg1 = __lfpd(&A[42]) ; + + Breg0 = __lfpd(&B[14]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[22]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[36]) ; + Areg1 = __lfpd(&A[44]) ; + + Breg0 = __lfpd(&B[30]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[38]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + Areg0 = __lfpd(&A[38]) ; + Areg1 = __lfpd(&A[46]) ; + + Breg0 = __lfpd(&B[46]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__creal(Areg1)) ; + + + Breg0 = __lfpd(&B[54]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + Creg10 = __fxcpmadd(Creg10,Breg0,__cimag(Areg1)) ; + + + __stfpd(&C[38],Creg00) ; + __stfpd(&C[46],Creg10) ; + + + /* Computing C(6:6,0:1) */ + + Areg0 = __lfpd(&A[48]) ; + + Breg0 = __lfpd(&B[0]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + + Areg0 = __lfpd(&A[50]) ; + + Breg0 = __lfpd(&B[8]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + + Breg0 = __lfpd(&B[16]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + + Areg0 = __lfpd(&A[52]) ; + + Breg0 = __lfpd(&B[24]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + + Breg0 = __lfpd(&B[32]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + + Areg0 = __lfpd(&A[54]) ; + + Breg0 = __lfpd(&B[40]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + + Breg0 = __lfpd(&B[48]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + + __stfpd(&C[48],Creg00) ; + + + /* Computing C(6:6,2:3) */ + + Areg0 = __lfpd(&A[48]) ; + + Breg0 = __lfpd(&B[2]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + + Areg0 = __lfpd(&A[50]) ; + + Breg0 = __lfpd(&B[10]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + + Breg0 = __lfpd(&B[18]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + + Areg0 = __lfpd(&A[52]) ; + + Breg0 = __lfpd(&B[26]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + + Breg0 = __lfpd(&B[34]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + + Areg0 = __lfpd(&A[54]) ; + + Breg0 = __lfpd(&B[42]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + + Breg0 = __lfpd(&B[50]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + + __stfpd(&C[50],Creg00) ; + + + /* Computing C(6:6,4:5) */ + + Areg0 = __lfpd(&A[48]) ; + + Breg0 = __lfpd(&B[4]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + + Areg0 = __lfpd(&A[50]) ; + + Breg0 = __lfpd(&B[12]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + + Breg0 = __lfpd(&B[20]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + + Areg0 = __lfpd(&A[52]) ; + + Breg0 = __lfpd(&B[28]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + + Breg0 = __lfpd(&B[36]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + + Areg0 = __lfpd(&A[54]) ; + + Breg0 = __lfpd(&B[44]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + + Breg0 = __lfpd(&B[52]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + + __stfpd(&C[52],Creg00) ; + + + /* Computing C(6:6,6:7) */ + + Areg0 = __lfpd(&A[48]) ; + + Breg0 = __lfpd(&B[6]) ; + + Creg00 = __fxsmul(Breg0,__cimag(Areg0)) ; + + + Areg0 = __lfpd(&A[50]) ; + + Breg0 = __lfpd(&B[14]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + + Breg0 = __lfpd(&B[22]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + + Areg0 = __lfpd(&A[52]) ; + + Breg0 = __lfpd(&B[30]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + + Breg0 = __lfpd(&B[38]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + + Areg0 = __lfpd(&A[54]) ; + + Breg0 = __lfpd(&B[46]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__creal(Areg0)) ; + + + Breg0 = __lfpd(&B[54]) ; + + Creg00 = __fxcpmadd(Creg00,Breg0,__cimag(Areg0)) ; + + + __stfpd(&C[54],Creg00) ; + + +} diff --git a/src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h b/src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h new file mode 100644 index 0000000000..2e38b5b0cf --- /dev/null +++ b/src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h @@ -0,0 +1,236 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + +#define vector vector4double +#define const +#define vec_fma vec_madd + +void mmul_bgq_n5_lda8_2x8(const double * restrict A, + const double * restrict B, + double * restrict C) { + vector + Creg00,Creg04, + Creg10,Creg14; + vector Areg0,Areg1; + vector Breg0,Breg4; + vector Atmp; + + + /* Computing C(0:1,0:5) */ + + Areg0 = vec_ld(8*0,A) ; + Areg1 = vec_ld(8*8,A) ; + + Breg0 = vec_ld(8*0,B) ; + Breg4 = vec_ld(8*4,B) ; + + Atmp = vec_splat(Areg0,1) ; + Creg00 = vec_mul(Atmp,Breg0) ; + Creg04 = vec_mul(Atmp,Breg4) ; + + Atmp = vec_splat(Areg1,1) ; + Creg10 = vec_mul(Atmp,Breg0) ; + Creg14 = vec_mul(Atmp,Breg4) ; + + + Breg0 = vec_ld(8*8,B) ; + Breg4 = vec_ld(8*12,B) ; + + Atmp = vec_splat(Areg0,2) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,2) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + + Breg0 = vec_ld(8*16,B) ; + Breg4 = vec_ld(8*20,B) ; + + Atmp = vec_splat(Areg0,3) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,3) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + + Areg0 = vec_ld(8*4,A) ; + Areg1 = vec_ld(8*12,A) ; + + Breg0 = vec_ld(8*24,B) ; + Breg4 = vec_ld(8*28,B) ; + + Atmp = vec_splat(Areg0,0) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,0) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + + Breg0 = vec_ld(8*32,B) ; + Breg4 = vec_ld(8*36,B) ; + + Atmp = vec_splat(Areg0,1) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,1) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + + vec_st(Creg00,8*0,C) ; + vec_st(Creg04,8*4,C) ; + vec_st(Creg10,8*8,C) ; + vec_st(Creg14,8*12,C) ; + + + /* Computing C(2:3,0:5) */ + + Areg0 = vec_ld(8*16,A) ; + Areg1 = vec_ld(8*24,A) ; + + Breg0 = vec_ld(8*0,B) ; + Breg4 = vec_ld(8*4,B) ; + + Atmp = vec_splat(Areg0,1) ; + Creg00 = vec_mul(Atmp,Breg0) ; + Creg04 = vec_mul(Atmp,Breg4) ; + + Atmp = vec_splat(Areg1,1) ; + Creg10 = vec_mul(Atmp,Breg0) ; + Creg14 = vec_mul(Atmp,Breg4) ; + + + Breg0 = vec_ld(8*8,B) ; + Breg4 = vec_ld(8*12,B) ; + + Atmp = vec_splat(Areg0,2) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,2) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + + Breg0 = vec_ld(8*16,B) ; + Breg4 = vec_ld(8*20,B) ; + + Atmp = vec_splat(Areg0,3) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,3) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + + Areg0 = vec_ld(8*20,A) ; + Areg1 = vec_ld(8*28,A) ; + + Breg0 = vec_ld(8*24,B) ; + Breg4 = vec_ld(8*28,B) ; + + Atmp = vec_splat(Areg0,0) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,0) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + + Breg0 = vec_ld(8*32,B) ; + Breg4 = vec_ld(8*36,B) ; + + Atmp = vec_splat(Areg0,1) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,1) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + + vec_st(Creg00,8*16,C) ; + vec_st(Creg04,8*20,C) ; + vec_st(Creg10,8*24,C) ; + vec_st(Creg14,8*28,C) ; + + + /* Computing C(4:4,0:5) */ + + Areg0 = vec_ld(8*32,A) ; + + Breg0 = vec_ld(8*0,B) ; + Breg4 = vec_ld(8*4,B) ; + + Atmp = vec_splat(Areg0,1) ; + Creg00 = vec_mul(Atmp,Breg0) ; + Creg04 = vec_mul(Atmp,Breg4) ; + + + Breg0 = vec_ld(8*8,B) ; + Breg4 = vec_ld(8*12,B) ; + + Atmp = vec_splat(Areg0,2) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + + Breg0 = vec_ld(8*16,B) ; + Breg4 = vec_ld(8*20,B) ; + + Atmp = vec_splat(Areg0,3) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + + Areg0 = vec_ld(8*36,A) ; + + Breg0 = vec_ld(8*24,B) ; + Breg4 = vec_ld(8*28,B) ; + + Atmp = vec_splat(Areg0,0) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + + Breg0 = vec_ld(8*32,B) ; + Breg4 = vec_ld(8*36,B) ; + + Atmp = vec_splat(Areg0,1) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + + vec_st(Creg00,8*32,C) ; + vec_st(Creg04,8*36,C) ; + + +} + +#undef vector +#undef const +#undef vec_fma diff --git a/src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h b/src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h new file mode 100644 index 0000000000..26f36c4844 --- /dev/null +++ b/src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h @@ -0,0 +1,332 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + +#define vector vector4double +#define const +#define vec_fma vec_madd + +void mmul_bgq_n7_lda8_4x8(const double * restrict A, + const double * restrict B, + double * restrict C) { + vector + Creg00,Creg04, + Creg10,Creg14, + Creg20,Creg24, + Creg30,Creg34; + vector Areg0,Areg1,Areg2,Areg3; + vector Breg0,Breg4; + vector Atmp; + + + /* Computing C(0:3,0:7) */ + + Areg0 = vec_ld(8*0,A) ; + Areg1 = vec_ld(8*8,A) ; + Areg2 = vec_ld(8*16,A) ; + Areg3 = vec_ld(8*24,A) ; + + Breg0 = vec_ld(8*0,B) ; + Breg4 = vec_ld(8*4,B) ; + + Atmp = vec_splat(Areg0,1) ; + Creg00 = vec_mul(Atmp,Breg0) ; + Creg04 = vec_mul(Atmp,Breg4) ; + + Atmp = vec_splat(Areg1,1) ; + Creg10 = vec_mul(Atmp,Breg0) ; + Creg14 = vec_mul(Atmp,Breg4) ; + + Atmp = vec_splat(Areg2,1) ; + Creg20 = vec_mul(Atmp,Breg0) ; + Creg24 = vec_mul(Atmp,Breg4) ; + + Atmp = vec_splat(Areg3,1) ; + Creg30 = vec_mul(Atmp,Breg0) ; + Creg34 = vec_mul(Atmp,Breg4) ; + + + Breg0 = vec_ld(8*8,B) ; + Breg4 = vec_ld(8*12,B) ; + + Atmp = vec_splat(Areg0,2) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,2) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + Atmp = vec_splat(Areg2,2) ; + Creg20 = vec_fma(Atmp,Breg0,Creg20) ; + Creg24 = vec_fma(Atmp,Breg4,Creg24) ; + + Atmp = vec_splat(Areg3,2) ; + Creg30 = vec_fma(Atmp,Breg0,Creg30) ; + Creg34 = vec_fma(Atmp,Breg4,Creg34) ; + + + Breg0 = vec_ld(8*16,B) ; + Breg4 = vec_ld(8*20,B) ; + + Atmp = vec_splat(Areg0,3) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,3) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + Atmp = vec_splat(Areg2,3) ; + Creg20 = vec_fma(Atmp,Breg0,Creg20) ; + Creg24 = vec_fma(Atmp,Breg4,Creg24) ; + + Atmp = vec_splat(Areg3,3) ; + Creg30 = vec_fma(Atmp,Breg0,Creg30) ; + Creg34 = vec_fma(Atmp,Breg4,Creg34) ; + + + Areg0 = vec_ld(8*4,A) ; + Areg1 = vec_ld(8*12,A) ; + Areg2 = vec_ld(8*20,A) ; + Areg3 = vec_ld(8*28,A) ; + + Breg0 = vec_ld(8*24,B) ; + Breg4 = vec_ld(8*28,B) ; + + Atmp = vec_splat(Areg0,0) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,0) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + Atmp = vec_splat(Areg2,0) ; + Creg20 = vec_fma(Atmp,Breg0,Creg20) ; + Creg24 = vec_fma(Atmp,Breg4,Creg24) ; + + Atmp = vec_splat(Areg3,0) ; + Creg30 = vec_fma(Atmp,Breg0,Creg30) ; + Creg34 = vec_fma(Atmp,Breg4,Creg34) ; + + + Breg0 = vec_ld(8*32,B) ; + Breg4 = vec_ld(8*36,B) ; + + Atmp = vec_splat(Areg0,1) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,1) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + Atmp = vec_splat(Areg2,1) ; + Creg20 = vec_fma(Atmp,Breg0,Creg20) ; + Creg24 = vec_fma(Atmp,Breg4,Creg24) ; + + Atmp = vec_splat(Areg3,1) ; + Creg30 = vec_fma(Atmp,Breg0,Creg30) ; + Creg34 = vec_fma(Atmp,Breg4,Creg34) ; + + + Breg0 = vec_ld(8*40,B) ; + Breg4 = vec_ld(8*44,B) ; + + Atmp = vec_splat(Areg0,2) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,2) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + Atmp = vec_splat(Areg2,2) ; + Creg20 = vec_fma(Atmp,Breg0,Creg20) ; + Creg24 = vec_fma(Atmp,Breg4,Creg24) ; + + Atmp = vec_splat(Areg3,2) ; + Creg30 = vec_fma(Atmp,Breg0,Creg30) ; + Creg34 = vec_fma(Atmp,Breg4,Creg34) ; + + + Breg0 = vec_ld(8*48,B) ; + Breg4 = vec_ld(8*52,B) ; + + Atmp = vec_splat(Areg0,3) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,3) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + Atmp = vec_splat(Areg2,3) ; + Creg20 = vec_fma(Atmp,Breg0,Creg20) ; + Creg24 = vec_fma(Atmp,Breg4,Creg24) ; + + Atmp = vec_splat(Areg3,3) ; + Creg30 = vec_fma(Atmp,Breg0,Creg30) ; + Creg34 = vec_fma(Atmp,Breg4,Creg34) ; + + + vec_st(Creg00,8*0,C) ; + vec_st(Creg04,8*4,C) ; + vec_st(Creg10,8*8,C) ; + vec_st(Creg14,8*12,C) ; + vec_st(Creg20,8*16,C) ; + vec_st(Creg24,8*20,C) ; + vec_st(Creg30,8*24,C) ; + vec_st(Creg34,8*28,C) ; + + + /* Computing C(4:6,0:7) */ + + Areg0 = vec_ld(8*32,A) ; + Areg1 = vec_ld(8*40,A) ; + Areg2 = vec_ld(8*48,A) ; + + Breg0 = vec_ld(8*0,B) ; + Breg4 = vec_ld(8*4,B) ; + + Atmp = vec_splat(Areg0,1) ; + Creg00 = vec_mul(Atmp,Breg0) ; + Creg04 = vec_mul(Atmp,Breg4) ; + + Atmp = vec_splat(Areg1,1) ; + Creg10 = vec_mul(Atmp,Breg0) ; + Creg14 = vec_mul(Atmp,Breg4) ; + + Atmp = vec_splat(Areg2,1) ; + Creg20 = vec_mul(Atmp,Breg0) ; + Creg24 = vec_mul(Atmp,Breg4) ; + + + Breg0 = vec_ld(8*8,B) ; + Breg4 = vec_ld(8*12,B) ; + + Atmp = vec_splat(Areg0,2) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,2) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + Atmp = vec_splat(Areg2,2) ; + Creg20 = vec_fma(Atmp,Breg0,Creg20) ; + Creg24 = vec_fma(Atmp,Breg4,Creg24) ; + + + Breg0 = vec_ld(8*16,B) ; + Breg4 = vec_ld(8*20,B) ; + + Atmp = vec_splat(Areg0,3) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,3) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + Atmp = vec_splat(Areg2,3) ; + Creg20 = vec_fma(Atmp,Breg0,Creg20) ; + Creg24 = vec_fma(Atmp,Breg4,Creg24) ; + + + Areg0 = vec_ld(8*36,A) ; + Areg1 = vec_ld(8*44,A) ; + Areg2 = vec_ld(8*52,A) ; + + Breg0 = vec_ld(8*24,B) ; + Breg4 = vec_ld(8*28,B) ; + + Atmp = vec_splat(Areg0,0) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,0) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + Atmp = vec_splat(Areg2,0) ; + Creg20 = vec_fma(Atmp,Breg0,Creg20) ; + Creg24 = vec_fma(Atmp,Breg4,Creg24) ; + + + Breg0 = vec_ld(8*32,B) ; + Breg4 = vec_ld(8*36,B) ; + + Atmp = vec_splat(Areg0,1) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,1) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + Atmp = vec_splat(Areg2,1) ; + Creg20 = vec_fma(Atmp,Breg0,Creg20) ; + Creg24 = vec_fma(Atmp,Breg4,Creg24) ; + + + Breg0 = vec_ld(8*40,B) ; + Breg4 = vec_ld(8*44,B) ; + + Atmp = vec_splat(Areg0,2) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,2) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + Atmp = vec_splat(Areg2,2) ; + Creg20 = vec_fma(Atmp,Breg0,Creg20) ; + Creg24 = vec_fma(Atmp,Breg4,Creg24) ; + + + Breg0 = vec_ld(8*48,B) ; + Breg4 = vec_ld(8*52,B) ; + + Atmp = vec_splat(Areg0,3) ; + Creg00 = vec_fma(Atmp,Breg0,Creg00) ; + Creg04 = vec_fma(Atmp,Breg4,Creg04) ; + + Atmp = vec_splat(Areg1,3) ; + Creg10 = vec_fma(Atmp,Breg0,Creg10) ; + Creg14 = vec_fma(Atmp,Breg4,Creg14) ; + + Atmp = vec_splat(Areg2,3) ; + Creg20 = vec_fma(Atmp,Breg0,Creg20) ; + Creg24 = vec_fma(Atmp,Breg4,Creg24) ; + + + vec_st(Creg00,8*32,C) ; + vec_st(Creg04,8*36,C) ; + vec_st(Creg10,8*40,C) ; + vec_st(Creg14,8*44,C) ; + vec_st(Creg20,8*48,C) ; + vec_st(Creg24,8*52,C) ; + + +} + +#undef vector +#undef const +#undef vec_fma diff --git a/src/USER-MGPT/mgpt_readpot.cpp b/src/USER-MGPT/mgpt_readpot.cpp new file mode 100644 index 0000000000..bfbb15ddcb --- /dev/null +++ b/src/USER-MGPT/mgpt_readpot.cpp @@ -0,0 +1,566 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include + +#include "mgpt_splinetab.h" + +#include "mgpt_readpot.h" + +static double fgauss(double x,double al) { + return exp(-al * pow(x-1.0, 2)); +} +static double hgauss(double x,double al) { + return (1.0 + al * pow(x-1.0, 2)) * exp(-al * pow(x-1.0, 2)); +} +static double fl(double r,int mode,double rp,double p1,double al,double r0,double pn) +{ + double term; + //double pn=1.0; + if (mode <= 4) + term = pow(rp/r, p1); + else + term = exp(-p1*(pow(r/rp, pn) - 1.0)/pn); + + if (r <= r0) return term; + double quan = al*(r/r0 - 1.0)*(r/r0 - 1.0); + if(mode <= 2) + return term*exp(-quan); + else + return term*(1.0 + quan)*exp(-quan); +} + +static int cmp_double(const void *ap,const void *bp) { + double a = *((const double *) ap); + double b = *((const double *) bp); + if(a < b) + return -1; + else if(a > b) + return 1; + else + return 0; +} +static void getparmindata(const char *potin_file,int nvol[1],double vol0[1],double x0[1],double x1[1]) { + int n,vsize; + double *volarr; + char metal[80],metalx[80]; + int ipot,ipotx,mode,modex; + FILE *in = fopen(potin_file,"r"); + char line[1024]; + + if(in == NULL) { + fprintf(stderr,"@%s:%d: Error reading potin file. Can not open file \'%s\'.\n", + __FILE__,__LINE__,potin_file); + exit(1); + } + + vsize = 10; + volarr = (double *) malloc(sizeof(double) * vsize); + n = 0; + while(fgets(line,sizeof(line),in) != NULL) { + double zval,ivol,rws,mass; + double r0x,r1x,drx; + int nrx,i; + + if(line[strspn(line," \t")] == '#') continue; + + if(n == 0) { + metal[0] = 0; + if(sscanf(line,"%s %d %d",metal,&ipot,&mode) != 3) { + fprintf(stderr,"@%s:%d: Error on potin file. line = %s\n", + __FILE__,__LINE__,line); + exit(1); + } + } else { + metalx[0] = 0; + if(sscanf(line,"%s %d %d",metalx,&ipotx,&modex) != 3) { + fprintf(stderr,"@%s:%d: Error on potin file. line = %s\n", + __FILE__,__LINE__,line); + exit(1); + } else if(strcmp(metal,metalx) != 0 || ipot != ipotx || mode != modex) { + fprintf(stderr,"@%s:%d: Error on potin file, parameter mismatch:\n" + " metal = \'%s\' ipot = %d mode = %d\n" + " metalx = \'%s\' ipotx = %d modex = %d\n", + __FILE__,__LINE__, + metal,ipot,mode, + metalx,ipotx,modex); + exit(1); + } + } + + fgets(line,sizeof(line),in); + sscanf(line,"%lf %lf %lf %lf",&zval,&ivol,&rws,&mass); + if(n >= vsize) { + vsize = 2*vsize; + volarr = (double *) realloc(volarr,sizeof(double) * vsize); + } + volarr[n] = ivol; + n = n + 1; + + for(i = 0; i<5; i++) + fgets(line,sizeof(line),in); + sscanf(line,"%lf %lf %lf",&r0x,&r1x,&drx); + nrx = (int) ((r1x-r0x)/drx + 1.1); /* Really: 1+round((r1-r0)/dr) */ + for(i = 0; i nvol = %d, vol0 = %.6f, x0= %.6f, x1 = %.6f, dx = %.6f\n", + nvol,vol0,x0,x1,dx); + } + } else { + /* Two-line version, reparse this line, and read second line */ + sscanf(line,"%lf %lf %lf %lf",&x0,&x1,&dx,&vol0); + fgets(line,sizeof(line),in); + sscanf(line,"%lf %lf %lf %lf %d",&ddl[1],&ddl[2],&ddl[3],&ddl[4],&L); + + } + double rws_scale = pow(3.0*vol0/(16.0*atan(1.0)),1.0/3.0); + fclose(in); + + lang = L+1; + lmax = 2*L+1; + double s = ddl[1],p = ddl[2],d = ddl[3],f = ddl[4]; + double ss = s*s, pp = p*p, dd = d*d, ff = f*f; + anorm3 = s*ss + 2.0*( p*pp + d*dd + f*ff); + anorm4 = ss*ss + 2.0*(pp*pp + dd*dd + ff*ff); + /* + for(i = 1; i<=lmax; i++) { + for(j = 1; j<=lmax; j++) + del0.m[i][j] = 0.0; + del0[i][i] = 1.0; + } + Matrix::sz = lmax; + */ + nx = (int) ((x1-x0)/dx + 1.1); /* Really: 1+round((x1-x0)/dx) */ + vatab = new double[nx]; + vbtab = new double[nx]; + vctab = new double[nx]; + vdtab = new double[nx]; + vetab = new double[nx]; + + p1tab = new double[nx]; + altab = new double[nx]; + + r0rwstab = new double[nx]; + evol0tab = new double[nx]; + + in = fopen(potin_file,"r"); + + int *tag = new int[nx]; + for(i = 0; i 1e-3) + printf("Wrong volume guess, i=%d volgues=%15.5e ivol=%15.5e\n", + i,volguess,ivol); + }*/ + + double ifrac = (pow(ivol/vol0,1.0/3.0) - x0)/((x1-x0)/(nx-1)); + i = (int) (ifrac + 0.1); + if(fabs(i - ifrac) > 0.01) { + printf("Volume point not in table... ii=%d i=%d ifrac=%15.5e vol=%15.5e\n", + ii,i,ifrac,ivol); + printf("vol0 = %15.5e zval = %15.5e mass = %15.5e\n",vol0,zval,mass); + exit(1); + } else if(tag[i] == 1) { + printf("Duplicate volume point in table.... ii=%d i=%d ifrac=%15.5e vol=%15.5e\n", + ii,i,ifrac,ivol); + exit(1); + } else tag[i] = 1; + + fgets(line,sizeof(line),in); + sscanf(line,"%lf %lf %lf %lf",&r0rwstab[i],&altab[i],&rcrws,&rmrws); + fgets(line,sizeof(line),in); + sscanf(line,"%lf %lf %lf",&p1tab[i],&unused,&evol0tab[i]); + + fgets(line,sizeof(line),in); + sscanf(line,"%lf %lf %lf %lf %lf", + &vatab[i],&vbtab[i],&vctab[i],&vdtab[i],&vetab[i]); + if(ipot == 1) { + vatab[i] *= vdtab[i]; + vctab[i] *= vctab[i]; + vetab[i] *= vetab[i]; + } + + fgets(line,sizeof(line),in); + + fgets(line,sizeof(line),in); + sscanf(line,"%lf %lf %lf",&r0x,&r1x,&drx); + nrx = (int) ((r1x-r0x)/drx + 1.1); /* Really: 1+round((r1-r0)/dr) */ + + if(ii == 0) { + r0 = r0x; r1 = r1x; dr = drx; nr = nrx; + vpairtab = new double[nx*nr]; + } else { + /* Check that {r0,r1,dr,nr}x == {r0,r1,dr,nr} */ + } + + for(j = 0; j 0.0); + + double xi = x0 + i/((double) (nx-1)) * (x1-x0); + double rws = rws_scale * xi; + + double r0rws = r0rwstab[i]; + double r00 = r0rws*rws,rp = 1.8*rws; + if(bscreen == 0) r0rws = 10.0; + double alp = al,alm = al; + if(mode == 2 || mode == 4 || mode == 6) alm = 125.0; + al = alp; + + double r = r0 + j*(r1-r0)/(nr-1); + + double rrws = r/rws; + //double rsqr = r*r; + // double fl(double r,int mode,double rp,double p1,double al,double r0) + double flr = fl(r,mode,rp,p1,al,r00,pn); + double fl2 = flr*flr; + double v2a = vatab[i]*fl2*fl2; + double v2b = vbtab[i]*fl2; + double fscr = 1.0; + + if(bscreen == 1 && rrws >= r0rws) { + double arg = rrws/r0rwstab[i]; + double arg1 = arg - 1.0; + double arg12 = arg1*arg1; + double f,dp; + if(mode <= 2) { + f = fgauss(arg,al); + dp=2.*al*arg*arg1; + } + else { + f = hgauss(arg,al); + double arg13 = arg1*arg12; + dp=2.0*al*al*arg*arg13/(1.+al*arg12); + } + fscr = f*f; + } + + double vpair_tmp = vpairtab[i*nr+j]; + vpairtab[i*nr+j] = vpairtab[i*nr+j]*fscr + v2a - v2b; + + if(0) if(fabs(vol-ivol) < 0.01) { + static FILE *xfile = NULL; + if(j == 0) { + xfile = fopen("mgpt5-pot.dat","w"); + fprintf(xfile,"%%%% vol = %15.5e ivol = %15.5e i = %d ii = %d\n", + vol,ivol,i,ii); + } + fprintf(xfile,"%15.5e %15.5e %15.5e %15.5e %15.5e %20.10e\n", + r,vpair_tmp,fscr,v2a,v2b,flr); + if(j == nr-1) fclose(xfile); + } + + + } + + } + } + fclose(in); + + for(i = 0; i nx) ? nr : nx][4]; + makespline(nx,1,vatab,C); + evalspline(nx-1,x0,x1,C,x,&va,&dva,&unused); + dva *= dxdv; + + makespline(nx,1,vbtab,C); + evalspline(nx-1,x0,x1,C,x,&vb,&dvb,&unused); + dvb *= dxdv; + + makespline(nx,1,vctab,C); + evalspline(nx-1,x0,x1,C,x,&vc,&dvc,&unused); + dvc *= dxdv; + + makespline(nx,1,vdtab,C); + evalspline(nx-1,x0,x1,C,x,&vd,&dvd,&unused); + dvd *= dxdv; + + makespline(nx,1,vetab,C); + evalspline(nx-1,x0,x1,C,x,&ve,&dve,&unused); + dve *= dxdv; + + makespline(nx,1,p1tab,C); + evalspline(nx-1,x0,x1,C,x,&p1,&dp1,&unused); + dp1 *= dxdv; + + makespline(nx,1,altab,C); + evalspline(nx-1,x0,x1,C,x,&al,&dal,&unused); + dal *= dxdv; + if(mode == 2 || mode == 4 || mode == 6) { + al = 125.0; + dal = 0.0; + } + + + { + double dr0rws; + makespline(nx,1,r0rwstab,C); + evalspline(nx-1,x0,x1,C,x,&r0rws,&dr0rws,&unused); + dr0rws *= dxdv; + rws = rws_scale*x; + r00 = r0rws * rws; + dr00 = dr0rws*rws + r0rws*rws_scale*dxdv; + rp = 1.8 * rws; + drp = 1.8 * rws_scale*dxdv; + } + + makespline(nx,1,evol0tab,C); + evalspline(nx-1,x0,x1,C,x,&evol0,&devol0,&unused); + devol0 *= dxdv; + + if(1) { + printf("%% READPOT PARAMETERS:\n"); + + printf("%% ddl = %15.5e %15.5e %15.5e %15.5e\n",ddl[1],ddl[2],ddl[3],ddl[4]); + printf("%% anorm3 = %15.5e anorm4 = %15.5e\n",anorm3,anorm4); + + printf("%% x = %15.5e pn = %15.5e\n",x,pn); + printf("%% va = %15.5e dva = %15.5e\n",va,dva); + printf("%% vb = %15.5e dvb = %15.5e\n",vb,dvb); + printf("%% vc = %15.5e dvc = %15.5e\n",vc,dvc); + printf("%% vd = %15.5e dvd = %15.5e\n",vd,dvd); + printf("%% ve = %15.5e dve = %15.5e\n",ve,dve); + printf("%% p1 = %15.5e dp1 = %15.5e\n",p1,dp1); + printf("%% al = %15.5e dal = %15.5e\n",al,dal); + printf("%% rp = %15.5e drp = %15.5e\n",rp,drp); + printf("%% r00= %15.5e dr00= %15.5e\n",r00,dr00); + printf("\n"); + } + + y = new double[nr]; + dy = new double[nr]; + + for(j = 0; j + +#include "mgpt_splinetab.h" + +struct potdata { + double va,vb,vc,vd,ve,p1,al,rp,r00,pn; + double dva,dvb,dvc,dvd,dve,dp1,dal,drp,dr00; + double evol0,devol0; + double (*vpair_spline)[4],(*dvpair_spline)[4]; + double r0,r1; + int nr; + + double mass,rcrit,rmax; + + int lang,lmax; + double anorm3,anorm4; + double ddl[5]; + + int ipot,mode; + char metal[80]; + + double input_vol; + + void readpot(const char *parmin_file,const char *potin_file,double vol); + + void eval_pot(double r,double *e_p,double *f_p) { + double d2y; + evalspline(nr-1,r0,r1,vpair_spline,r,e_p,f_p,&d2y); + } + + void eval_vir(double r,double *v_p) { + double dy,d2y; + evalspline(nr-1,r0,r1,dvpair_spline,r,v_p,&dy,&d2y); + } +}; + + +struct potdata2 { + typedef double (*spline)[4]; + spline va,vb,vc,vd,ve,p1,al,rp,r00; + spline dva,dvb,dvc,dvd,dve,dp1,dal,drp,dr00; + spline evol0,devol0; + double (*vpair)[4][4],(*dvpair)[4][4]; + double r0,r1,T0,T1; + int nr,nt; + + potdata *potlist; + + double mass,rcrit,rmax; + + int lang,lmax; + spline ddl[5]; + + int ipot,mode; + char metal[80]; + + double input_vol; + + /* Functions to retrieve temperature dependent parameters */ + + double eval_tdep(spline y,double T) { + double f,df,d2f; + + if(0) if(T != 3000.0) + printf("%s:%d: Error, T = %.3f\n",__FILE__,__LINE__,T); + evalspline(nt-1,T0,T1,y,T,&f,&df,&d2f); + return f; + } + double eval_tdepderiv(spline y,double T) { + double f,df,d2f; + + if(0) if(T != 3000.0) + printf("%s:%d: Error, T = %.3f\n",__FILE__,__LINE__,T); + evalspline(nt-1,T0,T1,y,T,&f,&df,&d2f); + return df; + } + + +#define make_get(param) \ + double get_##param(double T) { return eval_tdep(param,T); } \ + double get_d##param(double T) { return eval_tdep(d##param,T); } \ + double get_##param##_Tderiv(double T) { return eval_tdepderiv(param,T); } + + /* +#define make_get(param) \ + double get_##param(double T) { if(T != 3000.0) printf("%s:%d: Error, T = %.3f\n",__FILE__,__LINE__,T); return potlist[3].param; } \ + double get_d##param(double T) { if(T != 3000.0) printf("%s:%d: Error, T = %.3f\n",__FILE__,__LINE__,T); return potlist[3].d##param; } \ + double get_##param##_Tderiv(double T) { if(T != 3000.0) printf("%s:%d: Error, T = %.3f\n",__FILE__,__LINE__,T); return 0.0; } + */ + + make_get(va) make_get(vb) make_get(vc) make_get(vd) make_get(ve) + make_get(p1) make_get(al) make_get(rp) make_get(r00) make_get(evol0) +#undef make_get + + void get_anorm34(double T,double anorm3_p[1],double anorm4_p[1]) { + double + s = eval_tdep(ddl[1],T), + p = eval_tdep(ddl[2],T), + d = eval_tdep(ddl[3],T), + f = eval_tdep(ddl[4],T); + double ss = s*s, pp = p*p, dd = d*d, ff = f*f; + anorm3_p[0] = s*ss + 2.0*( p*pp + d*dd + f*ff); + anorm4_p[0] = ss*ss + 2.0*(pp*pp + dd*dd + ff*ff); + } + double get_anorm3(double T) { + double a3,a4; + get_anorm34(T,&a3,&a4); + return a3; + } + double get_anorm4(double T) { + double a3,a4; + get_anorm34(T,&a3,&a4); + return a4; + } + void get_anorm34_Tderiv(double T,double danorm3_p[1],double danorm4_p[1]) { + double + s = eval_tdep(ddl[1],T), ds = eval_tdepderiv(ddl[1],T), + p = eval_tdep(ddl[2],T), dp = eval_tdepderiv(ddl[2],T), + d = eval_tdep(ddl[3],T), d_d = eval_tdepderiv(ddl[3],T), + f = eval_tdep(ddl[4],T), df = eval_tdepderiv(ddl[4],T); + double ss = s*s, pp = p*p, dd = d*d, ff = f*f; + danorm3_p[0] = 3.0*ds*ss + 6.0*( dp*pp + d_d*dd + df*ff); + danorm4_p[0] = 4.0*ds*s*ss + 8.0*(dp*p*pp + d_d*d*dd + df*f*ff); + } + double get_anorm3_Tderiv(double T) { + double da3,da4; + get_anorm34_Tderiv(T,&da3,&da4); + return da3; + } + double get_anorm4_Tderiv(double T) { + double da3,da4; + get_anorm34_Tderiv(T,&da3,&da4); + return da4; + } + + /* ... */ + + + + char * parsefname(const char *nametemplate,int *i0,int *i1,int *stride) { + char *s,*p; + + if(0) { + s = new char[strlen(nametemplate)+1]; + } else { + int len = 0; + while(nametemplate[len] != '\0') len = len + 1; + s = new char[len+1]; + } + strcpy(s,nametemplate); + + p = strchr(s,'{'); + if(p != NULL) { + if(sscanf(p+1,"%d:%d:%d",i0,stride,i1) != 3) { + fprintf(stderr,"Error in template (\'%s\'), can not parse range.\n",nametemplate); + exit(1); + } + *p = '\0'; + } else { + *i0 = -1; + *i1 = -1; + *stride = 1; + } + return s; + } + + spline maketempspline(int n,potdata data[],double *ptr) { + int stride = &(data[1].va) - &(data[0].va); + spline s = new double[n-1][4]; + + makespline(n,stride,ptr,s); + return s; + } + + void readpot2(const char *parmin_template,const char *potin_template,double vol) { + int i0,i1,stride,i0x,i1x,stridex; + char *parmin_file = parsefname(parmin_template,&i0 ,&i1 ,&stride ); + char *potin_file = parsefname( potin_template,&i0x,&i1x,&stridex); + int ntemp; + + potdata2 &tdeppot = *this; + + if(i0x != i0 || i1x != i1 || stridex != stride) { + fprintf(stderr,"Inconsistent templates. parmin_template=\'%s\', potin_template=\'%s\'\n", + parmin_template,potin_template); + exit(1); + } + if(i0 < 0 || i1 < i0 || stride <= 0 || (i1-i0)/stride+1 < 4) { + fprintf(stderr,"Improper temperature range. Need at least 4 temperature samples. " + "i0=%d,i1=%d,stride=%d,basename=\'%s\'\n", + i0,i1,stride,parmin_file); + exit(1); + } + + const char *parmin_suffix = strchr(parmin_template,'}')+1; + const char * potin_suffix = strchr( potin_template,'}')+1; + + if(parmin_suffix-1 == NULL) { + fprintf(stderr,"No closing }. parmin_template=\'%s\'\n", + parmin_template); + exit(1); + } + if(potin_suffix-1 == NULL) { + fprintf(stderr,"No closing }. potin_template=\'%s\'\n", + potin_template); + exit(1); + } + + printf("parmin_template = %s\n" + "parmin_file = %s\n" + "parmin_suffix = %s\n" + "T0=%d , T1=%d , stride=%d\n", + parmin_template,parmin_file,parmin_suffix,i0,i1,stride); + + ntemp = (i1-i0)/stride + 1; + /*potdata **/potlist = new potdata[ntemp]; + char *parend = parmin_file+strlen(parmin_file); + char *potend = potin_file +strlen( potin_file); + for(int k=0; k 0) { + if(potlist[k].nr != potlist[k-1].nr) { + fprintf(stderr,"nr differs between file %d and %d. Exiting.\n", + k,k-1); + exit(1); + } + + if(potlist[k].r0 != potlist[k-1].r0) { + fprintf(stderr,"r0 differs between file %d and %d. Exiting.\n", + k,k-1); + exit(1); + } + + if(potlist[k].r1 != potlist[k-1].r1) { + fprintf(stderr,"r1 differs between file %d and %d. Exiting.\n", + k,k-1); + exit(1); + } + } + } + tdeppot.r0 = potlist[0].r0; + tdeppot.r1 = potlist[0].r1; + tdeppot.nr = potlist[0].nr; + tdeppot.T0 = i0; + tdeppot.T1 = i1; + tdeppot.nt = ntemp; + + tdeppot.mass = potlist[0].mass; + tdeppot.rcrit = potlist[0].rcrit; + tdeppot.rmax = potlist[0].rmax; + + tdeppot.lang = potlist[0].lang; + tdeppot.lmax = potlist[0].lmax; + tdeppot.ipot = potlist[0].ipot; + tdeppot.mode = potlist[0].mode; + tdeppot.input_vol = potlist[0].input_vol; + + strncpy(tdeppot.metal,potlist[0].metal,sizeof(tdeppot.metal)/sizeof(char)); + tdeppot.metal[sizeof(tdeppot.metal)/sizeof(char) - 1] = '\0'; + + delete[] parmin_file; + delete[] potin_file; + + // Base parameters + tdeppot.va = maketempspline(ntemp,potlist,&(potlist[0].va)); + tdeppot.vb = maketempspline(ntemp,potlist,&(potlist[0].vb)); + tdeppot.vc = maketempspline(ntemp,potlist,&(potlist[0].vc)); + tdeppot.vd = maketempspline(ntemp,potlist,&(potlist[0].vd)); + tdeppot.ve = maketempspline(ntemp,potlist,&(potlist[0].ve)); + + tdeppot.p1 = maketempspline(ntemp,potlist,&(potlist[0].p1)); + tdeppot.al = maketempspline(ntemp,potlist,&(potlist[0].al)); + tdeppot.rp = maketempspline(ntemp,potlist,&(potlist[0].rp)); + tdeppot.r00 = maketempspline(ntemp,potlist,&(potlist[0].r00)); + + tdeppot.evol0 = maketempspline(ntemp,potlist,&(potlist[0].evol0)); + + // Volume derivatives of base parameters + tdeppot.dva = maketempspline(ntemp,potlist,&(potlist[0].dva)); + tdeppot.dvb = maketempspline(ntemp,potlist,&(potlist[0].dvb)); + tdeppot.dvc = maketempspline(ntemp,potlist,&(potlist[0].dvc)); + tdeppot.dvd = maketempspline(ntemp,potlist,&(potlist[0].dvd)); + tdeppot.dve = maketempspline(ntemp,potlist,&(potlist[0].dve)); + + tdeppot.dp1 = maketempspline(ntemp,potlist,&(potlist[0].dp1)); + tdeppot.dal = maketempspline(ntemp,potlist,&(potlist[0].dal)); + tdeppot.drp = maketempspline(ntemp,potlist,&(potlist[0].drp)); + tdeppot.dr00 = maketempspline(ntemp,potlist,&(potlist[0].dr00)); + + tdeppot.devol0 = maketempspline(ntemp,potlist,&(potlist[0].devol0)); + + + tdeppot.ddl[0] = 0; + for(int k = 1; k<=4; k++) + tdeppot.ddl[k] = maketempspline(ntemp,potlist,&(potlist[0].ddl[k])); + + { + double *v = new double[ntemp]; + double (*C)[4] = new double[ntemp-1][4]; + + int sz = (nr-1)*(ntemp-1); + //printf("Allocation:: nr=%d ntemp=%d size=%d\n",nr,ntemp,sz); + tdeppot.vpair = new double[sz][4][4]; + tdeppot.dvpair = new double[sz][4][4]; + /* + printf("vpair = %llx , dvpair = %llx", + (unsigned long long int) tdeppot.vpair, + (unsigned long long int) tdeppot.dvpair); + printf(" @@@@@@@@@@@@@@ nr = %d\n",nr); + */ + for(int i = 0; i= potlist[k].nr-1) + printf("Index error, local_nr=%d, k=%d, i=%d, nr=%d\n",nr,k,i,potlist[k].nr); + v[k] = potlist[k].vpair_spline[i][j]; + } + makespline(ntemp,1,v,C); + + for(int k = 0; k nt-2) k = nt-2; + + if(i < 0) i = 0; + else if(i > nr-2) i = nr-2; + + /* + printf("eval_pot nr=%d nt=%d\n",nr,nt); + printf("eval_pot r=%.3f T=%.3f k=%d i=%d\n", + r,T,k,i); + printf("Tfrac=%.3f Tfrac-k=%.3f\n",Tfrac,Tfrac-k); + printf("rfrac=%.3f rfrac-i=%.3f\n",rfrac,rfrac-i); + */ + for(j = 0; j<4; j++) { + evalcubic(fun[k*(nr-1) + i][j],Tfrac-k,&C[j],&dC[j],&dd); + dC[j] = dC[j] * ((nt-1) / (T1-T0)); + } + /* + printf("C coeff: %.3e %.3e %.3e %.3e\n", + C[0],C[1],C[2],C[3]); + */ + evalcubic(C,rfrac-i,e_p,f_p,&dd); + evalcubic(dC,rfrac-i,dedT_p,&dd,&dd); + *f_p *= (nr-1) / (r1-r0); + } + void eval_pot(double r,double T,double *e_p,double *f_p,double *dedT_p) { + eval2Dspline(vpair,r,T,e_p,f_p,dedT_p); + } + void eval_vir(double r,double T,double *v_p) { + double vf,dvdT; + eval2Dspline(dvpair,r,T,v_p,&vf,&dvdT); + } +}; + + +#endif diff --git a/src/USER-MGPT/mgpt_splinetab.cpp b/src/USER-MGPT/mgpt_splinetab.cpp new file mode 100644 index 0000000000..22df495f9e --- /dev/null +++ b/src/USER-MGPT/mgpt_splinetab.cpp @@ -0,0 +1,125 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + +#include "mgpt_splinetab.h" + +static void trisolve(int n,double A[][3],double y[]) { + /* Backward elimination */ + for(int i = n-1; i>0; i--) { + double q = A[i-1][2] / A[i][1]; + A[i-1][1] = A[i-1][1] - q*A[i][0]; + y[i-1] = y[i-1] - q*y[i]; + } + + /* Forward substitution */ + y[0] = y[0] / A[0][1]; + for(int i = 1; i n-1) idx = n-1; + xhat = xhat - idx; + p = C[idx]; + + if(0) { + *y = p[0] + xhat*(p[1] + xhat*(p[2] + xhat*p[3])); + + *dy = p[1] + xhat*(2*p[2] + xhat*3*p[3]); + *d2y = 2*p[2] + xhat*6*p[3]; + + *dy *= dxinv; + *d2y *= dxinv*dxinv; + } else { + t1 = p[2] + xhat*p[3]; + t2 = p[1] + xhat*t1; + + t3 = t1 + xhat*p[3]; + + *y = p[0] + xhat*t2; + *dy = (t2 + xhat*t3)*dxinv; + *d2y = 2.0*(t3 + xhat*p[3])*(dxinv*dxinv); + } +} diff --git a/src/USER-MGPT/mgpt_splinetab.h b/src/USER-MGPT/mgpt_splinetab.h new file mode 100644 index 0000000000..e719f34218 --- /dev/null +++ b/src/USER-MGPT/mgpt_splinetab.h @@ -0,0 +1,62 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + +#ifndef SPLINETAB__ +#define SPLINETAB__ + + +/* + Given a table of ntab data points tab, assumed to be sampled + on an equidistant grid, compute coefficients of interpolating + cubic polynimials, one per interval (i.e. ntab-1 polynomials). + + Input point i is located at tab[i*stride]. + + Coefficients of output polynomial j are at C[j][0..3]; + + The piecewise polynimials form a C^2 function which + approximates the input function to fourth order. + + The computational cost of this routine is O(ntab). +*/ +void makespline(int ntab,int stride,double tab[],double C[][4]); + + +/* + Evaluate the spline function with coefficients in C (as returned + by makespline()) in point x. + x0 and x1 are the end points of the x points corresponding to + original input interval tab of makespline(). n is ntab-1. + + The output is the value (y) of the interpolating spline, and the + first (dy) and second (d2y) dervatives. + + The computational cost of this routine is O(1). +*/ +void evalspline(int n,double x0,double x1,double C[][4], + double x,double *y,double *dy,double *d2y); + + +/* Evaluate cubic polynomial represented by p in point x. + The first and second derivatives are also returned. + This can be used to evaluate one of the sub-polynomials + in a spline. */ +void evalcubic(double p[4],double x,double *y,double *dy,double *d2y); + +#endif + diff --git a/src/USER-MGPT/mgpt_ttr_5022.c.h b/src/USER-MGPT/mgpt_ttr_5022.c.h new file mode 100644 index 0000000000..2b697c6b84 --- /dev/null +++ b/src/USER-MGPT/mgpt_ttr_5022.c.h @@ -0,0 +1,202 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + +#include + +#include + +void ttr_5_8_3_v2r2(const double * restrict A, + const double * restrict B0,double * restrict tout0, + const double * restrict B1,double * restrict tout1, + const double * restrict B2,double * restrict tout2) { +__m128d Areg1,Areg2; +__m128d B0reg1,B0reg2,B1reg1,B1reg2,B2reg1,B2reg2; +__m128d T0reg1,T0reg2,T1reg1,T1reg2,T2reg1,T2reg2; + +Areg1 = _mm_load_pd(&A[0]) ; +T0reg1 = _mm_load_pd(&B0[0]) ; +T1reg1 = _mm_load_pd(&B1[0]) ; +T2reg1 = _mm_load_pd(&B2[0]) ; +T0reg1 = _mm_mul_pd(T0reg1,Areg1) ; +T1reg1 = _mm_mul_pd(T1reg1,Areg1) ; +T2reg1 = _mm_mul_pd(T2reg1,Areg1) ; + +Areg2 = _mm_load_pd(&A[2]) ; +T0reg2 = _mm_load_pd(&B0[2]) ; +T1reg2 = _mm_load_pd(&B1[2]) ; +T2reg2 = _mm_load_pd(&B2[2]) ; +T0reg2 = _mm_mul_pd(T0reg2,Areg2) ; +T1reg2 = _mm_mul_pd(T1reg2,Areg2) ; +T2reg2 = _mm_mul_pd(T2reg2,Areg2) ; + +Areg1 = _mm_load_pd(&A[4]) ; +B0reg1 = _mm_load_pd(&B0[4]) ; +B1reg1 = _mm_load_pd(&B1[4]) ; +B2reg1 = _mm_load_pd(&B2[4]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[8]) ; +B0reg2 = _mm_load_pd(&B0[8]) ; +B1reg2 = _mm_load_pd(&B1[8]) ; +B2reg2 = _mm_load_pd(&B2[8]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[10]) ; +B0reg1 = _mm_load_pd(&B0[10]) ; +B1reg1 = _mm_load_pd(&B1[10]) ; +B2reg1 = _mm_load_pd(&B2[10]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[12]) ; +B0reg2 = _mm_load_pd(&B0[12]) ; +B1reg2 = _mm_load_pd(&B1[12]) ; +B2reg2 = _mm_load_pd(&B2[12]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[16]) ; +B0reg1 = _mm_load_pd(&B0[16]) ; +B1reg1 = _mm_load_pd(&B1[16]) ; +B2reg1 = _mm_load_pd(&B2[16]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[18]) ; +B0reg2 = _mm_load_pd(&B0[18]) ; +B1reg2 = _mm_load_pd(&B1[18]) ; +B2reg2 = _mm_load_pd(&B2[18]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[20]) ; +B0reg1 = _mm_load_pd(&B0[20]) ; +B1reg1 = _mm_load_pd(&B1[20]) ; +B2reg1 = _mm_load_pd(&B2[20]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[24]) ; +B0reg2 = _mm_load_pd(&B0[24]) ; +B1reg2 = _mm_load_pd(&B1[24]) ; +B2reg2 = _mm_load_pd(&B2[24]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[26]) ; +B0reg1 = _mm_load_pd(&B0[26]) ; +B1reg1 = _mm_load_pd(&B1[26]) ; +B2reg1 = _mm_load_pd(&B2[26]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[28]) ; +B0reg2 = _mm_load_pd(&B0[28]) ; +B1reg2 = _mm_load_pd(&B1[28]) ; +B2reg2 = _mm_load_pd(&B2[28]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[32]) ; +B0reg1 = _mm_load_pd(&B0[32]) ; +B1reg1 = _mm_load_pd(&B1[32]) ; +B2reg1 = _mm_load_pd(&B2[32]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[34]) ; +B0reg2 = _mm_load_pd(&B0[34]) ; +B1reg2 = _mm_load_pd(&B1[34]) ; +B2reg2 = _mm_load_pd(&B2[34]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[36]) ; +B0reg1 = _mm_load_pd(&B0[36]) ; +B1reg1 = _mm_load_pd(&B1[36]) ; +B2reg1 = _mm_load_pd(&B2[36]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + + +T0reg1 = _mm_add_pd(T0reg1,T0reg2) ; +T1reg1 = _mm_add_pd(T1reg1,T1reg2) ; +T2reg1 = _mm_add_pd(T2reg1,T2reg2) ; + +T0reg1 = _mm_hadd_pd(T0reg1,T0reg1) ; +_mm_store_sd(tout0,T0reg1) ; +T1reg1 = _mm_hadd_pd(T1reg1,T1reg1) ; +_mm_store_sd(tout1,T1reg1) ; +T2reg1 = _mm_hadd_pd(T2reg1,T2reg1) ; +_mm_store_sd(tout2,T2reg1) ; + +} diff --git a/src/USER-MGPT/mgpt_ttr_5042.c.h b/src/USER-MGPT/mgpt_ttr_5042.c.h new file mode 100644 index 0000000000..4d77a49c9d --- /dev/null +++ b/src/USER-MGPT/mgpt_ttr_5042.c.h @@ -0,0 +1,150 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + +#include + +#include + +void ttr_5_8_3_v4r2(const float * restrict A, + const float * restrict B0,float * restrict tout0, + const float * restrict B1,float * restrict tout1, + const float * restrict B2,float * restrict tout2) { +__m128 Areg1,Areg2; +__m128 B0reg1,B0reg2,B1reg1,B1reg2,B2reg1,B2reg2; +__m128 T0reg1,T0reg2,T1reg1,T1reg2,T2reg1,T2reg2; + +Areg1 = _mm_load_ps(&A[0]) ; +T0reg1 = _mm_load_ps(&B0[0]) ; +T1reg1 = _mm_load_ps(&B1[0]) ; +T2reg1 = _mm_load_ps(&B2[0]) ; +T0reg1 = _mm_mul_ps(T0reg1,Areg1) ; +T1reg1 = _mm_mul_ps(T1reg1,Areg1) ; +T2reg1 = _mm_mul_ps(T2reg1,Areg1) ; + +Areg2 = _mm_load_ps(&A[4]) ; +T0reg2 = _mm_load_ps(&B0[4]) ; +T1reg2 = _mm_load_ps(&B1[4]) ; +T2reg2 = _mm_load_ps(&B2[4]) ; +T0reg2 = _mm_mul_ps(T0reg2,Areg2) ; +T1reg2 = _mm_mul_ps(T1reg2,Areg2) ; +T2reg2 = _mm_mul_ps(T2reg2,Areg2) ; + +Areg1 = _mm_load_ps(&A[8]) ; +B0reg1 = _mm_load_ps(&B0[8]) ; +B1reg1 = _mm_load_ps(&B1[8]) ; +B2reg1 = _mm_load_ps(&B2[8]) ; +B0reg1 = _mm_mul_ps(B0reg1,Areg1) ; +T0reg1 = _mm_add_ps(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_ps(B1reg1,Areg1) ; +T1reg1 = _mm_add_ps(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_ps(B2reg1,Areg1) ; +T2reg1 = _mm_add_ps(T2reg1,B2reg1) ; + +Areg2 = _mm_load_ps(&A[12]) ; +B0reg2 = _mm_load_ps(&B0[12]) ; +B1reg2 = _mm_load_ps(&B1[12]) ; +B2reg2 = _mm_load_ps(&B2[12]) ; +B0reg2 = _mm_mul_ps(B0reg2,Areg2) ; +T0reg2 = _mm_add_ps(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_ps(B1reg2,Areg2) ; +T1reg2 = _mm_add_ps(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_ps(B2reg2,Areg2) ; +T2reg2 = _mm_add_ps(T2reg2,B2reg2) ; + +Areg1 = _mm_load_ps(&A[16]) ; +B0reg1 = _mm_load_ps(&B0[16]) ; +B1reg1 = _mm_load_ps(&B1[16]) ; +B2reg1 = _mm_load_ps(&B2[16]) ; +B0reg1 = _mm_mul_ps(B0reg1,Areg1) ; +T0reg1 = _mm_add_ps(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_ps(B1reg1,Areg1) ; +T1reg1 = _mm_add_ps(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_ps(B2reg1,Areg1) ; +T2reg1 = _mm_add_ps(T2reg1,B2reg1) ; + +Areg2 = _mm_load_ps(&A[20]) ; +B0reg2 = _mm_load_ps(&B0[20]) ; +B1reg2 = _mm_load_ps(&B1[20]) ; +B2reg2 = _mm_load_ps(&B2[20]) ; +B0reg2 = _mm_mul_ps(B0reg2,Areg2) ; +T0reg2 = _mm_add_ps(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_ps(B1reg2,Areg2) ; +T1reg2 = _mm_add_ps(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_ps(B2reg2,Areg2) ; +T2reg2 = _mm_add_ps(T2reg2,B2reg2) ; + +Areg1 = _mm_load_ps(&A[24]) ; +B0reg1 = _mm_load_ps(&B0[24]) ; +B1reg1 = _mm_load_ps(&B1[24]) ; +B2reg1 = _mm_load_ps(&B2[24]) ; +B0reg1 = _mm_mul_ps(B0reg1,Areg1) ; +T0reg1 = _mm_add_ps(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_ps(B1reg1,Areg1) ; +T1reg1 = _mm_add_ps(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_ps(B2reg1,Areg1) ; +T2reg1 = _mm_add_ps(T2reg1,B2reg1) ; + +Areg2 = _mm_load_ps(&A[28]) ; +B0reg2 = _mm_load_ps(&B0[28]) ; +B1reg2 = _mm_load_ps(&B1[28]) ; +B2reg2 = _mm_load_ps(&B2[28]) ; +B0reg2 = _mm_mul_ps(B0reg2,Areg2) ; +T0reg2 = _mm_add_ps(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_ps(B1reg2,Areg2) ; +T1reg2 = _mm_add_ps(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_ps(B2reg2,Areg2) ; +T2reg2 = _mm_add_ps(T2reg2,B2reg2) ; + +Areg1 = _mm_load_ps(&A[32]) ; +B0reg1 = _mm_load_ps(&B0[32]) ; +B1reg1 = _mm_load_ps(&B1[32]) ; +B2reg1 = _mm_load_ps(&B2[32]) ; +B0reg1 = _mm_mul_ps(B0reg1,Areg1) ; +T0reg1 = _mm_add_ps(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_ps(B1reg1,Areg1) ; +T1reg1 = _mm_add_ps(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_ps(B2reg1,Areg1) ; +T2reg1 = _mm_add_ps(T2reg1,B2reg1) ; + +Areg2 = _mm_load_ps(&A[36]) ; +B0reg2 = _mm_load_ps(&B0[36]) ; +B1reg2 = _mm_load_ps(&B1[36]) ; +B2reg2 = _mm_load_ps(&B2[36]) ; +B0reg2 = _mm_mul_ps(B0reg2,Areg2) ; +T0reg2 = _mm_add_ps(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_ps(B1reg2,Areg2) ; +T1reg2 = _mm_add_ps(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_ps(B2reg2,Areg2) ; +T2reg2 = _mm_add_ps(T2reg2,B2reg2) ; + + +T0reg1 = _mm_add_ps(T0reg1,T0reg2) ; +T1reg1 = _mm_add_ps(T1reg1,T1reg2) ; +T2reg1 = _mm_add_ps(T2reg1,T2reg2) ; + +T0reg1 = _mm_hadd_ps(T0reg1,T0reg1) ; +T0reg1 = _mm_hadd_ps(T0reg1,T0reg1) ; +_mm_store_ss(tout0,T0reg1) ; +T1reg1 = _mm_hadd_ps(T1reg1,T1reg1) ; +T1reg1 = _mm_hadd_ps(T1reg1,T1reg1) ; +_mm_store_ss(tout1,T1reg1) ; +T2reg1 = _mm_hadd_ps(T2reg1,T2reg1) ; +T2reg1 = _mm_hadd_ps(T2reg1,T2reg1) ; +_mm_store_ss(tout2,T2reg1) ; + +} diff --git a/src/USER-MGPT/mgpt_ttr_5123.c.h b/src/USER-MGPT/mgpt_ttr_5123.c.h new file mode 100644 index 0000000000..e8237f4eb2 --- /dev/null +++ b/src/USER-MGPT/mgpt_ttr_5123.c.h @@ -0,0 +1,245 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + + +//#define TESTING + +#ifdef TESTING + +typedef struct { + double x,y; +} pair; + + +#define CPLX pair + +static double my_creal(CPLX x) { + return ((double *) &x)[0]; +} +static double my_cimag(CPLX x) { + return ((double *) &x)[1]; +} +static CPLX my_lfpd(const double *p) { + return ((CPLX *) p)[0]; +} + +/* +// Not needed for trace calculations. +static void my_stfpd(double *p,CPLX x) { + ((CPLX *) p)[0] = x; +} +static CPLX my_fxsmul(CPLX x,double a) { + double y[2]; + y[0] = a * my_creal(x); + y[1] = a * my_cimag(x); + return ((CPLX *) y)[0]; +} +static CPLX my_fxcpmadd(CPLX t,CPLX x,double a) { + double y[2]; + y[0] = my_creal(t) + a * my_creal(x); + y[1] = my_cimag(t) + a * my_cimag(x); + return ((CPLX *) y)[0]; +} +*/ + +static CPLX my_fpmul(CPLX x,CPLX y) { + union { + double z[2]; + CPLX c; + } U; + U.z[0] = my_creal(y) * my_creal(x); + U.z[1] = my_cimag(y) * my_cimag(x); + return U.c; +} +static CPLX my_fpadd(CPLX x,CPLX y) { + union { + double z[2]; + CPLX c; + } U; + U.z[0] = my_creal(y) + my_creal(x); + U.z[1] = my_cimag(y) + my_cimag(x); + return U.c; +} +static CPLX my_fpmadd(CPLX t,CPLX x,CPLX y) { + union { + double z[2]; + CPLX c; + } U; + U.z[0] = my_creal(t) + my_creal(y) * my_creal(x); + U.z[1] = my_cimag(t) + my_cimag(y) * my_cimag(x); + return U.c; +} + +#define __creal my_creal +#define __cimag my_cimag +#define __lfpd my_lfpd +#define __stfpd my_stfpd +#define __fxsmul my_fxsmul +#define __fxcpmadd my_fxcpmadd + +#define __fpadd my_fpadd +#define __fpmul my_fpmul +#define __fpmadd my_fpmadd + +#else + +#define CPLX double _Complex + +#endif + +void ttr_bg_5_8_3_v2r3(const double * restrict A, + const double * restrict B0,double * restrict tout0, + const double * restrict B1,double * restrict tout1, + const double * restrict B2,double * restrict tout2) { +CPLX Areg1,Areg2,Areg3; +CPLX B0reg1,B0reg2,B0reg3,B1reg1,B1reg2,B1reg3,B2reg1,B2reg2,B2reg3; +CPLX T0reg1,T0reg2,T0reg3,T1reg1,T1reg2,T1reg3,T2reg1,T2reg2,T2reg3; + +Areg1 = __lfpd(&A[0]) ; +B0reg1 = __lfpd(&B0[0]) ; +B1reg1 = __lfpd(&B1[0]) ; +B2reg1 = __lfpd(&B2[0]) ; +T0reg1 = __fpmul(Areg1,B0reg1) ; +T1reg1 = __fpmul(Areg1,B1reg1) ; +T2reg1 = __fpmul(Areg1,B2reg1) ; + +Areg2 = __lfpd(&A[2]) ; +B0reg2 = __lfpd(&B0[2]) ; +B1reg2 = __lfpd(&B1[2]) ; +B2reg2 = __lfpd(&B2[2]) ; +T0reg2 = __fpmul(Areg2,B0reg2) ; +T1reg2 = __fpmul(Areg2,B1reg2) ; +T2reg2 = __fpmul(Areg2,B2reg2) ; + +Areg3 = __lfpd(&A[4]) ; +B0reg3 = __lfpd(&B0[4]) ; +B1reg3 = __lfpd(&B1[4]) ; +B2reg3 = __lfpd(&B2[4]) ; +T0reg3 = __fpmul(Areg3,B0reg3) ; +T1reg3 = __fpmul(Areg3,B1reg3) ; +T2reg3 = __fpmul(Areg3,B2reg3) ; + +Areg1 = __lfpd(&A[8]) ; +B0reg1 = __lfpd(&B0[8]) ; +B1reg1 = __lfpd(&B1[8]) ; +B2reg1 = __lfpd(&B2[8]) ; +T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ; +T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ; +T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ; + +Areg2 = __lfpd(&A[10]) ; +B0reg2 = __lfpd(&B0[10]) ; +B1reg2 = __lfpd(&B1[10]) ; +B2reg2 = __lfpd(&B2[10]) ; +T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ; +T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ; +T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ; + +Areg3 = __lfpd(&A[12]) ; +B0reg3 = __lfpd(&B0[12]) ; +B1reg3 = __lfpd(&B1[12]) ; +B2reg3 = __lfpd(&B2[12]) ; +T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ; +T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ; +T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ; + +Areg1 = __lfpd(&A[16]) ; +B0reg1 = __lfpd(&B0[16]) ; +B1reg1 = __lfpd(&B1[16]) ; +B2reg1 = __lfpd(&B2[16]) ; +T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ; +T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ; +T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ; + +Areg2 = __lfpd(&A[18]) ; +B0reg2 = __lfpd(&B0[18]) ; +B1reg2 = __lfpd(&B1[18]) ; +B2reg2 = __lfpd(&B2[18]) ; +T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ; +T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ; +T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ; + +Areg3 = __lfpd(&A[20]) ; +B0reg3 = __lfpd(&B0[20]) ; +B1reg3 = __lfpd(&B1[20]) ; +B2reg3 = __lfpd(&B2[20]) ; +T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ; +T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ; +T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ; + +Areg1 = __lfpd(&A[24]) ; +B0reg1 = __lfpd(&B0[24]) ; +B1reg1 = __lfpd(&B1[24]) ; +B2reg1 = __lfpd(&B2[24]) ; +T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ; +T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ; +T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ; + +Areg2 = __lfpd(&A[26]) ; +B0reg2 = __lfpd(&B0[26]) ; +B1reg2 = __lfpd(&B1[26]) ; +B2reg2 = __lfpd(&B2[26]) ; +T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ; +T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ; +T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ; + +Areg3 = __lfpd(&A[28]) ; +B0reg3 = __lfpd(&B0[28]) ; +B1reg3 = __lfpd(&B1[28]) ; +B2reg3 = __lfpd(&B2[28]) ; +T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ; +T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ; +T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ; + +Areg1 = __lfpd(&A[32]) ; +B0reg1 = __lfpd(&B0[32]) ; +B1reg1 = __lfpd(&B1[32]) ; +B2reg1 = __lfpd(&B2[32]) ; +T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ; +T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ; +T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ; + +Areg2 = __lfpd(&A[34]) ; +B0reg2 = __lfpd(&B0[34]) ; +B1reg2 = __lfpd(&B1[34]) ; +B2reg2 = __lfpd(&B2[34]) ; +T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ; +T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ; +T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ; + +Areg3 = __lfpd(&A[36]) ; +B0reg3 = __lfpd(&B0[36]) ; +B1reg3 = __lfpd(&B1[36]) ; +B2reg3 = __lfpd(&B2[36]) ; +T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ; +T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ; +T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ; + + +T0reg1 = __fpadd(T0reg1,T0reg2) ; +T1reg1 = __fpadd(T1reg1,T1reg2) ; +T2reg1 = __fpadd(T2reg1,T2reg2) ; +T0reg1 = __fpadd(T0reg1,T0reg3) ; +T1reg1 = __fpadd(T1reg1,T1reg3) ; +T2reg1 = __fpadd(T2reg1,T2reg3) ; + +*tout0 = __creal(T0reg1) + __cimag(T0reg1) ; +*tout1 = __creal(T1reg1) + __cimag(T1reg1) ; +*tout2 = __creal(T2reg1) + __cimag(T2reg1) ; + +} diff --git a/src/USER-MGPT/mgpt_ttr_5141.c.h b/src/USER-MGPT/mgpt_ttr_5141.c.h new file mode 100644 index 0000000000..d77c6935f3 --- /dev/null +++ b/src/USER-MGPT/mgpt_ttr_5141.c.h @@ -0,0 +1,142 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + +#define vector vector4double +#define my_vec_add(a,b) vec_add(a,b) +#define my_vec_mul(a,b) vec_mul(a,b) +#define my_vec_fma(a,b,c) vec_madd(b,c,a) +#define my_vec_ld(ptr) vec_lda(0,ptr) +#define my_vec_sldw(x,y,n) vec_sldw(x,y,n) +#define my_vec_sts(x,ptr) vec_sts(x,0,ptr) + +#define const +#define real double + +void ttr_bg_5_8_3_v4r1(const real * restrict A, + const real * restrict B0,real * restrict tout0, + const real * restrict B1,real * restrict tout1, + const real * restrict B2,real * restrict tout2) { +vector Areg1; +vector B0reg1,B1reg1,B2reg1; +vector T0reg1,T1reg1,T2reg1; + +Areg1 = my_vec_ld(&A[0]) ; +B0reg1 = my_vec_ld(&B0[0]) ; +B1reg1 = my_vec_ld(&B1[0]) ; +B2reg1 = my_vec_ld(&B2[0]) ; +T0reg1 = my_vec_mul(Areg1,B0reg1) ; +T1reg1 = my_vec_mul(Areg1,B1reg1) ; +T2reg1 = my_vec_mul(Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[4]) ; +B0reg1 = my_vec_ld(&B0[4]) ; +B1reg1 = my_vec_ld(&B1[4]) ; +B2reg1 = my_vec_ld(&B2[4]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[8]) ; +B0reg1 = my_vec_ld(&B0[8]) ; +B1reg1 = my_vec_ld(&B1[8]) ; +B2reg1 = my_vec_ld(&B2[8]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[12]) ; +B0reg1 = my_vec_ld(&B0[12]) ; +B1reg1 = my_vec_ld(&B1[12]) ; +B2reg1 = my_vec_ld(&B2[12]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[16]) ; +B0reg1 = my_vec_ld(&B0[16]) ; +B1reg1 = my_vec_ld(&B1[16]) ; +B2reg1 = my_vec_ld(&B2[16]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[20]) ; +B0reg1 = my_vec_ld(&B0[20]) ; +B1reg1 = my_vec_ld(&B1[20]) ; +B2reg1 = my_vec_ld(&B2[20]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[24]) ; +B0reg1 = my_vec_ld(&B0[24]) ; +B1reg1 = my_vec_ld(&B1[24]) ; +B2reg1 = my_vec_ld(&B2[24]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[28]) ; +B0reg1 = my_vec_ld(&B0[28]) ; +B1reg1 = my_vec_ld(&B1[28]) ; +B2reg1 = my_vec_ld(&B2[28]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[32]) ; +B0reg1 = my_vec_ld(&B0[32]) ; +B1reg1 = my_vec_ld(&B1[32]) ; +B2reg1 = my_vec_ld(&B2[32]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[36]) ; +B0reg1 = my_vec_ld(&B0[36]) ; +B1reg1 = my_vec_ld(&B1[36]) ; +B2reg1 = my_vec_ld(&B2[36]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + + + +T0reg1 = my_vec_add(T0reg1,my_vec_sldw(T0reg1,T0reg1,2)); +T0reg1 = my_vec_add(T0reg1,my_vec_sldw(T0reg1,T0reg1,1)); +my_vec_sts(T0reg1,tout0); +T1reg1 = my_vec_add(T1reg1,my_vec_sldw(T1reg1,T1reg1,2)); +T1reg1 = my_vec_add(T1reg1,my_vec_sldw(T1reg1,T1reg1,1)); +my_vec_sts(T1reg1,tout1); +T2reg1 = my_vec_add(T2reg1,my_vec_sldw(T2reg1,T2reg1,2)); +T2reg1 = my_vec_add(T2reg1,my_vec_sldw(T2reg1,T2reg1,1)); +my_vec_sts(T2reg1,tout2); + +} + + +#undef vector +#undef my_vec_add +#undef my_vec_mul +#undef my_vec_fma +#undef my_vec_ld +#undef my_vec_sldw +#undef my_vec_sts + +#undef const +#undef real diff --git a/src/USER-MGPT/mgpt_ttr_7022.c.h b/src/USER-MGPT/mgpt_ttr_7022.c.h new file mode 100644 index 0000000000..99aeaec504 --- /dev/null +++ b/src/USER-MGPT/mgpt_ttr_7022.c.h @@ -0,0 +1,345 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + +#include + +#include + +void ttr_7_8_3_v2r2(const double * restrict A, + const double * restrict B0,double * restrict tout0, + const double * restrict B1,double * restrict tout1, + const double * restrict B2,double * restrict tout2) { +__m128d Areg1,Areg2; +__m128d B0reg1,B0reg2,B1reg1,B1reg2,B2reg1,B2reg2; +__m128d T0reg1,T0reg2,T1reg1,T1reg2,T2reg1,T2reg2; + +Areg1 = _mm_load_pd(&A[0]) ; +T0reg1 = _mm_load_pd(&B0[0]) ; +T1reg1 = _mm_load_pd(&B1[0]) ; +T2reg1 = _mm_load_pd(&B2[0]) ; +T0reg1 = _mm_mul_pd(T0reg1,Areg1) ; +T1reg1 = _mm_mul_pd(T1reg1,Areg1) ; +T2reg1 = _mm_mul_pd(T2reg1,Areg1) ; + +Areg2 = _mm_load_pd(&A[2]) ; +T0reg2 = _mm_load_pd(&B0[2]) ; +T1reg2 = _mm_load_pd(&B1[2]) ; +T2reg2 = _mm_load_pd(&B2[2]) ; +T0reg2 = _mm_mul_pd(T0reg2,Areg2) ; +T1reg2 = _mm_mul_pd(T1reg2,Areg2) ; +T2reg2 = _mm_mul_pd(T2reg2,Areg2) ; + +Areg1 = _mm_load_pd(&A[4]) ; +B0reg1 = _mm_load_pd(&B0[4]) ; +B1reg1 = _mm_load_pd(&B1[4]) ; +B2reg1 = _mm_load_pd(&B2[4]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[6]) ; +B0reg2 = _mm_load_pd(&B0[6]) ; +B1reg2 = _mm_load_pd(&B1[6]) ; +B2reg2 = _mm_load_pd(&B2[6]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[8]) ; +B0reg1 = _mm_load_pd(&B0[8]) ; +B1reg1 = _mm_load_pd(&B1[8]) ; +B2reg1 = _mm_load_pd(&B2[8]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[10]) ; +B0reg2 = _mm_load_pd(&B0[10]) ; +B1reg2 = _mm_load_pd(&B1[10]) ; +B2reg2 = _mm_load_pd(&B2[10]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[12]) ; +B0reg1 = _mm_load_pd(&B0[12]) ; +B1reg1 = _mm_load_pd(&B1[12]) ; +B2reg1 = _mm_load_pd(&B2[12]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[14]) ; +B0reg2 = _mm_load_pd(&B0[14]) ; +B1reg2 = _mm_load_pd(&B1[14]) ; +B2reg2 = _mm_load_pd(&B2[14]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[16]) ; +B0reg1 = _mm_load_pd(&B0[16]) ; +B1reg1 = _mm_load_pd(&B1[16]) ; +B2reg1 = _mm_load_pd(&B2[16]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[18]) ; +B0reg2 = _mm_load_pd(&B0[18]) ; +B1reg2 = _mm_load_pd(&B1[18]) ; +B2reg2 = _mm_load_pd(&B2[18]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[20]) ; +B0reg1 = _mm_load_pd(&B0[20]) ; +B1reg1 = _mm_load_pd(&B1[20]) ; +B2reg1 = _mm_load_pd(&B2[20]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[22]) ; +B0reg2 = _mm_load_pd(&B0[22]) ; +B1reg2 = _mm_load_pd(&B1[22]) ; +B2reg2 = _mm_load_pd(&B2[22]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[24]) ; +B0reg1 = _mm_load_pd(&B0[24]) ; +B1reg1 = _mm_load_pd(&B1[24]) ; +B2reg1 = _mm_load_pd(&B2[24]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[26]) ; +B0reg2 = _mm_load_pd(&B0[26]) ; +B1reg2 = _mm_load_pd(&B1[26]) ; +B2reg2 = _mm_load_pd(&B2[26]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[28]) ; +B0reg1 = _mm_load_pd(&B0[28]) ; +B1reg1 = _mm_load_pd(&B1[28]) ; +B2reg1 = _mm_load_pd(&B2[28]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[30]) ; +B0reg2 = _mm_load_pd(&B0[30]) ; +B1reg2 = _mm_load_pd(&B1[30]) ; +B2reg2 = _mm_load_pd(&B2[30]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[32]) ; +B0reg1 = _mm_load_pd(&B0[32]) ; +B1reg1 = _mm_load_pd(&B1[32]) ; +B2reg1 = _mm_load_pd(&B2[32]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[34]) ; +B0reg2 = _mm_load_pd(&B0[34]) ; +B1reg2 = _mm_load_pd(&B1[34]) ; +B2reg2 = _mm_load_pd(&B2[34]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[36]) ; +B0reg1 = _mm_load_pd(&B0[36]) ; +B1reg1 = _mm_load_pd(&B1[36]) ; +B2reg1 = _mm_load_pd(&B2[36]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[38]) ; +B0reg2 = _mm_load_pd(&B0[38]) ; +B1reg2 = _mm_load_pd(&B1[38]) ; +B2reg2 = _mm_load_pd(&B2[38]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[40]) ; +B0reg1 = _mm_load_pd(&B0[40]) ; +B1reg1 = _mm_load_pd(&B1[40]) ; +B2reg1 = _mm_load_pd(&B2[40]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[42]) ; +B0reg2 = _mm_load_pd(&B0[42]) ; +B1reg2 = _mm_load_pd(&B1[42]) ; +B2reg2 = _mm_load_pd(&B2[42]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[44]) ; +B0reg1 = _mm_load_pd(&B0[44]) ; +B1reg1 = _mm_load_pd(&B1[44]) ; +B2reg1 = _mm_load_pd(&B2[44]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[46]) ; +B0reg2 = _mm_load_pd(&B0[46]) ; +B1reg2 = _mm_load_pd(&B1[46]) ; +B2reg2 = _mm_load_pd(&B2[46]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[48]) ; +B0reg1 = _mm_load_pd(&B0[48]) ; +B1reg1 = _mm_load_pd(&B1[48]) ; +B2reg1 = _mm_load_pd(&B2[48]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[50]) ; +B0reg2 = _mm_load_pd(&B0[50]) ; +B1reg2 = _mm_load_pd(&B1[50]) ; +B2reg2 = _mm_load_pd(&B2[50]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + +Areg1 = _mm_load_pd(&A[52]) ; +B0reg1 = _mm_load_pd(&B0[52]) ; +B1reg1 = _mm_load_pd(&B1[52]) ; +B2reg1 = _mm_load_pd(&B2[52]) ; +B0reg1 = _mm_mul_pd(B0reg1,Areg1) ; +T0reg1 = _mm_add_pd(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_pd(B1reg1,Areg1) ; +T1reg1 = _mm_add_pd(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_pd(B2reg1,Areg1) ; +T2reg1 = _mm_add_pd(T2reg1,B2reg1) ; + +Areg2 = _mm_load_pd(&A[54]) ; +B0reg2 = _mm_load_pd(&B0[54]) ; +B1reg2 = _mm_load_pd(&B1[54]) ; +B2reg2 = _mm_load_pd(&B2[54]) ; +B0reg2 = _mm_mul_pd(B0reg2,Areg2) ; +T0reg2 = _mm_add_pd(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_pd(B1reg2,Areg2) ; +T1reg2 = _mm_add_pd(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_pd(B2reg2,Areg2) ; +T2reg2 = _mm_add_pd(T2reg2,B2reg2) ; + + +T0reg1 = _mm_add_pd(T0reg1,T0reg2) ; +T1reg1 = _mm_add_pd(T1reg1,T1reg2) ; +T2reg1 = _mm_add_pd(T2reg1,T2reg2) ; + +T0reg1 = _mm_hadd_pd(T0reg1,T0reg1) ; +_mm_store_sd(tout0,T0reg1) ; +T1reg1 = _mm_hadd_pd(T1reg1,T1reg1) ; +_mm_store_sd(tout1,T1reg1) ; +T2reg1 = _mm_hadd_pd(T2reg1,T2reg1) ; +_mm_store_sd(tout2,T2reg1) ; + +} diff --git a/src/USER-MGPT/mgpt_ttr_7042.c.h b/src/USER-MGPT/mgpt_ttr_7042.c.h new file mode 100644 index 0000000000..36ffe6714b --- /dev/null +++ b/src/USER-MGPT/mgpt_ttr_7042.c.h @@ -0,0 +1,194 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + +#include + +#include + +void ttr_7_8_3_v4r2(const float * restrict A, + const float * restrict B0,float * restrict tout0, + const float * restrict B1,float * restrict tout1, + const float * restrict B2,float * restrict tout2) { +__m128 Areg1,Areg2; +__m128 B0reg1,B0reg2,B1reg1,B1reg2,B2reg1,B2reg2; +__m128 T0reg1,T0reg2,T1reg1,T1reg2,T2reg1,T2reg2; + +Areg1 = _mm_load_ps(&A[0]) ; +T0reg1 = _mm_load_ps(&B0[0]) ; +T1reg1 = _mm_load_ps(&B1[0]) ; +T2reg1 = _mm_load_ps(&B2[0]) ; +T0reg1 = _mm_mul_ps(T0reg1,Areg1) ; +T1reg1 = _mm_mul_ps(T1reg1,Areg1) ; +T2reg1 = _mm_mul_ps(T2reg1,Areg1) ; + +Areg2 = _mm_load_ps(&A[4]) ; +T0reg2 = _mm_load_ps(&B0[4]) ; +T1reg2 = _mm_load_ps(&B1[4]) ; +T2reg2 = _mm_load_ps(&B2[4]) ; +T0reg2 = _mm_mul_ps(T0reg2,Areg2) ; +T1reg2 = _mm_mul_ps(T1reg2,Areg2) ; +T2reg2 = _mm_mul_ps(T2reg2,Areg2) ; + +Areg1 = _mm_load_ps(&A[8]) ; +B0reg1 = _mm_load_ps(&B0[8]) ; +B1reg1 = _mm_load_ps(&B1[8]) ; +B2reg1 = _mm_load_ps(&B2[8]) ; +B0reg1 = _mm_mul_ps(B0reg1,Areg1) ; +T0reg1 = _mm_add_ps(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_ps(B1reg1,Areg1) ; +T1reg1 = _mm_add_ps(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_ps(B2reg1,Areg1) ; +T2reg1 = _mm_add_ps(T2reg1,B2reg1) ; + +Areg2 = _mm_load_ps(&A[12]) ; +B0reg2 = _mm_load_ps(&B0[12]) ; +B1reg2 = _mm_load_ps(&B1[12]) ; +B2reg2 = _mm_load_ps(&B2[12]) ; +B0reg2 = _mm_mul_ps(B0reg2,Areg2) ; +T0reg2 = _mm_add_ps(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_ps(B1reg2,Areg2) ; +T1reg2 = _mm_add_ps(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_ps(B2reg2,Areg2) ; +T2reg2 = _mm_add_ps(T2reg2,B2reg2) ; + +Areg1 = _mm_load_ps(&A[16]) ; +B0reg1 = _mm_load_ps(&B0[16]) ; +B1reg1 = _mm_load_ps(&B1[16]) ; +B2reg1 = _mm_load_ps(&B2[16]) ; +B0reg1 = _mm_mul_ps(B0reg1,Areg1) ; +T0reg1 = _mm_add_ps(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_ps(B1reg1,Areg1) ; +T1reg1 = _mm_add_ps(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_ps(B2reg1,Areg1) ; +T2reg1 = _mm_add_ps(T2reg1,B2reg1) ; + +Areg2 = _mm_load_ps(&A[20]) ; +B0reg2 = _mm_load_ps(&B0[20]) ; +B1reg2 = _mm_load_ps(&B1[20]) ; +B2reg2 = _mm_load_ps(&B2[20]) ; +B0reg2 = _mm_mul_ps(B0reg2,Areg2) ; +T0reg2 = _mm_add_ps(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_ps(B1reg2,Areg2) ; +T1reg2 = _mm_add_ps(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_ps(B2reg2,Areg2) ; +T2reg2 = _mm_add_ps(T2reg2,B2reg2) ; + +Areg1 = _mm_load_ps(&A[24]) ; +B0reg1 = _mm_load_ps(&B0[24]) ; +B1reg1 = _mm_load_ps(&B1[24]) ; +B2reg1 = _mm_load_ps(&B2[24]) ; +B0reg1 = _mm_mul_ps(B0reg1,Areg1) ; +T0reg1 = _mm_add_ps(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_ps(B1reg1,Areg1) ; +T1reg1 = _mm_add_ps(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_ps(B2reg1,Areg1) ; +T2reg1 = _mm_add_ps(T2reg1,B2reg1) ; + +Areg2 = _mm_load_ps(&A[28]) ; +B0reg2 = _mm_load_ps(&B0[28]) ; +B1reg2 = _mm_load_ps(&B1[28]) ; +B2reg2 = _mm_load_ps(&B2[28]) ; +B0reg2 = _mm_mul_ps(B0reg2,Areg2) ; +T0reg2 = _mm_add_ps(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_ps(B1reg2,Areg2) ; +T1reg2 = _mm_add_ps(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_ps(B2reg2,Areg2) ; +T2reg2 = _mm_add_ps(T2reg2,B2reg2) ; + +Areg1 = _mm_load_ps(&A[32]) ; +B0reg1 = _mm_load_ps(&B0[32]) ; +B1reg1 = _mm_load_ps(&B1[32]) ; +B2reg1 = _mm_load_ps(&B2[32]) ; +B0reg1 = _mm_mul_ps(B0reg1,Areg1) ; +T0reg1 = _mm_add_ps(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_ps(B1reg1,Areg1) ; +T1reg1 = _mm_add_ps(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_ps(B2reg1,Areg1) ; +T2reg1 = _mm_add_ps(T2reg1,B2reg1) ; + +Areg2 = _mm_load_ps(&A[36]) ; +B0reg2 = _mm_load_ps(&B0[36]) ; +B1reg2 = _mm_load_ps(&B1[36]) ; +B2reg2 = _mm_load_ps(&B2[36]) ; +B0reg2 = _mm_mul_ps(B0reg2,Areg2) ; +T0reg2 = _mm_add_ps(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_ps(B1reg2,Areg2) ; +T1reg2 = _mm_add_ps(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_ps(B2reg2,Areg2) ; +T2reg2 = _mm_add_ps(T2reg2,B2reg2) ; + +Areg1 = _mm_load_ps(&A[40]) ; +B0reg1 = _mm_load_ps(&B0[40]) ; +B1reg1 = _mm_load_ps(&B1[40]) ; +B2reg1 = _mm_load_ps(&B2[40]) ; +B0reg1 = _mm_mul_ps(B0reg1,Areg1) ; +T0reg1 = _mm_add_ps(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_ps(B1reg1,Areg1) ; +T1reg1 = _mm_add_ps(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_ps(B2reg1,Areg1) ; +T2reg1 = _mm_add_ps(T2reg1,B2reg1) ; + +Areg2 = _mm_load_ps(&A[44]) ; +B0reg2 = _mm_load_ps(&B0[44]) ; +B1reg2 = _mm_load_ps(&B1[44]) ; +B2reg2 = _mm_load_ps(&B2[44]) ; +B0reg2 = _mm_mul_ps(B0reg2,Areg2) ; +T0reg2 = _mm_add_ps(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_ps(B1reg2,Areg2) ; +T1reg2 = _mm_add_ps(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_ps(B2reg2,Areg2) ; +T2reg2 = _mm_add_ps(T2reg2,B2reg2) ; + +Areg1 = _mm_load_ps(&A[48]) ; +B0reg1 = _mm_load_ps(&B0[48]) ; +B1reg1 = _mm_load_ps(&B1[48]) ; +B2reg1 = _mm_load_ps(&B2[48]) ; +B0reg1 = _mm_mul_ps(B0reg1,Areg1) ; +T0reg1 = _mm_add_ps(T0reg1,B0reg1) ; +B1reg1 = _mm_mul_ps(B1reg1,Areg1) ; +T1reg1 = _mm_add_ps(T1reg1,B1reg1) ; +B2reg1 = _mm_mul_ps(B2reg1,Areg1) ; +T2reg1 = _mm_add_ps(T2reg1,B2reg1) ; + +Areg2 = _mm_load_ps(&A[52]) ; +B0reg2 = _mm_load_ps(&B0[52]) ; +B1reg2 = _mm_load_ps(&B1[52]) ; +B2reg2 = _mm_load_ps(&B2[52]) ; +B0reg2 = _mm_mul_ps(B0reg2,Areg2) ; +T0reg2 = _mm_add_ps(T0reg2,B0reg2) ; +B1reg2 = _mm_mul_ps(B1reg2,Areg2) ; +T1reg2 = _mm_add_ps(T1reg2,B1reg2) ; +B2reg2 = _mm_mul_ps(B2reg2,Areg2) ; +T2reg2 = _mm_add_ps(T2reg2,B2reg2) ; + + +T0reg1 = _mm_add_ps(T0reg1,T0reg2) ; +T1reg1 = _mm_add_ps(T1reg1,T1reg2) ; +T2reg1 = _mm_add_ps(T2reg1,T2reg2) ; + +T0reg1 = _mm_hadd_ps(T0reg1,T0reg1) ; +T0reg1 = _mm_hadd_ps(T0reg1,T0reg1) ; +_mm_store_ss(tout0,T0reg1) ; +T1reg1 = _mm_hadd_ps(T1reg1,T1reg1) ; +T1reg1 = _mm_hadd_ps(T1reg1,T1reg1) ; +_mm_store_ss(tout1,T1reg1) ; +T2reg1 = _mm_hadd_ps(T2reg1,T2reg1) ; +T2reg1 = _mm_hadd_ps(T2reg1,T2reg1) ; +_mm_store_ss(tout2,T2reg1) ; + +} diff --git a/src/USER-MGPT/mgpt_ttr_7123.c.h b/src/USER-MGPT/mgpt_ttr_7123.c.h new file mode 100644 index 0000000000..39828ab481 --- /dev/null +++ b/src/USER-MGPT/mgpt_ttr_7123.c.h @@ -0,0 +1,349 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + + +//#define TESTING + +#ifdef TESTING + +typedef struct { + double x,y; +} pair; + + +#define CPLX pair + +static double my_creal(CPLX x) { + return ((double *) &x)[0]; +} +static double my_cimag(CPLX x) { + return ((double *) &x)[1]; +} +static CPLX my_lfpd(const double *p) { + return ((CPLX *) p)[0]; +} + +/* +// Not needed for trace calculations. +static void my_stfpd(double *p,CPLX x) { + ((CPLX *) p)[0] = x; +} +static CPLX my_fxsmul(CPLX x,double a) { + double y[2]; + y[0] = a * my_creal(x); + y[1] = a * my_cimag(x); + return ((CPLX *) y)[0]; +} +static CPLX my_fxcpmadd(CPLX t,CPLX x,double a) { + double y[2]; + y[0] = my_creal(t) + a * my_creal(x); + y[1] = my_cimag(t) + a * my_cimag(x); + return ((CPLX *) y)[0]; +} +*/ + +static CPLX my_fpmul(CPLX x,CPLX y) { + union { + double z[2]; + CPLX c; + } U; + U.z[0] = my_creal(y) * my_creal(x); + U.z[1] = my_cimag(y) * my_cimag(x); + return U.c; +} +static CPLX my_fpadd(CPLX x,CPLX y) { + union { + double z[2]; + CPLX c; + } U; + U.z[0] = my_creal(y) + my_creal(x); + U.z[1] = my_cimag(y) + my_cimag(x); + return U.c; +} +static CPLX my_fpmadd(CPLX t,CPLX x,CPLX y) { + union { + double z[2]; + CPLX c; + } U; + U.z[0] = my_creal(t) + my_creal(y) * my_creal(x); + U.z[1] = my_cimag(t) + my_cimag(y) * my_cimag(x); + return U.c; +} + +#define __creal my_creal +#define __cimag my_cimag +#define __lfpd my_lfpd +#define __stfpd my_stfpd +#define __fxsmul my_fxsmul +#define __fxcpmadd my_fxcpmadd + +#define __fpadd my_fpadd +#define __fpmul my_fpmul +#define __fpmadd my_fpmadd + +#else + +#define CPLX double _Complex + +#endif + +void ttr_bg_7_8_3_v2r3(const double * restrict A, + const double * restrict B0,double * restrict tout0, + const double * restrict B1,double * restrict tout1, + const double * restrict B2,double * restrict tout2) { +CPLX Areg1,Areg2,Areg3; +CPLX B0reg1,B0reg2,B0reg3,B1reg1,B1reg2,B1reg3,B2reg1,B2reg2,B2reg3; +CPLX T0reg1,T0reg2,T0reg3,T1reg1,T1reg2,T1reg3,T2reg1,T2reg2,T2reg3; + +Areg1 = __lfpd(&A[0]) ; +B0reg1 = __lfpd(&B0[0]) ; +B1reg1 = __lfpd(&B1[0]) ; +B2reg1 = __lfpd(&B2[0]) ; +T0reg1 = __fpmul(Areg1,B0reg1) ; +T1reg1 = __fpmul(Areg1,B1reg1) ; +T2reg1 = __fpmul(Areg1,B2reg1) ; + +Areg2 = __lfpd(&A[2]) ; +B0reg2 = __lfpd(&B0[2]) ; +B1reg2 = __lfpd(&B1[2]) ; +B2reg2 = __lfpd(&B2[2]) ; +T0reg2 = __fpmul(Areg2,B0reg2) ; +T1reg2 = __fpmul(Areg2,B1reg2) ; +T2reg2 = __fpmul(Areg2,B2reg2) ; + +Areg3 = __lfpd(&A[4]) ; +B0reg3 = __lfpd(&B0[4]) ; +B1reg3 = __lfpd(&B1[4]) ; +B2reg3 = __lfpd(&B2[4]) ; +T0reg3 = __fpmul(Areg3,B0reg3) ; +T1reg3 = __fpmul(Areg3,B1reg3) ; +T2reg3 = __fpmul(Areg3,B2reg3) ; + +Areg1 = __lfpd(&A[6]) ; +B0reg1 = __lfpd(&B0[6]) ; +B1reg1 = __lfpd(&B1[6]) ; +B2reg1 = __lfpd(&B2[6]) ; +T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ; +T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ; +T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ; + +Areg2 = __lfpd(&A[8]) ; +B0reg2 = __lfpd(&B0[8]) ; +B1reg2 = __lfpd(&B1[8]) ; +B2reg2 = __lfpd(&B2[8]) ; +T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ; +T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ; +T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ; + +Areg3 = __lfpd(&A[10]) ; +B0reg3 = __lfpd(&B0[10]) ; +B1reg3 = __lfpd(&B1[10]) ; +B2reg3 = __lfpd(&B2[10]) ; +T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ; +T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ; +T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ; + +Areg1 = __lfpd(&A[12]) ; +B0reg1 = __lfpd(&B0[12]) ; +B1reg1 = __lfpd(&B1[12]) ; +B2reg1 = __lfpd(&B2[12]) ; +T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ; +T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ; +T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ; + +Areg2 = __lfpd(&A[14]) ; +B0reg2 = __lfpd(&B0[14]) ; +B1reg2 = __lfpd(&B1[14]) ; +B2reg2 = __lfpd(&B2[14]) ; +T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ; +T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ; +T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ; + +Areg3 = __lfpd(&A[16]) ; +B0reg3 = __lfpd(&B0[16]) ; +B1reg3 = __lfpd(&B1[16]) ; +B2reg3 = __lfpd(&B2[16]) ; +T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ; +T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ; +T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ; + +Areg1 = __lfpd(&A[18]) ; +B0reg1 = __lfpd(&B0[18]) ; +B1reg1 = __lfpd(&B1[18]) ; +B2reg1 = __lfpd(&B2[18]) ; +T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ; +T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ; +T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ; + +Areg2 = __lfpd(&A[20]) ; +B0reg2 = __lfpd(&B0[20]) ; +B1reg2 = __lfpd(&B1[20]) ; +B2reg2 = __lfpd(&B2[20]) ; +T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ; +T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ; +T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ; + +Areg3 = __lfpd(&A[22]) ; +B0reg3 = __lfpd(&B0[22]) ; +B1reg3 = __lfpd(&B1[22]) ; +B2reg3 = __lfpd(&B2[22]) ; +T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ; +T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ; +T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ; + +Areg1 = __lfpd(&A[24]) ; +B0reg1 = __lfpd(&B0[24]) ; +B1reg1 = __lfpd(&B1[24]) ; +B2reg1 = __lfpd(&B2[24]) ; +T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ; +T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ; +T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ; + +Areg2 = __lfpd(&A[26]) ; +B0reg2 = __lfpd(&B0[26]) ; +B1reg2 = __lfpd(&B1[26]) ; +B2reg2 = __lfpd(&B2[26]) ; +T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ; +T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ; +T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ; + +Areg3 = __lfpd(&A[28]) ; +B0reg3 = __lfpd(&B0[28]) ; +B1reg3 = __lfpd(&B1[28]) ; +B2reg3 = __lfpd(&B2[28]) ; +T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ; +T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ; +T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ; + +Areg1 = __lfpd(&A[30]) ; +B0reg1 = __lfpd(&B0[30]) ; +B1reg1 = __lfpd(&B1[30]) ; +B2reg1 = __lfpd(&B2[30]) ; +T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ; +T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ; +T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ; + +Areg2 = __lfpd(&A[32]) ; +B0reg2 = __lfpd(&B0[32]) ; +B1reg2 = __lfpd(&B1[32]) ; +B2reg2 = __lfpd(&B2[32]) ; +T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ; +T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ; +T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ; + +Areg3 = __lfpd(&A[34]) ; +B0reg3 = __lfpd(&B0[34]) ; +B1reg3 = __lfpd(&B1[34]) ; +B2reg3 = __lfpd(&B2[34]) ; +T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ; +T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ; +T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ; + +Areg1 = __lfpd(&A[36]) ; +B0reg1 = __lfpd(&B0[36]) ; +B1reg1 = __lfpd(&B1[36]) ; +B2reg1 = __lfpd(&B2[36]) ; +T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ; +T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ; +T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ; + +Areg2 = __lfpd(&A[38]) ; +B0reg2 = __lfpd(&B0[38]) ; +B1reg2 = __lfpd(&B1[38]) ; +B2reg2 = __lfpd(&B2[38]) ; +T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ; +T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ; +T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ; + +Areg3 = __lfpd(&A[40]) ; +B0reg3 = __lfpd(&B0[40]) ; +B1reg3 = __lfpd(&B1[40]) ; +B2reg3 = __lfpd(&B2[40]) ; +T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ; +T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ; +T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ; + +Areg1 = __lfpd(&A[42]) ; +B0reg1 = __lfpd(&B0[42]) ; +B1reg1 = __lfpd(&B1[42]) ; +B2reg1 = __lfpd(&B2[42]) ; +T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ; +T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ; +T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ; + +Areg2 = __lfpd(&A[44]) ; +B0reg2 = __lfpd(&B0[44]) ; +B1reg2 = __lfpd(&B1[44]) ; +B2reg2 = __lfpd(&B2[44]) ; +T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ; +T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ; +T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ; + +Areg3 = __lfpd(&A[46]) ; +B0reg3 = __lfpd(&B0[46]) ; +B1reg3 = __lfpd(&B1[46]) ; +B2reg3 = __lfpd(&B2[46]) ; +T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ; +T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ; +T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ; + +Areg1 = __lfpd(&A[48]) ; +B0reg1 = __lfpd(&B0[48]) ; +B1reg1 = __lfpd(&B1[48]) ; +B2reg1 = __lfpd(&B2[48]) ; +T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ; +T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ; +T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ; + +Areg2 = __lfpd(&A[50]) ; +B0reg2 = __lfpd(&B0[50]) ; +B1reg2 = __lfpd(&B1[50]) ; +B2reg2 = __lfpd(&B2[50]) ; +T0reg2 = __fpmadd(T0reg2,Areg2,B0reg2) ; +T1reg2 = __fpmadd(T1reg2,Areg2,B1reg2) ; +T2reg2 = __fpmadd(T2reg2,Areg2,B2reg2) ; + +Areg3 = __lfpd(&A[52]) ; +B0reg3 = __lfpd(&B0[52]) ; +B1reg3 = __lfpd(&B1[52]) ; +B2reg3 = __lfpd(&B2[52]) ; +T0reg3 = __fpmadd(T0reg3,Areg3,B0reg3) ; +T1reg3 = __fpmadd(T1reg3,Areg3,B1reg3) ; +T2reg3 = __fpmadd(T2reg3,Areg3,B2reg3) ; + +Areg1 = __lfpd(&A[54]) ; +B0reg1 = __lfpd(&B0[54]) ; +B1reg1 = __lfpd(&B1[54]) ; +B2reg1 = __lfpd(&B2[54]) ; +T0reg1 = __fpmadd(T0reg1,Areg1,B0reg1) ; +T1reg1 = __fpmadd(T1reg1,Areg1,B1reg1) ; +T2reg1 = __fpmadd(T2reg1,Areg1,B2reg1) ; + + +T0reg1 = __fpadd(T0reg1,T0reg2) ; +T1reg1 = __fpadd(T1reg1,T1reg2) ; +T2reg1 = __fpadd(T2reg1,T2reg2) ; +T0reg1 = __fpadd(T0reg1,T0reg3) ; +T1reg1 = __fpadd(T1reg1,T1reg3) ; +T2reg1 = __fpadd(T2reg1,T2reg3) ; + +*tout0 = __creal(T0reg1) + __cimag(T0reg1) ; +*tout1 = __creal(T1reg1) + __cimag(T1reg1) ; +*tout2 = __creal(T2reg1) + __cimag(T2reg1) ; + +} diff --git a/src/USER-MGPT/mgpt_ttr_7141.c.h b/src/USER-MGPT/mgpt_ttr_7141.c.h new file mode 100644 index 0000000000..8309422333 --- /dev/null +++ b/src/USER-MGPT/mgpt_ttr_7141.c.h @@ -0,0 +1,174 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This file is part of the MGPT implementation. See further comments + in pair_mgpt.cpp and pair_mgpt.h. +------------------------------------------------------------------------- */ + +#define vector vector4double +#define my_vec_add(a,b) vec_add(a,b) +#define my_vec_mul(a,b) vec_mul(a,b) +#define my_vec_fma(a,b,c) vec_madd(b,c,a) +#define my_vec_ld(ptr) vec_lda(0,ptr) +#define my_vec_sldw(x,y,n) vec_sldw(x,y,n) +#define my_vec_sts(x,ptr) vec_sts(x,0,ptr) + +#define const +#define real double + +void ttr_bg_7_8_3_v4r1(const real * restrict A, + const real * restrict B0,real * restrict tout0, + const real * restrict B1,real * restrict tout1, + const real * restrict B2,real * restrict tout2) { +vector Areg1; +vector B0reg1,B1reg1,B2reg1; +vector T0reg1,T1reg1,T2reg1; + +Areg1 = my_vec_ld(&A[0]) ; +B0reg1 = my_vec_ld(&B0[0]) ; +B1reg1 = my_vec_ld(&B1[0]) ; +B2reg1 = my_vec_ld(&B2[0]) ; +T0reg1 = my_vec_mul(Areg1,B0reg1) ; +T1reg1 = my_vec_mul(Areg1,B1reg1) ; +T2reg1 = my_vec_mul(Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[4]) ; +B0reg1 = my_vec_ld(&B0[4]) ; +B1reg1 = my_vec_ld(&B1[4]) ; +B2reg1 = my_vec_ld(&B2[4]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[8]) ; +B0reg1 = my_vec_ld(&B0[8]) ; +B1reg1 = my_vec_ld(&B1[8]) ; +B2reg1 = my_vec_ld(&B2[8]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[12]) ; +B0reg1 = my_vec_ld(&B0[12]) ; +B1reg1 = my_vec_ld(&B1[12]) ; +B2reg1 = my_vec_ld(&B2[12]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[16]) ; +B0reg1 = my_vec_ld(&B0[16]) ; +B1reg1 = my_vec_ld(&B1[16]) ; +B2reg1 = my_vec_ld(&B2[16]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[20]) ; +B0reg1 = my_vec_ld(&B0[20]) ; +B1reg1 = my_vec_ld(&B1[20]) ; +B2reg1 = my_vec_ld(&B2[20]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[24]) ; +B0reg1 = my_vec_ld(&B0[24]) ; +B1reg1 = my_vec_ld(&B1[24]) ; +B2reg1 = my_vec_ld(&B2[24]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[28]) ; +B0reg1 = my_vec_ld(&B0[28]) ; +B1reg1 = my_vec_ld(&B1[28]) ; +B2reg1 = my_vec_ld(&B2[28]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[32]) ; +B0reg1 = my_vec_ld(&B0[32]) ; +B1reg1 = my_vec_ld(&B1[32]) ; +B2reg1 = my_vec_ld(&B2[32]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[36]) ; +B0reg1 = my_vec_ld(&B0[36]) ; +B1reg1 = my_vec_ld(&B1[36]) ; +B2reg1 = my_vec_ld(&B2[36]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[40]) ; +B0reg1 = my_vec_ld(&B0[40]) ; +B1reg1 = my_vec_ld(&B1[40]) ; +B2reg1 = my_vec_ld(&B2[40]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[44]) ; +B0reg1 = my_vec_ld(&B0[44]) ; +B1reg1 = my_vec_ld(&B1[44]) ; +B2reg1 = my_vec_ld(&B2[44]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[48]) ; +B0reg1 = my_vec_ld(&B0[48]) ; +B1reg1 = my_vec_ld(&B1[48]) ; +B2reg1 = my_vec_ld(&B2[48]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + +Areg1 = my_vec_ld(&A[52]) ; +B0reg1 = my_vec_ld(&B0[52]) ; +B1reg1 = my_vec_ld(&B1[52]) ; +B2reg1 = my_vec_ld(&B2[52]) ; +T0reg1 = my_vec_fma(T0reg1,Areg1,B0reg1) ; +T1reg1 = my_vec_fma(T1reg1,Areg1,B1reg1) ; +T2reg1 = my_vec_fma(T2reg1,Areg1,B2reg1) ; + + + +T0reg1 = my_vec_add(T0reg1,my_vec_sldw(T0reg1,T0reg1,2)); +T0reg1 = my_vec_add(T0reg1,my_vec_sldw(T0reg1,T0reg1,1)); +my_vec_sts(T0reg1,tout0); +T1reg1 = my_vec_add(T1reg1,my_vec_sldw(T1reg1,T1reg1,2)); +T1reg1 = my_vec_add(T1reg1,my_vec_sldw(T1reg1,T1reg1,1)); +my_vec_sts(T1reg1,tout1); +T2reg1 = my_vec_add(T2reg1,my_vec_sldw(T2reg1,T2reg1,2)); +T2reg1 = my_vec_add(T2reg1,my_vec_sldw(T2reg1,T2reg1,1)); +my_vec_sts(T2reg1,tout2); + +} + + +#undef vector +#undef my_vec_add +#undef my_vec_mul +#undef my_vec_fma +#undef my_vec_ld +#undef my_vec_sldw +#undef my_vec_sts + +#undef const +#undef real diff --git a/src/USER-MGPT/pair_mgpt.cpp b/src/USER-MGPT/pair_mgpt.cpp new file mode 100644 index 0000000000..596e66f488 --- /dev/null +++ b/src/USER-MGPT/pair_mgpt.cpp @@ -0,0 +1,2927 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Tomas Oppelstrup, LLNL (oppelstrup2@llnl.gov) + and John Moriarty, LLNL (moriarty2@llnl.gov) + + Fast MGPT algorithm developed by Tomas Oppelstrup (2015) based on the + matrix MGPT v4.4 FORTRAN routine of John Moriarty (2006) as converted + to C++ for LAMMPS application by Jamie Marian and Alexander Stukowski + (2011). See LLNL copyright notice at bottom of this file. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include + +#include "pair_mgpt.h" +#include "atom.h" +#include "force.h" +#include "comm.h" +#include "memory.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "memory.h" +#include "error.h" + + +using namespace LAMMPS_NS; + +//#define TIMING_ON + +#ifdef TIMING_ON +#include +#include +//#include "rdtsc.h" +#ifdef __bgq__ +#include +#endif + +static double gettime(int x = 0) { + if(1) { + /* + struct timeval tv; + gettimeofday(&tv,NULL); + return tv.tv_sec + 1e-6 * tv.tv_usec; + */ + /* + const double x = 1.0 / CLOCKS_PER_SEC; + return clock() * x; + */ + + //const double invfreq = 1.0 / 2394.108e6; + /* + const double invfreq = 1.0 / 700e6; + unsigned long long int x = rdtsc(); + return x*invfreq; + */ + + const double invfreq = 1.0 / 1.6e9; + unsigned long long int x = GetTimeBase(); + return x*invfreq; + + + } else + return 0.0; +} +#else +static double gettime(int x = 0) { return 0.0; } +#endif + + +/* ---------------------------------------------------------------------- */ + +PairMGPT::PairMGPT(LAMMPS *lmp) : Pair(lmp) +{ + single_enable = 0; + one_coeff = 1; + ghostneigh = 1; +} + +PairMGPT::~PairMGPT() +{ + if(allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(cutghost); + } +} + +/* ---------------------------------------------------------------------- */ + + +static double t_make_b2 = 0.0,n_make_b2 = 0.0; + +template void fmatconv(intype *array) { + outtype *cast = (outtype *) array; + for(int i = 0; iH.m )) & 31) == 0 ); + assert( (((unsigned long long int) (bptr->Hx.m)) & 31) == 0 ); + assert( (((unsigned long long int) (bptr->Hy.m)) & 31) == 0 ); + assert( (((unsigned long long int) (bptr->Hz.m)) & 31) == 0 ); + + rij = 0.0; + for(p = 0; p<3; p++) { + rrij[p] = xx[i][p] - xx[j][p]; + rij = rij + rrij[p]*rrij[p]; + } + + /* Zero all matrix elements */ + for(i = 0; i<8; i++) + for(j = 0; j<8; j++) { + bptr->H.m[i][j] = 0.0; + bptr->Hx.m[i][j] = 0.0; + bptr->Hy.m[i][j] = 0.0; + bptr->Hz.m[i][j] = 0.0; + bptr->Hz.m[j][i] = 0.0; + } + + if(rij <= rcrit*rcrit) { + t0 = gettime(); + if(lang == 3) { + hamltn_5_raw(rrij[0],rrij[1],rrij[2], + bptr->H.m ,bptr->Hx.m, + bptr->Hy.m,bptr->Hz.m,&bptr->fl_deriv_sum); + } else { + hamltn_7_raw(rrij[0],rrij[1],rrij[2], + bptr->H.m ,bptr->Hx.m, + bptr->Hy.m,bptr->Hz.m,&bptr->fl_deriv_sum); + } + + t1 = gettime(); + t_make_b2 += t1-t0; + n_make_b2++; + } else { + bptr->fl_deriv_sum = 0.0; + } + + if(linalg.single) { + fmatconv(&(bptr->H.m[1][0])); + fmatconv(&(bptr->Hx.m[1][0])); + fmatconv(&(bptr->Hy.m[1][0])); + fmatconv(&(bptr->Hz.m[1][0])); + } +} + +static double t_trace = 0.0,n_trace = 0.0; +/* +static inline double mtrace(int n,double A[8][8],double B[8][8]) { + double t0,t1; + double s; + + t0 = gettime(); + if(n == 5) s = mtrace_5(A,B); + else if(n == 7) s = mtrace_7(A,B); + else { + s = 0.0; + for(int i = 1; i<=n; i++) + for(int j = 1; j<=n; j++) + s = s + A[i][j]*B[i][j]; + } + t1 = gettime(); + t_trace += t1-t0; + n_trace++; + + return s; +} +*/ + +void PairMGPT::make_triplet(bond_data *ij_bond,bond_data *ik_bond, + triplet_data *triptr) { + if(1) { + const trmul_fun tr_mul = linalg.tr_mul; + tr_mul(&(ij_bond->H.m[1][0]), &(ik_bond->H.m[1][0]) ,&(triptr->H1H2.m[1][0]) ); + tr_mul(&(ij_bond->Hx.m[1][0]),&(ik_bond->H.m[1][0]) ,&(triptr->H1xH2.m[1][0])); + tr_mul(&(ij_bond->Hy.m[1][0]),&(ik_bond->H.m[1][0]) ,&(triptr->H1yH2.m[1][0])); + tr_mul(&(ij_bond->Hz.m[1][0]),&(ik_bond->H.m[1][0]) ,&(triptr->H1zH2.m[1][0])); + tr_mul(&(ij_bond->H.m[1][0]) ,&(ik_bond->Hx.m[1][0]),&(triptr->H1H2x.m[1][0])); + tr_mul(&(ij_bond->H.m[1][0]) ,&(ik_bond->Hy.m[1][0]),&(triptr->H1H2y.m[1][0])); + tr_mul(&(ij_bond->H.m[1][0]) ,&(ik_bond->Hz.m[1][0]),&(triptr->H1H2z.m[1][0])); + } else { + transprod(ij_bond->H, ik_bond->H ,triptr->H1H2 ); + transprod(ij_bond->Hx,ik_bond->H ,triptr->H1xH2); + transprod(ij_bond->Hy,ik_bond->H ,triptr->H1yH2); + transprod(ij_bond->Hz,ik_bond->H ,triptr->H1zH2); + transprod(ij_bond->H ,ik_bond->Hx,triptr->H1H2x); + transprod(ij_bond->H ,ik_bond->Hy,triptr->H1H2y); + transprod(ij_bond->H ,ik_bond->Hz,triptr->H1H2z); + } +} + +static double t_make_t = 0.0,t_make_b = 0.0,n_make = 0.0; + +PairMGPT::triplet_data *PairMGPT::get_triplet(const double xx[][3],int i,int j,int k, + Hash *bhash, + triplet_data *twork, + double *dvir_ij_p,double *dvir_ik_p) { + const int recompute = 0; + static bond_data bij_work,bik_work; + + double t0,t1; + + bond_data *bij = 0,*bik = 0; + triplet_data *tptr = 0; + + t0 = gettime(); + if(recompute == 0) { + bij = bhash->Lookup(Doublet(i,j)); + bik = bhash->Lookup(Doublet(i,k)); + } + + if(bij == 0) { + if(recompute == 0) + bij = bhash->Insert(Doublet(i,j)); + else + bij = &bij_work; + if(i < j) + make_bond(xx,i,j,bij); + else + make_bond(xx,j,i,bij); + } + + if(bik == 0) { + if(recompute == 0) + bik = bhash->Insert(Doublet(i,k)); + else + bik = &bik_work; + if(i < k) + make_bond(xx,i,k,bik); + else + make_bond(xx,k,i,bik); + } + t1 = gettime(); + t_make_b += t1-t0; + + t0 = gettime(); + if(bij != 0 && bij != 0) { + tptr = twork; + make_triplet(bij,bik,tptr); + *dvir_ij_p = bij->fl_deriv_sum; + *dvir_ik_p = bik->fl_deriv_sum; + } else { + *dvir_ij_p = 0.0; + *dvir_ik_p = 0.0; + } + t1 = gettime(); + t_make_t += t1-t0; + n_make++; + return tptr; +} + + +double PairMGPT::numderiv3t(double xx[][3],int i,int j,int k,int p) { + static bond_data Bij,Bjk,Bki; + const double delta = 1e-5; + + const double xsave = xx[i][p]; + double e1,e2; + + const double vc = splinepot.vc; + + xx[i][p] = xsave + delta; + make_bond(xx,i,j,&Bij); + make_bond(xx,j,k,&Bjk); + make_bond(xx,k,i,&Bki); + e1 = trace(prodmat(Bij.H,Bjk.H),Bki.H) * (vc/anorm3); + + xx[i][p] = xsave - delta; + make_bond(xx,i,j,&Bij); + if(0) { /* This bond doesn't change when i is perturbed */ + make_bond(xx,j,k,&Bjk); + } + make_bond(xx,k,i,&Bki); + e2 = trace(prodmat(Bij.H,Bjk.H),Bki.H) * (vc/anorm3); + + xx[i][p] = xsave; + return (e1 - e2)/(2.0*delta); +} + +double PairMGPT::numderiv3v(double xx[][3],int i,int j,int k,int p,int ipert) { + static bond_data Bij,Bik; + const double delta = 1e-5; + + const double xsave = xx[ipert][p]; + double e1,e2; + + const double vd = splinepot.vd; + + xx[ipert][p] = xsave + delta; + make_bond(xx,i,j,&Bij); + make_bond(xx,i,k,&Bik); + e1 = trace(prodmat(Bij.H,Bij.H),prodmat(Bik.H,Bik.H)) * (vd/anorm4); + + xx[ipert][p] = xsave - delta; + make_bond(xx,i,j,&Bij); + make_bond(xx,i,k,&Bik); + e2 = trace(prodmat(Bij.H,Bij.H),prodmat(Bik.H,Bik.H)) * (vd/anorm4); + + xx[ipert][p] = xsave; + return (e1 - e2)/(2.0*delta); +} + + +double PairMGPT::numderiv4(double xx[][3],int i,int j,int k,int m,int p) { + static bond_data Bij,Bjk,Bkm,Bmi; + const double delta = 1e-5; + + const double xsave = xx[i][p]; + double e1,e2; + + const double ve = splinepot.ve; + + xx[i][p] = xsave + delta; + make_bond(xx,i,j,&Bij); + make_bond(xx,j,k,&Bjk); + make_bond(xx,k,m,&Bkm); + make_bond(xx,m,i,&Bmi); + e1 = trace(prodmat(Bij.H,Bjk.H),prodmat(Bkm.H,Bmi.H)) * (ve/anorm4); + + xx[i][p] = xsave - delta; + make_bond(xx,i,j,&Bij); + if(0) { /* Only the i coordinates changed... */ + make_bond(xx,j,k,&Bjk); + make_bond(xx,k,m,&Bkm); + } + make_bond(xx,m,i,&Bmi); + e2 = trace(prodmat(Bij.H,Bjk.H),prodmat(Bkm.H,Bmi.H)) * (ve/anorm4); + + xx[i][p] = xsave; + return (e1 - e2)/(2.0*delta); +} + +static double dtol = 1e-6; +void PairMGPT::force_debug_3t(double xx[][3], + int i0,int j0,int k0, + int i ,int j ,int k , + double dfix,double dfiy,double dfiz, + double dfjx,double dfjy,double dfjz, + double dfkx,double dfky,double dfkz) { + double dfi[3],dfj[3],dfk[3]; + dfi[0] = dfix; dfi[1] = dfiy; dfi[2] = dfiz; + dfj[0] = dfjx; dfj[1] = dfjy; dfj[2] = dfjz; + dfk[0] = dfkx; dfk[1] = dfky; dfk[2] = dfkz; + + for(int p = 0; p<3; p++) { + /* Compute numerical derivatives by displacing atoms i,j,k */ + double ndfi,ndfj,ndfk; + ndfi = -numderiv3t(xx,i,j,k,p); + ndfj = -numderiv3t(xx,j,k,i,p); + ndfk = -numderiv3t(xx,k,i,j,p); + + if((fabs(dfi[p] - ndfi) > dtol && + fabs(dfi[p] - ndfi) > dtol*fabs(ndfi)) || + (fabs(dfj[p] - ndfj) > dtol && + fabs(dfj[p] - ndfj) > dtol*fabs(ndfj)) || + (fabs(dfk[p] - ndfk) > dtol && + fabs(dfk[p] - ndfk) > dtol*fabs(ndfk))) { + printf("Force error in T12 & T23 & T31 :: i,j,k = %d,%d,%d\n",i0,j0,k0); + printf(" dE/d%c[i] = %20.10e %20.10e\n", 'x'+p,ndfi, dfi[p]); + printf(" dE/d%c[j] = %20.10e %20.10e\n", 'x'+p,ndfj, dfj[p]); + printf(" dE/d%c[k] = %20.10e %20.10e\n", 'x'+p,ndfk, dfk[p]); + printf("\n"); + } + } +} + +void PairMGPT::force_debug_3v(double xx[][3], + int i0,int j0,int k0, + int i ,int j ,int k , + double dfix,double dfiy,double dfiz, + double dfjx,double dfjy,double dfjz, + double dfkx,double dfky,double dfkz) { + double dfi[3],dfj[3],dfk[3]; + dfi[0] = dfix; dfi[1] = dfiy; dfi[2] = dfiz; + dfj[0] = dfjx; dfj[1] = dfjy; dfj[2] = dfjz; + dfk[0] = dfkx; dfk[1] = dfky; dfk[2] = dfkz; + + for(int p = 0; p<3; p++) { + /* Compute numerical derivatives by displacing atoms i,j,k */ + double ndfi,ndfj,ndfk; + ndfi = -numderiv3v(xx,i,j,k,p,i0); + ndfj = -numderiv3v(xx,i,j,k,p,j0); + ndfk = -numderiv3v(xx,i,j,k,p,k0); + + if((fabs(dfi[p] - ndfi) > dtol && + fabs(dfi[p] - ndfi) > dtol*fabs(ndfi)) || + (fabs(dfj[p] - ndfj) > dtol && + fabs(dfj[p] - ndfj) > dtol*fabs(ndfj)) || + (fabs(dfk[p] - ndfk) > dtol && + fabs(dfk[p] - ndfk) > dtol*fabs(ndfk))) { + printf("Force error in T12 :: i,j,k = %d,%d,%d\n",i0,j0,k0); + printf(" dE/d%c[i] = %20.10e %20.10e\n", 'x'+p,ndfi, dfi[p]); + printf(" dE/d%c[j] = %20.10e %20.10e\n", 'x'+p,ndfj, dfj[p]); + printf(" dE/d%c[k] = %20.10e %20.10e\n", 'x'+p,ndfk, dfk[p]); + printf("\n"); + } + } +} + +void PairMGPT::force_debug_4(double xx[][3], + int i0,int j0,int k0,int m0, + int i ,int j ,int k ,int m , + double dfix,double dfiy,double dfiz, + double dfjx,double dfjy,double dfjz, + double dfkx,double dfky,double dfkz, + double dfmx,double dfmy,double dfmz) { + + double dfi[3],dfj[3],dfk[3],dfm[3]; + dfi[0] = dfix; dfi[1] = dfiy; dfi[2] = dfiz; + dfj[0] = dfjx; dfj[1] = dfjy; dfj[2] = dfjz; + dfk[0] = dfkx; dfk[1] = dfky; dfk[2] = dfkz; + dfm[0] = dfmx; dfm[1] = dfmy; dfm[2] = dfmz; + + const int ii0[] = {i0,j0,k0,m0},ii[] = {i,j,k,m,i,j,k}; + + for(int p = 0; p<3; p++) { + /* Compute numerical derivatives by displacing atoms i,j,k,m */ + double ndfi,ndfj,ndfk,ndfm; + if(1) { + double ndf[] = {0.0,0.0,0.0,0.0}; + for(int s = 0; s<4; s++) + for(int t = 0; t<4; t++) + if(ii[s] == ii0[t]) + ndf[t] = -numderiv4(xx,ii[s],ii[s+1],ii[s+2],ii[s+3],p); + ndfi = ndf[0]; ndfj = ndf[1]; + ndfk = ndf[2]; ndfm = ndf[3]; + } else { + ndfi = -numderiv4(xx,i,j,k,m,p); + ndfj = -numderiv4(xx,j,k,m,i,p); + ndfk = -numderiv4(xx,k,m,i,j,p); + ndfm = -numderiv4(xx,m,i,j,k,p); + } + + if((fabs(dfi[p] - ndfi) > dtol && + fabs(dfi[p] - ndfi) > dtol*fabs(ndfi)) || + (fabs(dfj[p] - ndfj) > dtol && + fabs(dfj[p] - ndfj) > dtol*fabs(ndfj)) || + (fabs(dfk[p] - ndfk) > dtol && + fabs(dfk[p] - ndfk) > dtol*fabs(ndfk)) || + (fabs(dfm[p] - ndfm) > dtol && + fabs(dfm[p] - ndfm) > dtol*fabs(ndfm))) { + printf("Force error in T31 & T64 :: i,j,k,m = %d,%d,%d,%d\n",i0,j0,k0,m0); + printf(" dE/d%c[i] = %20.10e %20.10e\n", 'x'+p,ndfi, dfi[p]); + printf(" dE/d%c[j] = %20.10e %20.10e\n", 'x'+p,ndfj, dfj[p]); + printf(" dE/d%c[k] = %20.10e %20.10e\n", 'x'+p,ndfk, dfk[p]); + printf(" dE/d%c[m] = %20.10e %20.10e\n", 'x'+p,ndfm, dfm[p]); + printf("\n"); + } + } +} + + + +/* +#define trd_update_4(T12,T45,coord) \ + do { \ + trd1 = transtrace(T12->H1##coord##H2,T45->H1H2 ); \ + trd2 = transtrace(T12->H1H2##coord,T45->H1H2 ); \ + trd3 = transtrace(T12->H1H2 ,T45->H1##coord##H2); \ + trd4 = transtrace(T12->H1H2 ,T45->H1H2##coord ); \ + } while(0) +*/ +#define trd_update_4(T12,T45) \ + do { \ + tr_trace3(&(T45->H1H2.m[1][0]), \ + &(T12->H1xH2.m[1][0]),&utr1x.d, \ + &(T12->H1yH2.m[1][0]),&utr1y.d, \ + &(T12->H1zH2.m[1][0]),&utr1z.d); \ + tr_trace3(&(T45->H1H2.m[1][0]), \ + &(T12->H1H2x.m[1][0]),&utr2x.d, \ + &(T12->H1H2y.m[1][0]),&utr2y.d, \ + &(T12->H1H2z.m[1][0]),&utr2z.d); \ + tr_trace3(&(T12->H1H2.m[1][0]), \ + &(T45->H1xH2.m[1][0]),&utr3x.d, \ + &(T45->H1yH2.m[1][0]),&utr3y.d, \ + &(T45->H1zH2.m[1][0]),&utr3z.d); \ + tr_trace3(&(T12->H1H2.m[1][0]), \ + &(T45->H1H2x.m[1][0]),&utr4x.d, \ + &(T45->H1H2y.m[1][0]),&utr4y.d, \ + &(T45->H1H2z.m[1][0]),&utr4z.d); \ + if(linalg.single) { \ + trd1x = utr1x.f; trd2x = utr2x.f; trd3x = utr3x.f; trd4x = utr4x.f; \ + trd1y = utr1y.f; trd2y = utr2y.f; trd3y = utr3y.f; trd4y = utr4y.f; \ + trd1z = utr1z.f; trd2z = utr2z.f; trd3z = utr3z.f; trd4z = utr4z.f; \ + } else { \ + trd1x = utr1x.d; trd2x = utr2x.d; trd3x = utr3x.d; trd4x = utr4x.d; \ + trd1y = utr1y.d; trd2y = utr2y.d; trd3y = utr3y.d; trd4y = utr4y.d; \ + trd1z = utr1z.d; trd2z = utr2z.d; trd3z = utr3z.d; trd4z = utr4z.d; \ + } \ + } while(0) + +#define dfix_update_4a(coord) \ + do { \ + dfi##coord = ( (-sij)*trd1##coord + (-sim)*trd3##coord ) * (ve / anorm4); \ + dfj##coord = ( ( sij)*trd1##coord + (-sjk)*trd2##coord ) * (ve / anorm4); \ + dfk##coord = ( ( sjk)*trd2##coord + (-skm)*trd4##coord ) * (ve / anorm4); \ + dfm##coord = ( ( sim)*trd3##coord + ( skm)*trd4##coord ) * (ve / anorm4); \ + } while(0) + + +#define dfix_update_4b(coord) \ + do { \ + dfi##coord = ( ( ski)*trd1##coord + (-sim)*trd3##coord ) * (ve / anorm4); \ + dfj##coord = ( (-sjk)*trd2##coord + (-sjm)*trd4##coord ) * (ve / anorm4); \ + dfk##coord = ( (-ski)*trd1##coord + ( sjk)*trd2##coord ) * (ve / anorm4); \ + dfm##coord = ( ( sim)*trd3##coord + ( sjm)*trd4##coord ) * (ve / anorm4); \ + } while(0); + +#define dfix_update_4c(coord) \ + do { \ + dfi##coord = ( (-sij)*trd1##coord + ( ski)*trd2##coord ) * (ve / anorm4); \ + dfj##coord = ( ( sij)*trd1##coord + (-sjm)*trd3##coord ) * (ve / anorm4); \ + dfk##coord = ( (-ski)*trd2##coord + (-skm)*trd4##coord ) * (ve / anorm4); \ + dfm##coord = ( ( sjm)*trd3##coord + ( skm)*trd4##coord ) * (ve / anorm4); \ + } while(0); + +#define accumulate_forces_2(w) \ + do { \ + fix = fix + dfix*(w); \ + fiy = fiy + dfiy*(w); \ + fiz = fiz + dfiz*(w); \ + \ + fjx = fjx + dfjx*(w); \ + fjy = fjy + dfjy*(w); \ + fjz = fjz + dfjz*(w); \ + } while(0) + +#define accumulate_forces_3(w) \ + do { \ + accumulate_forces_2(w); \ + fkx = fkx + dfkx*(w); \ + fky = fky + dfky*(w); \ + fkz = fkz + dfkz*(w); \ + } while(0) + +#define accumulate_forces_4(w) \ + do { \ + accumulate_forces_3(w); \ + fmx = fmx + dfmx*(w); \ + fmy = fmy + dfmy*(w); \ + fmz = fmz + dfmz*(w); \ + } while(0) + + + +#define restrict __restrict__ +#ifdef __bg__ +#define const +#endif +static int ntr_calls = 0; +static trtrace3_fun tr_internal; +static void tr_count(const double * restrict A, + const double * restrict B1,double * restrict t1, + const double * restrict B2,double * restrict t2, + const double * restrict B3,double * restrict t3) { + tr_internal(A,B1,t1,B2,t2,B3,t3); + ntr_calls++; +} +#ifdef __bg__ +#undef const +#endif +#undef restrict + + +int PairMGPT::Matrix::sz; +void PairMGPT::compute_x(const int *nnei,const int * const *nlist, + double *e_s,double *e_p,double *e_t,double *e_q, + int evflag,int newton_pair) { + Hash bond_hash(100000); + int i,j,k,m,ix,jx,kx,mx,itag,jtag,p; + + double e_single,e_pair,e_triplet,e_triplet_c,e_quad; + double volvir2; + + double nbc = 0.0,tbl = 0.0,tbm = 0.0; + const int lmax_local = lmax; + + //if(evflag) printf("##### ev flag is set... wasting cycles...\n"); + + *e_s = -99.0; + *e_p = -99.0; + *e_t = -99.0; + *e_q = -99.0; + + double t0,t1; + + t0 = gettime(1); + e_single = e_pair = e_triplet = e_triplet_c = e_quad = 0.0; + volvir2 = 0.0; + + t_make_t = t_make_b = t_make_b2 = t_trace = 0.0; + n_make = n_make_b2 = n_trace = 0.0; + + double tx0,tx1,tsort = 0.0,tpair = 0.0,tlookup = 0.0; + double ttriplet = 0.0,tquad = 0.0,tmem = 0.0; + double ntsort = 0.0,ntpair = 0.0,ntlookup = 0.0; + double nttriplet = 0.0,ntquad = 0.0,ntmem = 0.0,ntquaditer = 0.0; + double mcount = 0.0,mcount2 = 0.0, qcount = 0.0; + + double fix,fjx,fkx,fmx,dfix,dfjx,dfkx,dfmx; + double fiy,fjy,fky,fmy,dfiy,dfjy,dfky,dfmy; + double fiz,fjz,fkz,fmz,dfiz,dfjz,dfkz,dfmz; + + double fsave[4][3] = { {0.0} } /* {{0.0}} is to get rid of uninitialized use warning */; + + //const int numerical_pair_forces = (nbody_flag/16)%2; + const int pair_forces = (nbody_flag/2)%2,three_body_forces = (nbody_flag/4)%2,four_body_forces = (nbody_flag/8)%2; + const int pair_energies = (nbody_flag/2)%2,three_body_energies = (nbody_flag/4)%2,four_body_energies = (nbody_flag/8)%2; + const int single_energies = nbody_flag%2; + + const int triplet_debug = 0,quad_debug = 0; + + /* Energy and force scale factor for unit conversion. */ + const double e_scale = 0.5; + +#ifdef NEIGHMASK +#define NIDX(x) (x) +#else +#define NIDX(x) ((x) & NEIGHMASK) +#endif + + int nneitot,*first,*nlist_short; + double w2,w3,w4; + triplet_data T12work,T23work,T31work,T45work,T56work,T64work; + triplet_data *T12,*T23,*T31,*T45,*T56,*T64; + int c_ij,c_jk,c_ki,c_im,c_jm,c_km; + int mi,mj,mk; + double tr0,tr1,tr2,tr3; + double v33,v43; + double rcut2_pair = rmax*rmax,rcut2_bond = rcrit*rcrit,rij2; + int ntot,nloc; + + double dvir_ij,dvir_jk,dvir_ki,dvir_im,dvir_jm,dvir_km; + double vir3t = 0.0,vir3v = 0.0,vir4 = 0.0; + + double (*xx)[3],(*ff)[3],(*ss)[3]; + +#ifdef TIMING_ON + tr_internal = linalg.tr_trace; ntr_calls = 0; + const trtrace3_fun tr_trace3 = tr_count; +#else + const trtrace3_fun tr_trace3 = linalg.tr_trace; +#endif + union { + double d; + float f; + } utr1x,utr2x,utr3x,utr4x,utr1y,utr2y,utr3y,utr4y,utr1z,utr2z,utr3z,utr4z; + double trd1x,trd2x,trd3x,trd4x; + double trd1y,trd2y,trd3y,trd4y; + double trd1z,trd2z,trd3z,trd4z; + + + tx0 = gettime(); + + double rhoinv; + { + double vtot = 1.0; + double ntot = atom->natoms; + for(i = 0; i<3; i++) + vtot = vtot * (domain->boxhi[i] - domain->boxlo[i]); + rhoinv = vtot / ntot; + } + + /* Make sure triplet data work area is aligned and zeroed out. */ { + assert(T12work.align_check() == 0); + assert(T23work.align_check() == 0); + assert(T31work.align_check() == 0); + assert(T45work.align_check() == 0); + assert(T56work.align_check() == 0); + assert(T64work.align_check() == 0); + + T12work.zero(); T23work.zero(); T31work.zero(); + T45work.zero(); T56work.zero(); T64work.zero(); + } + + ntot = atom->nlocal + atom->nghost; + nloc = atom->nlocal; + //printf("[%3d] Allocating local array, size is %d atoms...\n",comm->me,j); + xx = (double (*)[3]) memory->smalloc(sizeof(double [3]) * ntot,"mgpt: local position vector."); + ff = (double (*)[3]) memory->smalloc(sizeof(double [3]) * ntot,"mgpt: local force vector."); + //printf("[%3d] Initializing arrays...\n",comm->me); + + const int triclinic = domain->triclinic; + double alpha[3] = {0.0,0.0,0.0}; + if(triclinic) { + double E[3][3],EX[3][3]; + int cyc[] = {0,1,2,0,1}; + + ss = (double (*)[3]) memory->smalloc(sizeof(double [3]) * ntot, + "mgpt: local reduced coordinate vector."); + + for(i = 0; i<3; i++) { + for(j = 0; j<3; j++) + E[i][j] = 0.0; + E[i][i] = domain->subhi_lamda[i] - domain->sublo_lamda[i]; + domain->lamda2x(E[i],EX[i]); + } + for(i = 0; i<3; i++) { + int i1 = cyc[i+1],i2 = cyc[i+2]; + double dot = 0.0,ns2 = 0.0; + for(j = 0; j<3; j++) { + int j1 = cyc[j+1],j2 = cyc[j+2]; + double cj = EX[i1][j1]*EX[i2][j2] - EX[i1][j2]*EX[i2][j1]; + ns2 = ns2 + cj*cj; + dot = dot + EX[i][j]*cj; + } + alpha[i] = E[i][i] / (dot/sqrt(ns2)); + if(comm->me == 0) { + static int count = 0; + if(count < 3) + printf("@@@ alpha(%d) = %15.5e\n",i+1,alpha[i]); + count++; + } + if(alpha[i] < 0.0) alpha[i] = -alpha[i]; + } + } else + ss = xx; + + nneitot = 0; + for(ix = 0; ixx[ix][p]; + ff[ix][p] = 0.0; + } + if(triclinic) + domain->x2lamda(xx[ix],ss[ix]); + nneitot = nneitot + nnei[ix]; + } + + first = (int *) memory->smalloc(sizeof(int) * (ntot+1),"mgpt: first"); + nlist_short = (int *) memory->smalloc(sizeof(int) * nneitot,"mgpt: nlist_short"); + + tx1 = gettime(); + tmem += tx1-tx0; + ntmem++; + + //printf("[%3d] Starting calculation...\n",comm->me); + + + fix = fjx = fkx = fmx = 0.0; + fiy = fjy = fky = fmy = 0.0; + fiz = fjz = fkz = fmz = 0.0; + + int c_p = 0, c_t = 0, c_q = 0; + + if(0) + if(domain->triclinic) { + if(comm->me == 0) + printf("Can not handle triclinic box yet\n"); + error->all(__FILE__,__LINE__,"Can not handle triclinic cell with mgpt yet."); + } + + /* + for(i = 0; i 0.0) { + /* + Compute pair energy/force + */ + double de_pair,df,rij = sqrt(rij2); + splinepot.eval_pot(rij,&de_pair,&df); + de_pair = de_pair * e_scale * w2; + df = df / rij * w2; + + + if(pair_energies == 0) de_pair = 0.0; + e_pair = e_pair + de_pair; + c_p++; + + if(pair_forces == 0) df = 0.0; + + if(volpres_flag && pair_energies) { + double dvir; + splinepot.eval_vir(rij,&dvir); + volvir2 = volvir2 - dvir * w2; + + /* Per-atom virial contribution of volumetric energy term */ + if(vflag_atom) + for(int pp = 0; pp<3; pp++) { + //virial[i] = virial[i] + rhoinv*e_scale*volvir2; + vatom[i][pp] -= 0.5 * rhoinv*e_scale*dvir*w2; + vatom[j][pp] -= 0.5 * rhoinv*e_scale*dvir*w2; + } + } + + double drijx = xx[j][0] - xx[i][0]; + double drijy = xx[j][1] - xx[i][1]; + double drijz = xx[j][2] - xx[i][2]; + + fix = fix + df*drijx; + fjx = fjx - df*drijx; + + fiy = fiy + df*drijy; + fjy = fjy - df*drijy; + + fiz = fiz + df*drijz; + fjz = fjz - df*drijz; + + if(evflag) { + //ev_tally(i,j,nloc,newton_pair,de_pair,0.0,df,-drijx,-drijy,-drijz); + /* To fix stress-per-atom scaling, and sign */ + ev_tally(i,j,nloc,newton_pair,de_pair,0.0,-df * e_scale,-drijx,-drijy,-drijz); + } + + ff[j][0] += fjx * e_scale; + ff[j][1] += fjy * e_scale; + ff[j][2] += fjz * e_scale; + + } + } + } + + if(rij2 < rcut2_bond && c2_outside(ss[i],ss[j],triclinic,alpha) == 0) { + /* + Add j to short neighbor list for i. + Insert j to keep list sorted. + */ + + p = first[i+1]-1; + while(p >= first[i] && nlist_short[p] > j) { + nlist_short[p+1] = nlist_short[p]; + p = p - 1; + } + nlist_short[p+1] = j; + first[i+1] = first[i+1] + 1; + if(first[i+1] > nneitot) { + printf("nneitot = %d, short list full. i=%d\n", + nneitot,i); + error->one(__FILE__,__LINE__,"Shit! Short list full\n"); + } + + } + } + + ff[i][0] += fix * e_scale; + ff[i][1] += fiy * e_scale; + ff[i][2] += fiz * e_scale; + + tx1 = gettime(); + tpair += tx1-tx0; + ntpair += nnei[i]; + } + + for(i = 0; i k and the list + is sorted, the loop below terminates:-) + */ + while(mj < first[j+1] && nlist_short[mj] < k) mj = mj + 1; + if(mj < first[j+1] && nlist_short[mj] == k) { + /* Closed triplet */ + c_jk = 1; + + if(j > i) continue; /* Require k 0.0) { + triplet_defer = 0; + + dvir_ij = dvir_jk = dvir_ki = 0.0; + if(c_ij && c_jk) + T12 = get_triplet(xx,j,i,k,&bond_hash,&T12work,&dvir_ij,&dvir_jk); + if(c_ki && c_jk) + T23 = get_triplet(xx,k,i,j,&bond_hash,&T23work,&dvir_ki,&dvir_jk); + if(c_ij && c_ki) + T31 = get_triplet(xx,i,j,k,&bond_hash,&T31work,&dvir_ij,&dvir_ki); + + if(evflag) { + fsave[0][0] = fix; fsave[0][1] = fiy; fsave[0][2] = fiz; + fsave[1][0] = fjx; fsave[1][1] = fjy; fsave[1][2] = fjz; + fsave[2][0] = fkx; fsave[2][1] = fky; fsave[2][2] = fkz; + fix = fiy = fiz = 0.0; + fjx = fjy = fjz = 0.0; + fkx = fky = fkz = 0.0; + } + + tr0 = tr1 = tr2 = tr3 = 0.0; + double xvir3t,xvir3v; + xvir3t = xvir3v = 0.0; + + if(T12 && T23) { + bond_data *bki = bond_hash.Lookup(Doublet(k,i)); + + if(three_body_energies && evflag) { + tr0 = transtrace(T12->H1H2,bki->H); + double dvir = ((dvir_ij + dvir_jk + bki->fl_deriv_sum)*splinepot.vc + + splinepot.dvc)*tr0*w3/anorm3; + vir3t = vir3t + dvir; + xvir3t = xvir3t + dvir; + } + mcount2++; + + { + const double vc = splinepot.vc; + tr_trace3(&(bki->H.m[1][0]), + &(T12->H1xH2.m[1][0]),&utr1x.d, + &(T12->H1yH2.m[1][0]),&utr1y.d, + &(T12->H1zH2.m[1][0]),&utr1z.d); + + tr_trace3(&(bki->H.m[1][0]), + &(T12->H1H2x.m[1][0]),&utr2x.d, + &(T12->H1H2y.m[1][0]),&utr2y.d, + &(T12->H1H2z.m[1][0]),&utr2z.d); + + tr_trace3(&(T12->H1H2.m[1][0]), + &(bki->Hx.m[1][0]),&utr3x.d, + &(bki->Hy.m[1][0]),&utr3y.d, + &(bki->Hz.m[1][0]),&utr3z.d); + + if(linalg.single) { + trd1x = utr1x.f; trd2x = utr2x.f; trd3x = utr3x.f; + trd1y = utr1y.f; trd2y = utr2y.f; trd3y = utr3y.f; + trd1z = utr1z.f; trd2z = utr2z.f; trd3z = utr3z.f; + } else { + trd1x = utr1x.d; trd2x = utr2x.d; trd3x = utr3x.d; + trd1y = utr1y.d; trd2y = utr2y.d; trd3y = utr3y.d; + trd1z = utr1z.d; trd2z = utr2z.d; trd3z = utr3z.d; + } + + dfix = ( (-sij)*trd1x + ( ski)*trd3x ) * (vc / anorm3); + dfjx = ( ( sij)*trd1x + (-sjk)*trd2x ) * (vc / anorm3); + dfkx = ( ( sjk)*trd2x + (-ski)*trd3x ) * (vc / anorm3); + + dfiy = ( (-sij)*trd1y + ( ski)*trd3y ) * (vc / anorm3); + dfjy = ( ( sij)*trd1y + (-sjk)*trd2y ) * (vc / anorm3); + dfky = ( ( sjk)*trd2y + (-ski)*trd3y ) * (vc / anorm3); + + dfiz = ( (-sij)*trd1z + ( ski)*trd3z ) * (vc / anorm3); + dfjz = ( ( sij)*trd1z + (-sjk)*trd2z ) * (vc / anorm3); + dfkz = ( ( sjk)*trd2z + (-ski)*trd3z ) * (vc / anorm3); + } + + if(triplet_debug) + force_debug_3t(xx,i,j,k, i,j,k, + dfix,dfiy,dfiz, + dfjx,dfjy,dfjz, + dfkx,dfky,dfkz); + + if(three_body_forces) + accumulate_forces_3(w3); + } + + if(T12 != 0) { + //printf("T12 i,j,k = %d,%d,%d\n",i,j,k); + mcount++; + if(three_body_energies && evflag) { + tr1 = transtrace(T12->H1H2,T12->H1H2); + double dvir = (2.0*(dvir_ij + dvir_jk)*splinepot.vd + + splinepot.dvd)*tr1*w3/anorm4; + vir3v = vir3v + dvir; + xvir3v = xvir3v + dvir; + } + + { + const double vd = splinepot.vd; + + tr_trace3(&(T12->H1H2.m[1][0]), + &(T12->H1xH2.m[1][0]),&utr1x.d, + &(T12->H1yH2.m[1][0]),&utr1y.d, + &(T12->H1zH2.m[1][0]),&utr1z.d); + tr_trace3(&(T12->H1H2.m[1][0]), + &(T12->H1H2x.m[1][0]),&utr2x.d, + &(T12->H1H2y.m[1][0]),&utr2y.d, + &(T12->H1H2z.m[1][0]),&utr2z.d); + if(linalg.single) { + trd1x = utr1x.f; trd2x = utr2x.f; + trd1y = utr1y.f; trd2y = utr2y.f; + trd1z = utr1z.f; trd2z = utr2z.f; + } else { + trd1x = utr1x.d; trd2x = utr2x.d; + trd1y = utr1y.d; trd2y = utr2y.d; + trd1z = utr1z.d; trd2z = utr2z.d; + } + + dfix = 2.0*(-sij)*trd1x * (vd / anorm4); + dfkx = 2.0*( sjk)*trd2x * (vd / anorm4); + dfjx = -(dfix + dfkx); + + dfiy = 2.0*(-sij)*trd1y * (vd / anorm4); + dfky = 2.0*( sjk)*trd2y * (vd / anorm4); + dfjy = -(dfiy + dfky); + + dfiz = 2.0*(-sij)*trd1z * (vd / anorm4); + dfkz = 2.0*( sjk)*trd2z * (vd / anorm4); + dfjz = -(dfiz + dfkz); + } + + if(triplet_debug) /* Compare forces to numerical derivatives */ + force_debug_3v(xx,i,j,k, j,i,k, + dfix,dfiy,dfiz, + dfjx,dfjy,dfjz, + dfkx,dfky,dfkz); + + + if(three_body_forces) + accumulate_forces_3(w3); + } + + if(T23 != 0) { + //printf("T23 i,j,k = %d,%d,%d\n",i,j,k); + mcount++; + if(three_body_energies && evflag) { + tr2 = transtrace(T23->H1H2,T23->H1H2); + double dvir = (2.0*(dvir_jk + dvir_ki)*splinepot.vd + + splinepot.dvd)*tr2*w3/anorm4; + vir3v = vir3v + dvir; + xvir3v = xvir3v + dvir; + } + + { + const double vd = splinepot.vd; + + tr_trace3(&(T23->H1H2.m[1][0]), + &(T23->H1xH2.m[1][0]),&utr1x.d, + &(T23->H1yH2.m[1][0]),&utr1y.d, + &(T23->H1zH2.m[1][0]),&utr1z.d); + tr_trace3(&(T23->H1H2.m[1][0]), + &(T23->H1H2x.m[1][0]),&utr2x.d, + &(T23->H1H2y.m[1][0]),&utr2y.d, + &(T23->H1H2z.m[1][0]),&utr2z.d); + if(linalg.single) { + trd1x = utr1x.f; trd2x = utr2x.f; + trd1y = utr1y.f; trd2y = utr2y.f; + trd1z = utr1z.f; trd2z = utr2z.f; + } else { + trd1x = utr1x.d; trd2x = utr2x.d; + trd1y = utr1y.d; trd2y = utr2y.d; + trd1z = utr1z.d; trd2z = utr2z.d; + } + + dfix = 2.0*( ski)*trd1x * (vd / anorm4); + dfjx = 2.0*(-sjk)*trd2x * (vd / anorm4); + dfkx = -(dfix + dfjx); + + dfiy = 2.0*( ski)*trd1y * (vd / anorm4); + dfjy = 2.0*(-sjk)*trd2y * (vd / anorm4); + dfky = -(dfiy + dfjy); + + dfiz = 2.0*( ski)*trd1z * (vd / anorm4); + dfjz = 2.0*(-sjk)*trd2z * (vd / anorm4); + dfkz = -(dfiz + dfjz); + } + + if(triplet_debug) /* Compare forces to numerical derivatives */ + force_debug_3v(xx,i,j,k, k,i,j, + dfix,dfiy,dfiz, + dfjx,dfjy,dfjz, + dfkx,dfky,dfkz); + + if(three_body_forces) + accumulate_forces_3(w3); + + } + + if(T31 != 0) { + //printf("T31 i,j,k = %d,%d,%d\n",i,j,k); + mcount++; + if(three_body_energies && evflag) { + tr3 = transtrace(T31->H1H2,T31->H1H2); + double dvir = (2.0*(dvir_ki + dvir_ij)*splinepot.vd + + splinepot.dvd)*tr3*w3/anorm4; + vir3v = vir3v + dvir; + xvir3v = xvir3v + dvir; + } + + { + const double vd = splinepot.vd; + + tr_trace3(&(T31->H1H2.m[1][0]), + &(T31->H1xH2.m[1][0]),&utr1x.d, + &(T31->H1yH2.m[1][0]),&utr1y.d, + &(T31->H1zH2.m[1][0]),&utr1z.d); + tr_trace3(&(T31->H1H2.m[1][0]), + &(T31->H1H2x.m[1][0]),&utr2x.d, + &(T31->H1H2y.m[1][0]),&utr2y.d, + &(T31->H1H2z.m[1][0]),&utr2z.d); + if(linalg.single) { + trd1x = utr1x.f; trd2x = utr2x.f; + trd1y = utr1y.f; trd2y = utr2y.f; + trd1z = utr1z.f; trd2z = utr2z.f; + } else { + trd1x = utr1x.d; trd2x = utr2x.d; + trd1y = utr1y.d; trd2y = utr2y.d; + trd1z = utr1z.d; trd2z = utr2z.d; + } + + dfjx = 2.0*( sij)*trd1x * (vd / anorm4); + dfkx = 2.0*(-ski)*trd2x * (vd / anorm4); + dfix = -(dfjx + dfkx); + + dfjy = 2.0*( sij)*trd1y * (vd / anorm4); + dfky = 2.0*(-ski)*trd2y * (vd / anorm4); + dfiy = -(dfjy + dfky); + + dfjz = 2.0*( sij)*trd1z * (vd / anorm4); + dfkz = 2.0*(-ski)*trd2z * (vd / anorm4); + dfiz = -(dfjz + dfkz); + + } + + if(triplet_debug) /* Compare forces to numerical derivatives */ + force_debug_3v(xx,i,j,k, i,j,k, + dfix,dfiy,dfiz, + dfjx,dfjy,dfjz, + dfkx,dfky,dfkz); + + if(three_body_forces) + accumulate_forces_3(w3); + } + + v33 = tr0 / anorm3; + v43 = (tr1 + tr2 + tr3) / anorm4; + double de_triplet = (splinepot.vc*v33 + splinepot.vd*v43) * e_scale * w3; + e_triplet = e_triplet + de_triplet; + e_triplet_c = e_triplet_c + splinepot.vc*v33 * e_scale * w3; + c_t++; + + //printf("xxxx %6d %6d %6d :: %20.10e\n",1,2,3,de_triplet); + + if(evflag) { + double drji[3],drki[3]; + double fj[3] = {fjx,fjy,fjz},fk[3] = {fkx,fky,fkz}; + for(int p = 0; p<3; p++) { + drji[p] = xx[j][p] - xx[i][p]; + drki[p] = xx[k][p] - xx[i][p]; + /* To fix stress-per-atom scaling. */ + fj[p] *= e_scale; + fk[p] *= e_scale; + } + + ev_tally3(i,j,k,de_triplet,0.0,fj,fk,drji,drki); + + if(volpres_flag && vflag_atom) { + //virial[i] = virial[i] - (vir3v + vir3t) * rhoinv*e_scale; + double dvir = -(xvir3v + xvir3t) * rhoinv*e_scale * (1.0/3.0); + for(int pp = 0; pp<3; pp++) { + vatom[i][pp] += dvir; + vatom[j][pp] += dvir; + vatom[k][pp] += dvir; + } + } + + fix = fix+fsave[0][0]; fiy = fiy+fsave[0][1]; fiz = fiz+fsave[0][2]; + fjx = fjx+fsave[1][0]; fjy = fjy+fsave[1][1]; fjz = fjz+fsave[1][2]; + fkx = fkx+fsave[2][0]; fky = fky+fsave[2][1]; fkz = fkz+fsave[2][2]; + } + + tx1 = gettime(); + ttriplet += tx1 - tx0; + nttriplet++; + } else { + triplet_defer = 1; + } + + if(four_body_energies || four_body_forces) + if(j < i) { /* Search for quadruplet */ + tx0 = gettime(); + + mj = first[j]; + mk = first[k]; + /* + i is in both the j-list and the k-list, and i > k, + and lists are sorted, so the loop terminates. + */ + while(nlist_short[mj] < i && nlist_short[mk] < i) { + + if(mj >= first[j+1] || mk >= first[k+1]) { + printf("Illegal quad...\n" + " j=%d first[j]=%d first[j+1]=%d mj=%d\n" + " k=%d first[k]=%d first[k+1]=%d mk=%d\n", + j,first[j],first[j+1],mj, + k,first[k],first[k+1],mk); + error->one(__FILE__,__LINE__,"Shit, brkoen quad loop"); + } + + if(nlist_short[mj] == nlist_short[mk]) { + /* Closed quadruplet */ + m = nlist_short[mj]; + c_jm = c_km = 1; + + const int sim = (i < m) ? 1 : -1; + const int sjm = (j < m) ? 1 : -1; + const int skm = (k < m) ? 1 : -1; + + w4 = get_weight(triclinic,ss[i],ss[j],ss[k],ss[m]); + + if(w4 > 0.0) { + + /* Alrady know ij,jk,ki,jm,km bonds. Look for im bond. */ + mi = first[i]; + while(mi < first[i+1] && nlist_short[mi] < m) mi = mi + 1; + if(mi < first[i+1] && nlist_short[mi] == m) + c_im = 1; + else + c_im = 0; + + if(c_im == 0 || c_jk == 0 || (c_jk && c_im && m < k)) { + + if(triplet_defer) { + dvir_ij = dvir_jk = dvir_ki = 0.0; + if(c_ij && c_jk) + T12 = get_triplet(xx,j,i,k,&bond_hash,&T12work,&dvir_ij,&dvir_jk); + if(c_ki && c_jk) + T23 = get_triplet(xx,k,i,j,&bond_hash,&T23work,&dvir_ki,&dvir_jk); + if(c_ij && c_ki) + T31 = get_triplet(xx,i,j,k,&bond_hash,&T31work,&dvir_ij,&dvir_ki); + triplet_defer = 0; + } + + + fmx = fmy = fmz = 0.0; + double xvir4 = 0.0; + + if(evflag) { + fsave[0][0] = fix; fsave[0][1] = fiy; fsave[0][2] = fiz; + fsave[1][0] = fjx; fsave[1][1] = fjy; fsave[1][2] = fjz; + fsave[2][0] = fkx; fsave[2][1] = fky; fsave[2][2] = fkz; + fsave[3][0] = fmx; fsave[3][1] = fmy; fsave[3][2] = fmz; + fix = fiy = fiz = 0.0; + fjx = fjy = fjz = 0.0; + fkx = fky = fkz = 0.0; + fmx = fmy = fmz = 0.0; + } + + tr1 = tr2 = tr3 = 0.0; + + dvir_im = dvir_jm = dvir_km = 0.0; + T45 = T56 = T64 = 0; + if(T12 != 0 && c_km && c_im) + T45 = get_triplet(xx,m,i,k,&bond_hash,&T45work,&dvir_im,&dvir_km); + if(T23 != 0 && c_im && c_jm) + T56 = get_triplet(xx,m,i,j,&bond_hash,&T56work,&dvir_im,&dvir_jm); + if(T31 != 0 && c_jm && c_km) + T64 = get_triplet(xx,m,j,k,&bond_hash,&T64work,&dvir_jm,&dvir_km); + + if(T12 != 0 && T45 != 0) { + if(four_body_energies && evflag) { + tr1 = transtrace(T12->H1H2,T45->H1H2); + double dvir = ( (dvir_ij + dvir_jk + dvir_im + dvir_km)*splinepot.ve + + splinepot.dve )*tr1*w4/anorm4; + vir4 = vir4 + dvir; + xvir4 = xvir4 + dvir; + } + qcount++; + + { + const double ve = splinepot.ve; + + trd_update_4(T12,T45); + + dfix_update_4a(x); + dfix_update_4a(y); + dfix_update_4a(z); + } + + if(quad_debug) /* Compare forces to numerical derivatives */ + force_debug_4(xx,i,j,k,m, i,j,k,m, + dfix,dfiy,dfiz , dfjx,dfjy,dfjz, + dfkx,dfky,dfkz , dfmx,dfmy,dfmz); + + if(four_body_forces) + accumulate_forces_4(w4); + } + + if(T23 != 0 && T56 != 0) { + if(four_body_energies && evflag) { + tr2 = transtrace(T23->H1H2,T56->H1H2); + double dvir = ( (dvir_ki + dvir_jk + dvir_im + dvir_jm)*splinepot.ve + + splinepot.dve )*tr2*w4/anorm4; + vir4 = vir4 + dvir; + xvir4 = xvir4 + dvir; + } + qcount++; + + { + const double ve = splinepot.ve; + + trd_update_4(T23,T56); + + dfix_update_4b(x); + dfix_update_4b(y); + dfix_update_4b(z); + } + + if(quad_debug) /* Compare forces to numerical derivatives */ + force_debug_4(xx,i,j,k,m, i,m,j,k, + dfix,dfiy,dfiz , dfjx,dfjy,dfjz, + dfkx,dfky,dfkz , dfmx,dfmy,dfmz); + + if(four_body_forces) + accumulate_forces_4(w4); + + } + + if(T31 != 0 && T64 != 0) { + if(four_body_energies && evflag) { + tr3 = transtrace(T31->H1H2,T64->H1H2); + double dvir = ( (dvir_ki + dvir_ij + dvir_jm + dvir_km)*splinepot.ve + + splinepot.dve )*tr3*w4/anorm4; + vir4 = vir4 + dvir; + xvir4 = xvir4 + dvir; + } + qcount++; + + { + const double ve = splinepot.ve; + + /* X */ + trd_update_4(T31,T64); + + dfix_update_4c(x); + dfix_update_4c(y); + dfix_update_4c(z); + } + + if(quad_debug) /* Compare forces to numerical derivatives */ + force_debug_4(xx,i,j,k,m, i,j,m,k, + dfix,dfiy,dfiz , dfjx,dfjy,dfjz, + dfkx,dfky,dfkz , dfmx,dfmy,dfmz); + + if(four_body_forces) + accumulate_forces_4(w4); + } + + double de_quad = splinepot.ve*(tr1 + tr2 + tr3)/anorm4 * e_scale * w4; + e_quad = e_quad + de_quad; + if((T12 && T45) || + (T23 && T56) || + (T31 && T64)) { + c_q++; + } + + if(evflag) { + double drim[3],drjm[3],drkm[3]; + double fi[3] = {fix,fiy,fiz}; + double fj[3] = {fjx,fjy,fjz}; + double fk[3] = {fkx,fky,fkz}; + for(int p = 0; p<3; p++) { + drim[p] = xx[i][p] - xx[m][p]; + drjm[p] = xx[j][p] - xx[m][p]; + drkm[p] = xx[k][p] - xx[m][p]; + fi[p] *= e_scale; + fj[p] *= e_scale; + fk[p] *= e_scale; + } + + ev_tally4(i,j,k,m,de_quad,fi,fj,fk,drim,drjm,drkm); + + if(volpres_flag && vflag_atom) { + //virial[i] = virial[i] - vir4 * rhoinv*e_scale; + double dvir = -xvir4 * rhoinv*e_scale * (1.0/4.0); + for(int pp = 0; pp<3; pp++) { + vatom[i][pp] += dvir; + vatom[j][pp] += dvir; + vatom[k][pp] += dvir; + vatom[m][pp] += dvir; + } + } + + fix = fix+fsave[0][0]; fiy = fiy+fsave[0][1]; fiz = fiz+fsave[0][2]; + fjx = fjx+fsave[1][0]; fjy = fjy+fsave[1][1]; fjz = fjz+fsave[1][2]; + fkx = fkx+fsave[2][0]; fky = fky+fsave[2][1]; fkz = fkz+fsave[2][2]; + fmx = fmx+fsave[3][0]; fmy = fmy+fsave[3][1]; fmz = fmz+fsave[3][2]; + } + + ff[m][0] += fmx * e_scale; + ff[m][1] += fmy * e_scale; + ff[m][2] += fmz * e_scale; + + } + } + mj = mj + 1; + mk = mk + 1; + } else if(nlist_short[mj] < nlist_short[mk]) { + mj = mj + 1; + } else { + mk = mk + 1; + } + + } + tx1 = gettime(); + tquad += tx1 - tx0; + ntquad++; + ntquaditer++; + } + + + ff[k][0] += fkx * e_scale; + ff[k][1] += fky * e_scale; + ff[k][2] += fkz * e_scale; + + } +#undef transtrace + + ff[j][0] += fjx * e_scale; + ff[j][1] += fjy * e_scale; + ff[j][2] += fjz * e_scale; + + } + + ff[i][0] += fix * e_scale; + ff[i][1] += fiy * e_scale; + ff[i][2] += fiz * e_scale; + + if(single_energies == 1 && i < nloc) { + const double evol0 = splinepot.evol0; + if(eflag_global) { + e_single = e_single + evol0 * e_scale; + eng_vdwl = eng_vdwl + evol0 * e_scale; + } + if(eflag_atom) eatom[i] = eatom[i] + evol0 * e_scale; + if(volpres_flag && vflag_atom) { + for(int pp = 0; pp<3; pp++) + vatom[i][pp] = vatom[i][pp] - rhoinv*splinepot.devol0*e_scale; + } + + } + + } + + tx0 = gettime(); + for(i = 0; if[i][p] = atom->f[i][p] + ff[i][p]; + + memory->sfree(nlist_short); + memory->sfree(first); + if(ss != xx) memory->sfree(ss); + memory->sfree(ff); + memory->sfree(xx); + tx1 = gettime(); + tmem += tx1-tx0; + ntmem++; + + t1 = gettime(1); + + //printf("compute_x: c_p = %d c_t = %d c_q = %d\n",c_p,c_t,c_q); + + +#ifdef TIMING_ON + if(comm->me == 0) { + double tsum = (tmem+tsort+tpair+tlookup+ttriplet+tquad); + double nsum = (ntmem+ntsort+ntpair+ntlookup+nttriplet+ntquad); + //double adj = ((t1-t0)-tsum)/nsum; + /* Use adj = 6ns for RDTSC, and 58ns for gettimeofday, + on monkfish.llnl.gov, 2.4GHz Intel + + Use adj = 35.945ns for RDTSC on uBGL (assumed rate set to 700MHz) + */ + double adj = 35.945e-9; + + double + memadj = tmem - adj*ntmem , + sortadj = tsort - adj*ntsort , + pairadj = tpair - adj*ntpair , + lookupadj = tlookup - adj*ntlookup , + tripletadj = ttriplet - adj*nttriplet, + quadadj = tquad - adj*ntquad , + + make_b_adj = t_make_b - adj*n_make, + make_t_adj = t_make_t - adj*n_make, + make_b2_adj = t_make_b2 - adj*n_make_b2, + trace_adj = t_trace - adj*n_trace; + + printf("mgpt engy = %10.3fms\n",(t1-t0)*1e3); + printf(" mem = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n", + tmem*1e3,ntmem,memadj*1e3,memadj/ntmem*1e9); + printf(" sort = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n", + tsort*1e3,ntsort,sortadj*1e3,sortadj/ntsort*1e9); + printf(" pair = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n", + tpair*1e3,ntpair,pairadj*1e3,pairadj/ntpair*1e9); + printf(" lookup = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n", + tlookup*1e3,ntlookup,lookupadj*1e3,lookupadj/ntlookup*1e9); + printf(" triplet = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n", + ttriplet*1e3,nttriplet,tripletadj*1e3,tripletadj/nttriplet*1e9); + printf(" quad = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n", + tquad*1e3,ntquaditer,quadadj*1e3,quadadj/ntquaditer*1e9); + printf(" sum = %10.3fms adj = %10.3fms\n", + tsum*1e3,(tsum - adj*nsum)*1e3); + printf("\n make_b = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n", + t_make_b*1e3,n_make,make_b_adj*1e3,make_b_adj/n_make*1e9); + printf(" make_b2 = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n", + t_make_b2*1e3,n_make_b2,make_b2_adj*1e3,make_b2_adj/n_make_b2*1e9); + printf(" make_t = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n\n", + t_make_t*1e3,n_make,make_t_adj*1e3,make_t_adj/n_make*1e9); + printf(" trace = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n\n", + t_trace*1e3,n_trace,trace_adj*1e3,trace_adj/n_trace*1e9); + + printf("mcount (transpose + trace for triplet) = %.0f , %.0f qcount = %.0f lmax = %d\n", + mcount,mcount2,qcount,lmax); + + printf("nbc=%.0f tbl=%.3fms tbm=%.3fms one tbl=%.3fns one tbm=%.3fns\n", + nbc,(tbl-adj*nbc)*1e3,(tbm-adj*nbc)*1e3,(tbl/nbc-adj)*1e9, + (tbm/nbc-adj)*1e9); + printf("\n\nForces:\n"); + printf("fix = %.3f fiy=%.3f fiz=%.3f\n",fix,fiy,fiz); + printf("fjx = %.3f fjy=%.3f fjz=%.3f\n",fjx,fjy,fjz); + printf("fkx = %.3f fky=%.3f fkz=%.3f\n",fkx,fky,fkz); + printf("\n"); + + printf("Bonds : nsearch=%d maxlen=%d avg.len=%.3f\n", + bond_hash.NSearch(),bond_hash.MaxLength(), + bond_hash.NStep()/(double) bond_hash.NSearch()); + + printf("compute_x: c_p = %d c_t = %d c_q = %d\n",c_p,c_t,c_q); + + printf("@@ Total number of trace3 calls is %d, total number of make_triplet is %.1f\n", + ntr_calls,n_make); + + { + Hash::Iterator iter = bond_hash.begin(); + int nitem = 0,nhit = 0; + while(iter != bond_hash.end()) { + nitem++; + nhit += iter.link()->hits; + iter.next(); + } + printf("bond_hash hits: nitems=%d nhits=%d hits/item = %.3f\n", + nitem,nhit,nhit/(double) nitem); + } + } +#endif + + if(volpres_flag) { + /* + Include contributions to the pressure due to derivatines + of the energy with respect to the potential input volume. + */ + + /* The following lines have moved to beginning of functions, + since they are used in calculating per-atom virial contributions */ + /* + double vtot = 1.0; + double ntot = atom->natoms; + for(i = 0; i<3; i++) + vtot = vtot * (domain->boxhi[i] - domain->boxlo[i]); + double rhoinv = vtot / ntot; + */ + + if(single_energies) // Virial correction for self energy + for(i = 0; i<3; i++) { + //virial[i] = virial[i] + nloc*pot_input_vol*pvol0*e_scale; + virial[i] = virial[i] - nloc*rhoinv*splinepot.devol0*e_scale; + } + + if(pair_energies) // Virial correction for pair energy + for(i = 0; i<3; i++) + virial[i] = virial[i] + rhoinv*e_scale*volvir2; + + if(three_body_energies) // Virial correction for three body enegries + for(i = 0; i<3; i++) { + //virial[i] = virial[i] - pot_input_vol*(e_triplet_c*pc + (e_triplet-e_triplet_c)*pd); + virial[i] = virial[i] - (vir3v + vir3t) * rhoinv*e_scale; + } + + if(four_body_energies) // Virial correction for four body enegries + for(i = 0; i<3; i++) { + //virial[i] = virial[i] - pot_input_vol*e_quad*pe; + virial[i] = virial[i] - vir4 * rhoinv*e_scale; + } + + } + + *e_s = e_single; + *e_p = e_pair; + *e_t = e_triplet; + *e_q = e_quad; +} + +void PairMGPT::compute(int eflag, int vflag) +{ + if(eflag || vflag) ev_setup(eflag, vflag); + else evflag = vflag_fdotr = eflag_global = vflag_global = eflag_atom = vflag_atom = 0; + + int newton_pair = force->newton_pair; + double e_s,e_p,e_t,e_q; + + //printf("newton_pair = %d, newton = %d, tag_enable = %d\n",force->newton_pair,force->newton,atom->tag_enable); + + if(newton_pair == 0) { + printf("This is a problem. MGPT requires newton_pair flag to be on. Exiting...\n"); + exit(1); + } + + if(atom->tag_enable == 0) { + printf("This is a problem. MGPT requires tag_enable flag to be on. Exiting...\n"); + exit(1); + } + + compute_x(listfull->numneigh,listfull->firstneigh,&e_s,&e_p,&e_t,&e_q,evflag,newton_pair); + + if(0) { // Stupid force calculation / verification + int ii,nmax=-1; + for(ii = 0; iiinum + listfull->gnum; ii++) { + int i = listfull->ilist[ii]; + if(i > nmax) nmax = i; + } + nmax++; + double *ffwork = new double[3*nmax]; + double *ffloc = new double[3*listfull->inum]; + double *ffloc2 = new double[3*listfull->inum]; + double **ffptr = new double *[nmax]; + for(ii = 0; iiinum + listfull->gnum; ii++) + ffptr[ii] = &ffwork[3*ii]; + + printf("Computing boundary forces\n"); + for(ii = 0; iiinum; ii++) { + ffloc2[3*ii] = 0.0; + ffloc2[3*ii+1] = 0.0; + ffloc2[3*ii+2] = 0.0; + int i = listfull->ilist[ii]; + for(int jj = 0; jjinum+listfull->gnum; jj++) { + int j = listfull->ilist[jj]; + if(atom->tag[i] == atom->tag[j]) + for(int p = 0; p<3; p++) + ffloc2[3*ii+p] += atom->f[j][p]; + } + } + + printf("Starting main displacement force calculation\n"); + for(ii = 0; iiinum; ii++) { + int i = listfull->ilist[ii]; + + double **atom_f_save = atom->f; + atom->f = ffptr; + + for(int p = 0; p<3; p++) { + double xsave = atom->x[i][p]; + const double delta = 1e-3; + + atom->x[i][p] = xsave + delta; + for(int jj = 0; jj<3*nmax; jj++) ffwork[jj] = 0.0; + compute_x(listfull->numneigh, + listfull->firstneigh, + &e_s,&e_p,&e_t,&e_q,evflag,newton_pair); + double e1 = e_s + e_p + e_t + e_q; + + atom->x[i][p] = xsave - delta; + for(int jj = 0; jj<3*nmax; jj++) ffwork[jj] = 0.0; + compute_x(listfull->numneigh, + listfull->firstneigh, + &e_s,&e_p,&e_t,&e_q,evflag,newton_pair); + double e2 = e_s + e_p + e_t + e_q; + + ffloc[3*ii+p] = -(e1-e2)/(2*delta); + + atom->x[i][p] = xsave; + } + + atom->f = atom_f_save; + printf("Force on i=%4d:\n",i); + printf(" Position %20.10e %20.10e %20.10e\n", + atom->x[i][0],atom->x[i][1],atom->x[i][2]); + printf(" Exact %20.10e %20.10e %20.10e\n", + atom->f[i][0],atom->f[i][1],atom->f[i][2]); + printf(" Numerical %20.10e %20.10e %20.10e\n", + ffloc[3*ii+0],ffloc[3*ii+1],ffloc[3*ii+2]); + printf(" Boundary %20.10e %20.10e %20.10e\n", + ffloc2[3*ii+0],ffloc2[3*ii+1],ffloc2[3*ii+2]); + } + + + delete[] ffloc2; + delete[] ffloc; + delete[] ffptr; + delete[] ffwork; + } + + + if(0) { + printf("\nForces MGPT:\n"); + const int iimax = (listfull->inum < 10) ? listfull->inum : 10; + for(int ii = 0; iiilist[ii]; + printf("%4d = %20.10e %20.10e %20.10e\n", + i,atom->f[i][0],atom->f[i][1],atom->f[i][2]); + } + printf("\n\n"); + } + + if(vflag_fdotr) { + //printf("##### Using virial_compute!!!\n"); + virial_fdotr_compute(); + } +} + +void PairMGPT::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for(int i = 0; i <= n; i++) + for(int j = 0; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(cutghost,n+1,n+1,"pair:cutsq"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ +void PairMGPT::settings(int narg, char **arg) +{ + if(narg != 0) error->all(__FILE__,__LINE__,"Illegal pair_style command"); +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairMGPT::coeff(int narg, char **arg) +{ + int single_precision = 0; + + if(narg < 5) + error->all(__FILE__,__LINE__, + "Not enough arguments for mgpt (MGPT) pair coefficients."); + + if(!allocated) allocate(); + + // Make sure I,J args are * * + if(strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) + error->all(__FILE__,__LINE__,"Incorrect args for pair coefficients"); + + double vol; + if(sscanf(arg[4], "%lg", &vol) != 1 || vol <= 0.0) + error->all(__FILE__,__LINE__,"Invalid volume in mgpt (MGPT) pair coefficients."); + + volpres_flag = 1; + single_precision = 0; + + /* Parse arguments */ { + int volpres_tag = 0,precision_tag = 0,nbody_tag = 0; + + int iarg = 5; + while (iarg < narg) { + if(strcmp(arg[iarg],"volpress") == 0) { /* Volumetric pressure flag */ + if (iarg+2 > narg) + error->all(FLERR,"Incorrect args for pair coefficients"); + if(strcmp(arg[iarg+1],"yes") == 0) volpres_flag = 1; + else if(strcmp(arg[iarg+1],"no") == 0) volpres_flag = 0; + else { + char line[1024]; + sprintf(line,"(In %s:%d) Invalid value for volumetric pressure argument.\n" + "It should be \"volpress yes\" or \"volpress no\".\n" + "The value is \"%s\".\n",__FILE__,__LINE__,arg[iarg+1]); + error->all(__FILE__,__LINE__,line); + } + volpres_tag = 1; + iarg += 2; + if(comm->me == 0) printf("* volpress: volpres_flag = %d [%s %s]\n",volpres_flag,arg[iarg-2],arg[iarg-1]); + } else if(strcmp(arg[iarg],"nbody") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Incorrect args for pair coefficients"); + if(strspn(arg[iarg+1],"1234") == strlen(arg[iarg+1])) { + nbody_flag = 0; + for(int i = 0; i<4; i++) + if(strchr(arg[iarg+1],'1'+i) != NULL) { + nbody_flag = nbody_flag + (1<me == 0) printf("Explicitly adding %d-tuple forces.\n",i+1); + } + } else { + char line[1024]; + sprintf(line,"(In %s:%d) Invalid value for nbody flag.\n" + "It should be e.g. \"nbody=1234\" (for single, pair, triple, and quad forces/energiers)\n" + "For e.g. only pair and triple forces/energies, use \"nbody=23\".\n" + "The default is \"nbody=1234\".\n" + "The current value is \"%s\".\n",__FILE__,__LINE__,arg[iarg+1]); + error->all(__FILE__,__LINE__,line); + } + nbody_tag = 1; + iarg += 2; + } else if(strcmp(arg[iarg],"precision") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Incorrect args for pair coefficients"); + if(strcmp(arg[iarg+1],"single") == 0) single_precision = 1; + else if(strcmp(arg[iarg+1],"double") == 0) single_precision = 0; + else { + char line[1024]; + sprintf(line,"(In %s:%d) Invalid value for precision argument.\n" + "It should be \"precision single\" or \"precision double\".\n" + "The value is \"%s\".\n",__FILE__,__LINE__,arg[iarg+1]); + error->all(__FILE__,__LINE__,line); + } + precision_tag = 1; + iarg += 2; + if(comm->me == 0) printf("* precision: single_flag = %d [%s %s]\n",single_precision,arg[iarg-2],arg[iarg-1]); + } else { + char line[1024]; + sprintf(line,"(In %s:%d) Invalid argument. Allowed arguments are:\n" + " volpress {yes|no} , default = yes\n" + " precision {single|double} , default = double\n" + " nbody {[1234,]*} , default = whichever terms potential require\n" + "The invalid argument is \"%s\".\n",__FILE__,__LINE__,arg[iarg]); + error->all(__FILE__,__LINE__,line); + } + } + + if(comm->me == 0) + printf("Volumetric pressure is %s.\n",volpres_flag ? "on" : "off"); + + if(comm->me == 0) { + FILE *parmin_fp = force->open_potential(arg[2]); + FILE *potin_fp = force->open_potential(arg[3]); + if (parmin_fp == NULL || potin_fp == NULL) { + char str[128]; + sprintf(str,"Cannot open MGPT potential files %s %s",arg[2],arg[3]); + error->one(FLERR,str); + } + fclose(parmin_fp); + fclose(potin_fp); + + splinepot.readpot(arg[2],arg[3],vol); + printf("evol0 = %.10e\n",splinepot.evol0); + + /* Set up default and requested nbody forces to include */ { + int nbody_default = (1<<0) + (1<<1) + (1<<2) + (1<<3); + + if(splinepot.vd == 0.0 && splinepot.dvd == 0.0) + nbody_default -= (1<<2); // No 3-body contributions + if(splinepot.ve == 0.0 && splinepot.dve == 0.0) + nbody_default -= (1<<3); // No 4-body contributions + + if(nbody_tag == 0) nbody_flag = nbody_default; + + if(nbody_flag != nbody_default) { + printf("Warning: nbody=%d (suggested=%d) set to disregard multibody-forces in potential.\n", + nbody_flag,nbody_default); + } + } + } + } + + MPI_Bcast(&nbody_flag,sizeof(nbody_flag),MPI_BYTE,0,world); + + /* + Broadcast structure to all processes. In receiving + processes, pointes will be screwed up. We allocate + memory, and then broadcast contents of arrays. + */ + MPI_Bcast(&splinepot,sizeof(splinepot),MPI_BYTE,0,world); + if(comm->me != 0) { + splinepot.vpair_spline = new double[splinepot.nr-1][4]; + splinepot.dvpair_spline = new double[splinepot.nr-1][4]; + } + MPI_Bcast(splinepot.vpair_spline,4*(splinepot.nr-1),MPI_DOUBLE,0,world); + MPI_Bcast(splinepot.dvpair_spline,4*(splinepot.nr-1),MPI_DOUBLE,0,world); + anorm3 = splinepot.anorm3; + anorm4 = splinepot.anorm4; + lmax = splinepot.lmax; + lang = splinepot.lang; + //ipot = splinepot.ipot; + for(int i = 0; i<(int) (sizeof(ddl)/sizeof(double)); i++) + ddl[i] = splinepot.ddl[i]; + for(int i = 0; i rmax) cutoff = rcrit; + + // Set LAMMPS pair interaction flags. + for(int i = 1; i <= atom->ntypes; i++) { + for(int j = 1; j <= atom->ntypes; j++) { + setflag[i][j] = 1; + cutsq[i][j] = cutoff; + cutghost[i][j] = cutoff; + } + } + + // Set atomic mass. + for(int i = 1; i <= atom->ntypes; i++) + atom->set_mass(i, splinepot.mass); + + // Initialize linear algebra routines. + linalg = mgpt_linalg(lmax,single_precision); + if(comm->me == 0) + printf("%s",linalg.msg); +} + + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ +void PairMGPT::init_style() +{ + if(force->newton_pair == 0) + error->all(__FILE__,__LINE__,"Pair style mgpt requires newton pair on."); + + // Need full neighbor list. + int irequest_full = neighbor->request(this); + neighbor->requests[irequest_full]->id = 1; + neighbor->requests[irequest_full]->half = 0; + neighbor->requests[irequest_full]->full = 1; + neighbor->requests[irequest_full]->ghost = 1; + + // Also need half neighbor list. + int irequest_half = neighbor->request(this); + neighbor->requests[irequest_half]->id = 2; + neighbor->requests[irequest_half]->half = 0; + neighbor->requests[irequest_half]->half_from_full = 1; + neighbor->requests[irequest_half]->otherlist = irequest_full; + +} + +/* ---------------------------------------------------------------------- + neighbor callback to inform pair style of neighbor list to use + half or full +------------------------------------------------------------------------- */ +void PairMGPT::init_list(int id, NeighList *ptr) +{ + if(id == 1) listfull = ptr; + else if(id == 2) listhalf = ptr; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ +double PairMGPT::init_one(int i, int j) +{ + return cutoff; +} + +/************************************************************************ + **** REIMPLEMENTATION OF FL AND HAMLTN WITH ANALYTICAL DERIVATIVES **** + ************************************************************************/ +/* + Reimplementation of bond length potential, including + derivatives with respect to x,y, and z. +*/ +void PairMGPT::fl_deriv_new(double r,double ri,double xhat,double yhat,double zhat, + double &fl_0,double &fl_x,double &fl_y,double &fl_z, + double &fl_rp,double &fl_p1,double &fl_r0,double &fl_al) { + const double rp = splinepot.rp,p1 = splinepot.p1,r0 = splinepot.r00,al = splinepot.al; + const int mode = splinepot.mode; + const double pn = splinepot.pn; + + double t,tx,ty,tz,t_rp_ti,t_p1_ti; + double s; + + /* + // Original code + double term; + double pn=1.0; + if (mode <= 4) + term = pow(rp/r, p1); + else + term = exp(-p1*(pow(r/rp, pn) - 1.0)/pn); + */ + + double rpi = 1.0/rp; + if(mode <= 4) { + t = pow(rp*ri,p1); + s = -p1 * t * ri; + t_rp_ti = p1*rpi; + t_p1_ti = log(rp*ri); + } else { + if(pn == 1.0) { + double p1_rpi = -p1*rpi; + t = exp(p1 + r*p1_rpi); + s = p1_rpi * t; + t_rp_ti = -r*p1_rpi*rpi; + t_p1_ti = 1.0 - r*rpi; + } else { + double pni = 1.0/pn; + double rprpn = pow(r*rpi,pn); + t = exp(-p1*pni*(rprpn - 1.0)); + s = -p1*rprpn*ri * t; + t_rp_ti = p1*rprpn*rpi; + t_p1_ti = pni - pni*rprpn;// -pni*(rprpn - 1.0); + } + } + tx = s * xhat; + ty = s * yhat; + tz = s * zhat; + + fl_rp = t_rp_ti; + fl_p1 = t_p1_ti; + + if (r <= r0) { + fl_0 = t; + fl_x = tx; + fl_y = ty; + fl_z = tz; + + fl_r0 = 0.0; + fl_al = 0.0; + } else { + double q,qx,qy,qz,exp_q,q_r0,q_al; + double r0i,u; + + r0i = 1.0/r0; + u = r*r0i - 1.0; + q = al*u*u; + s = 2*al*u*r0i; + qx = s * xhat; + qy = s * yhat; + qz = s * zhat; + q_r0 = -2.0*al*u*r*r0i*r0i; + q_al = u*u; + + exp_q = exp(-q); + if(mode <= 2) { + fl_0 = exp_q * t; + fl_x = exp_q*(tx - t*qx); + fl_y = exp_q*(ty - t*qy); + fl_z = exp_q*(tz - t*qz); + + fl_r0 = -q_r0; + fl_al = -q_al; + } else { + fl_0 = exp_q * (1.0 + q) * t; + fl_x = exp_q * (tx + q*(tx - t*qx)); + fl_y = exp_q * (ty + q*(ty - t*qy)); + fl_z = exp_q * (tz + q*(tz - t*qz)); + + fl_r0 = -q_r0 * q/(1.0 + q); + fl_al = -q_al * q/(1.0 + q); + } + } +} + + +/* + Macros to build elements of the bond matrix, and also + its derivatives with repsect to x,y, and z. +*/ +#define MAKE_ELEMENT_5(i,j) \ + do { \ + const double dl0 = del0.m[i][j]; \ + const double dl4 = gsl_##i * gsl_##j; \ + const double dl4x = gsl_##i##x * gsl_##j + gsl_##i * gsl_##j##x; \ + const double dl4y = gsl_##i##y * gsl_##j + gsl_##i * gsl_##j##y; \ + const double dl4z = gsl_##i##z * gsl_##j + gsl_##i * gsl_##j##z; \ + \ + const double tmp = w4*dl4 + w2*dl2 + w0*dl0; \ + const double tmpx = w4*dl4x + w2*dl2x; \ + const double tmpy = w4*dl4y + w2*dl2y; \ + const double tmpz = w4*dl4z + w2*dl2z; \ + const double tmpsum = tmpx*x + tmpy*y + tmpz*z; \ + M [j][i] = M[i][j] = fl *tmp; \ + Mx[j][i] = Mx[i][j] = fl_x*tmp + fl_ri*(tmpx - x*tmpsum); \ + My[j][i] = My[i][j] = fl_y*tmp + fl_ri*(tmpy - y*tmpsum); \ + Mz[j][i] = Mz[i][j] = fl_z*tmp + fl_ri*(tmpz - z*tmpsum); \ + } while(0) + +#define MAKE_ELEMENT_7(i,j) \ + do { \ + const double dl0 = del0.m[i][j]; \ + const double dl6 = gsl_##i * gsl_##j; \ + const double dl6x = gsl_##i##x * gsl_##j + gsl_##i * gsl_##j##x; \ + const double dl6y = gsl_##i##y * gsl_##j + gsl_##i * gsl_##j##y; \ + const double dl6z = gsl_##i##z * gsl_##j + gsl_##i * gsl_##j##z; \ + \ + const double tmp = w6*dl6 + w4*dl4 + w2*dl2 + w0*dl0; \ + const double tmpx = w6*dl6x + w4*dl4x + w2*dl2x; \ + const double tmpy = w6*dl6y + w4*dl4y + w2*dl2y; \ + const double tmpz = w6*dl6z + w4*dl4z + w2*dl2z; \ + const double tmpsum = tmpx*x + tmpy*y + tmpz*z; \ + M [j][i] = M[i][j] = fl *tmp; \ + Mx[j][i] = Mx[i][j] = fl_x*tmp + fl_ri*(tmpx - x*tmpsum); \ + My[j][i] = My[i][j] = fl_y*tmp + fl_ri*(tmpy - y*tmpsum); \ + Mz[j][i] = Mz[i][j] = fl_z*tmp + fl_ri*(tmpz - z*tmpsum); \ + } while(0) +/* End of bond matrix macros */ + + +/* + Construction of bond matrix, and its derivatives + with respect to the coordinates +*/ +void PairMGPT::hamltn_5_raw(const double xin,const double yin,const double zin, + double M [8][8],double Mx[8][8], + double My[8][8],double Mz[8][8], + double *fl_deriv_sum_p) { + + const double r = sqrt(xin*xin + yin*yin + zin*zin),ri = 1.0/r; + const double x = xin*ri,y = yin*ri,z = zin*ri; + + // d-d + // call delndd(x,y,z) + const double x2 = x*x,y2 = y*y,z2 = z*z; + const double xy = x*y,xz = x*z,yz = y*z; + + const double sr3 = sqrt(3.0),sr3i = 1.0/sr3; + const double frac_1_3 = 1.0/3.0,frac_2_3 = 2.0/3.0,frac_4_3 = 4.0/3.0; + + const double ddl_1 = ddl[1],ddl_2 = ddl[2],ddl_3 = ddl[3]; + const double w4 = ddl_1 - frac_4_3*ddl_2 + frac_1_3*ddl_3; + const double w2 = ddl_2 - ddl_3; + const double w0 = ddl_2; + + + //del4 + double gsl_1 ,gsl_2 ,gsl_3 ,gsl_4 ,gsl_5; + double gsl_1x,gsl_2x,gsl_3x,gsl_4x,gsl_5x; + double gsl_1y,gsl_2y,gsl_3y,gsl_4y,gsl_5y; + double gsl_1z,gsl_2z,gsl_3z,gsl_4z,gsl_5z; + + double dl2,dl2x,dl2y,dl2z; + + double fl,fl_x,fl_y,fl_z,fl_ri; + double fl_rp,fl_p1,fl_r0,fl_al; + + gsl_1 = 0.5*(3.0*z2 - 1.0); + gsl_1x = 0.0; + gsl_1y = 0.0; + gsl_1z = 3.0*z; + + gsl_2 = sr3*xz; + gsl_2x = sr3*z; + gsl_2y = 0.0; + gsl_2z = sr3*x; + + gsl_3 = sr3*yz; + gsl_3x = 0.0; + gsl_3y = sr3*z; + gsl_3z = sr3*y; + + gsl_4 = sr3*(x2 - y2)*0.5; + gsl_4x = sr3*x; + gsl_4y = -sr3*y; + gsl_4z = 0.0; + + gsl_5 = sr3*xy; + gsl_5x = sr3*y; + gsl_5y = sr3*x; + gsl_5z = 0.0; + + // Compute bond length potential + fl_deriv_new(r,ri,x,y,z,fl,fl_x,fl_y,fl_z , fl_rp,fl_p1,fl_r0,fl_al); + fl_ri = fl*ri; + + *fl_deriv_sum_p = + fl_rp*splinepot.drp + fl_p1*splinepot.dp1 + + fl_r0*splinepot.dr00 + fl_al*splinepot.dal; + + // del2 + + //del2.m[1][1] = z2 - 2.0/3.0; + dl2 = z2 - frac_2_3; + dl2x = 0.0; + dl2y = 0.0; + dl2z = 2*z; + MAKE_ELEMENT_5(1,1); + + //del2.m[1][2] = xz/sr3; + dl2 = xz*sr3i; + dl2x = z*sr3i; + dl2y = 0.0; + dl2z = x*sr3i; + MAKE_ELEMENT_5(1,2); + + //del2.m[1][3] = yz/sr3; + dl2 = yz*sr3i; + dl2x = 0.0; + dl2y = z*sr3i; + dl2z = y*sr3i; + MAKE_ELEMENT_5(1,3); + + //del2.m[1][4] = -(x2 - y2)*sr3i; + dl2 = -(x2 - y2)*sr3i; + dl2x = -2.0*sr3i*x; + dl2y = 2.0*sr3i*y; + dl2z = 0.0; + MAKE_ELEMENT_5(1,4); + + //del2.m[1][5] = -2.0*xy*sr3i; + dl2 = -2.0*xy*sr3i; + dl2x = -2.0*y*sr3i; + dl2y = -2.0*x*sr3i; + dl2z = 0.0; + MAKE_ELEMENT_5(1,5); + + //del2.m[2][2] = -y2; + dl2 = -y2; + dl2x = 0.0; + dl2y = -2.0*y; + dl2z = 0.0; + MAKE_ELEMENT_5(2,2); + + //del2.m[2][3] = xy; + dl2 = xy; + dl2x = y; + dl2y = x; + dl2z = 0.0; + MAKE_ELEMENT_5(2,3); + + //del2.m[2][4] = xz; + dl2 = xz; + dl2x = z; + dl2y = 0.0; + dl2z = x; + MAKE_ELEMENT_5(2,4); + + //del2.m[2][5] = yz; + dl2 = yz; + dl2x = 0.0; + dl2y = z; + dl2z = y; + MAKE_ELEMENT_5(2,5); + + //del2.m[3][3] = -x2; + dl2 = -x2; + dl2x = -2.0*x; + dl2y = 0.0; + dl2z = 0.0; + MAKE_ELEMENT_5(3,3); + + //del2.m[3][4] = -yz; + dl2 = -yz; + dl2x = 0.0; + dl2y = -z; + dl2z = -y; + MAKE_ELEMENT_5(3,4); + + //del2.m[3][5] = xz; + dl2 = xz; + dl2x = z; + dl2y = 0.0; + dl2z = x; + MAKE_ELEMENT_5(3,5); + + //del2.m[4][4] = -z2; + dl2 = -z2; + dl2x = 0.0; + dl2y = 0.0; + dl2z = -2.0*z; + MAKE_ELEMENT_5(4,4); + + //del2.m[4][5] = 0.0; + dl2 = 0.0; + dl2x = 0.0; + dl2y = 0.0; + dl2z = 0.0; + MAKE_ELEMENT_5(4,5); + + //del2.m[5][5] = -z2; + dl2 = -z2; + dl2x = 0.0; + dl2y = 0.0; + dl2z = -2.0*z; + MAKE_ELEMENT_5(5,5); +} + + +void PairMGPT::hamltn_7_raw(const double xin,const double yin,const double zin, + double M [8][8],double Mx[8][8], + double My[8][8],double Mz[8][8], + double *fl_deriv_sum_p) { + + const double r = sqrt(xin*xin + yin*yin + zin*zin),ri = 1.0/r; + const double x = xin*ri,y = yin*ri,z = zin*ri; + + // d-d + // call delndd(x,y,z) + const double x2 = x*x,y2 = y*y,z2 = z*z; + const double xy = x*y,xz = x*z,yz = y*z; + const double x4 = x2*x2,y4 = y2*y2; + + //const double sr3 = sqrt(3.0);//,sr3i = 1.0/sr3; + //const double frac_1_3 = 1.0/3.0,frac_2_3 = 2.0/3.0,frac_4_3 = 4.0/3.0; + + const double sr01 = sqrt(0.1); + const double sr015 = sqrt(0.15); + const double sr024 = sqrt(0.24); + const double sr0375 = sqrt(0.375); + const double sr06 = sqrt(0.6); + const double sr0625 = sqrt(0.625); + const double sr09 = sqrt(0.9); + const double sr15 = sqrt(1.5); + const double sr24 = sqrt(2.4); + const double sr36 = sqrt(3.6); + const double sr375 = sqrt(3.75); + const double sr96 = sqrt(9.6); + const double sr150 = sqrt(15.0); + + + + const double ddl_1 = ddl[1],ddl_2 = ddl[2],ddl_3 = ddl[3],ddl_4 = ddl[4]; + const double w6 = ddl_1 - 1.5*ddl_2 + 0.6*ddl_3 - 0.1*ddl_4; + const double w4 = 0.625*ddl_2 - ddl_3 + 0.375*ddl_4; + const double w2 = 0.625*(ddl_2 - ddl_4); + const double w0 = 0.625*ddl_2 + 0.375*ddl_4; + + + //del6 + double gsl_1 ,gsl_2 ,gsl_3 ,gsl_4 ,gsl_5 ,gsl_6, gsl_7; + double gsl_1x,gsl_2x,gsl_3x,gsl_4x,gsl_5x,gsl_6x,gsl_7x; + double gsl_1y,gsl_2y,gsl_3y,gsl_4y,gsl_5y,gsl_6y,gsl_7y; + double gsl_1z,gsl_2z,gsl_3z,gsl_4z,gsl_5z,gsl_6z,gsl_7z; + + double dl2,dl2x,dl2y,dl2z; + double dl4,dl4x,dl4y,dl4z; + double t1; + + double fl,fl_x,fl_y,fl_z,fl_ri; + double fl_rp,fl_p1,fl_r0,fl_al; + + //gslf[1] = 0.5*(5.0*n2 - 3.0)*n; + gsl_1 = 0.5*(5.0*z2 - 3.0)*z; + gsl_1x = 0.0; + gsl_1y = 0.0; + gsl_1z = 7.5*z2 - 1.5; + + //gslf[2] = sr0375*(5.0*n2 - 1.0)*l; + gsl_2 = sr0375*(5.0*z2 - 1.0)*x; + gsl_2x = sr0375*(5.0*z2 - 1.0); + gsl_2y = 0.0; + gsl_2z = sr0375*10.0*xz; + + //gslf[3] = sr0375*(5.0*n2 - 1.0)*m; + gsl_3 = sr0375*(5.0*z2 - 1.0)*y; + gsl_3x = 0.0; + gsl_3y = sr0375*(5.0*z2 - 1.0); + gsl_3z = sr0375*10.0*yz; + + //gslf[4] = sr375*(l2 - m2)*n; + gsl_4 = sr375*(x2 - y2)*z; + gsl_4x = 2.0*sr375*xz; + gsl_4y = -2.0*sr375*yz; + gsl_4z = sr375*(x2 - y2); + + //gslf[5] = sr150*lm*n; + gsl_5 = sr150*xy*z; + gsl_5x = sr150*yz; + gsl_5y = sr150*xz; + gsl_5z = sr150*xy; + + //gslf[6] = sr0625*(l2 - 3.0*m2)*l; + gsl_6 = sr0625*(x2 - 3.0*y2)*x; + gsl_6x = 3.0*sr0625*(x2 - y2); + gsl_6y = -6.0*sr0625*xy; + gsl_6z = 0.0; + + //gslf[7] = sr0625*(3.0*l2 - m2)*m; + gsl_7 = sr0625*(3.0*x2 - y2)*y; + gsl_7x = 6.0*sr0625*xy; + gsl_7y = 3.0*sr0625*(x2 - y2); + gsl_7z = 0.0; + + + // Compute bond length potential + fl_deriv_new(r,ri,x,y,z,fl,fl_x,fl_y,fl_z , fl_rp,fl_p1,fl_r0,fl_al); + fl_ri = fl*ri; + + *fl_deriv_sum_p = + fl_rp*splinepot.drp + fl_p1*splinepot.dp1 + + fl_r0*splinepot.dr00 + fl_al*splinepot.dal; + + // del2f + + //del2f.m[1][1] = 0.4*(3.0*n2 - 1.0); + dl2 = 0.4*(3.0*z2 - 1.0); + dl2x = 0.0; + dl2y = 0.0; + dl2z = 2.4*z; + + //del4f.m[1][1] = 0.60*(5.0*n2 - 4.0)*n2; + dl4 = 0.60*(5.0*z2 - 4.0)*z2; + dl4x = 0.0; + dl4y = 0.0; + dl4z = 0.60*(20.0*z2 - 8.0)*z; + + MAKE_ELEMENT_7(1,1); + + + //del2f.m[1][2] = sr024*ln; + dl2 = sr024*xz; + dl2x = sr024*z; + dl2y = 0.0; + dl2z = sr024*x; + + //del4f.m[1][2] = sr024*(5.0*n2 - 2.0)*ln; + dl4 = sr024*(5.0*z2 - 2.0)*xz; + dl4x = sr024*(5.0*z2 - 2.0)*z; + dl4y = 0.0; + dl4z = sr024*(15.0*z2 - 2.0)*x; + + MAKE_ELEMENT_7(1,2); + + + //del2f.m[1][3] = sr024*mn; + dl2 = sr024*yz; + dl2x = 0.0; + dl2y = sr024*z; + dl2z = sr024*y; + + //del4f.m[1][3] = sr024*(5.0*n2 - 2.0)*mn; + dl4 = sr024*(5.0*z2 - 2.0)*yz; + dl4x = 0.0; + dl4y = sr024*(5.0*z2 - 2.0)*z; + dl4z = sr024*(15.0*z2 - 2.0)*y; + + MAKE_ELEMENT_7(1,3); + + + //del2f.m[1][4] = -sr06*(l2 - m2); + dl2 = -sr06*(x2 - y2); + dl2x = -2.0*sr06*x; + dl2y = 2.0*sr06*y; + dl2z = 0.0; + + //del4f.m[1][4] = -sr06*(l2 - m2)*n2; + dl4 = -sr06*(x2 - y2)*z2; + dl4x = -2.0*sr06*x*z2; + dl4y = 2.0*sr06*y*z2; + dl4z = -2.0*sr06*(x2 - y2)*z; + + MAKE_ELEMENT_7(1,4); + + + //del2f.m[1][5] = -sr24*lm; + dl2 = -sr24*xy; + dl2x = -sr24*y; + dl2y = -sr24*x; + dl2z = 0.0; + + //del4f.m[1][5] = -sr24*lm*n2; + dl4 = -sr24*xy*z2; + dl4x = -sr24*y*z2; + dl4y = -sr24*x*z2; + dl4z = -2.0*sr24*xy*z; + + MAKE_ELEMENT_7(1,5); + + + //del2f.m[1][6] = 0.0; + dl2 = 0.0; + dl2x = 0.0; + dl2y = 0.0; + dl2z = 0.0; + + //del4f.m[1][6] = sr36*(3.0*m2 - l2)*ln; + dl4 = sr36*(3.0*y2 - x2)*xz; + dl4x = 3.0*sr36*(y2 - x2)*z; + dl4y = 6.0*sr36*y*xz; + dl4z = sr36*(3.0*y2 - x2)*x; + + MAKE_ELEMENT_7(1,6); + + + //del2f.m[1][7] = 0.0; + dl2 = 0.0; + dl2x = 0.0; + dl2y = 0.0; + dl2z = 0.0; + + //del4f.m[1][7] = -sr36*(3.0*l2 - m2)*mn; + dl4 = -sr36*(3.0*x2 - y2)*yz; + dl4x = -6.0*sr36*x*yz; + dl4y = -3.0*sr36*(x2 - y2)*z; + dl4z = -sr36*(3.0*x2 - y2)*y; + + MAKE_ELEMENT_7(1,7); + + + //del2f.m[2][2] = 0.3*(1.0 - 4.0*m2 + n2); + dl2 = 0.3 - 1.2*y2 + 0.3*z2; + dl2x = 0.0; + dl2y = -2.4*y; + dl2z = 0.6*z; + + //del4f.m[2][2] = -0.4*l*l - 2.5*(m2 - 0.6*l2)*n2; + dl4 = -0.4*x2 - 2.5*(y2 - 0.6*x2)*z2; + dl4x = -0.8*x + 3.0*x*z2; + dl4y = -5.0*y*z2; + dl4z = -5.0*(y2 - 0.6*x2)*z; + + MAKE_ELEMENT_7(2,2); + + + //del2f.m[2][3] = 1.2*lm; + dl2 = 1.2*xy; + dl2x = 1.2*y; + dl2y = 1.2*x; + dl2z = 0.0; + + //del4f.m[2][3] = 0.4*(10.0*n2 - 1.0)*lm; + dl4 = (4.0*z2 - 0.4)*xy; + dl4x = (4.0*z2 - 0.4)*y; + dl4y = (4.0*z2 - 0.4)*x; + dl4z = 8.0*z*xy; + + MAKE_ELEMENT_7(2,3); + + + //del2f.m[2][4] = sr09*ln; + dl2 = sr09*xz; + dl2x = sr09*z; + dl2y = 0.0; + dl2z = sr09*x; + + //del4f.m[2][4] = sr01*(6.0*n2 - 8.0*m2 - 1.0)*ln; + dl4 = sr01*(6.0*z2 - 8.0*y2 - 1.0)*xz; + dl4x = sr01*(6.0*z2 - 8.0*y2 - 1.0)*z; + dl4y = -16.0*sr01*y*xz; + dl4z = sr01*(18.0*z2 - 8.0*y2 - 1.0)*x; + + MAKE_ELEMENT_7(2,4); + + + //del2f.m[2][5] = sr09*mn; + dl2 = sr09*yz; + dl2x = 0.0; + dl2y = sr09*z; + dl2z = sr09*y; + + //del4f.m[2][5] = sr01*(2.0*n2 - 8.0*m2 + 3.0)*mn; + dl4 = sr01*(2.0*z2 - 8.0*y2 + 3.0)*yz; + dl4x = 0.0; + dl4y = sr01*(2.0*z2 - 24.0*y2 + 3.0)*z; + dl4z = sr01*(6.0*z2 - 8.0*y2 + 3.0)*y; + + MAKE_ELEMENT_7(2,5); + + + //del2f.m[2][6] = -sr015*(l2 - m2); + dl2 = -sr015*(x2 - y2); + dl2x = -2.0*sr015*x; + dl2y = 2.0*sr015*y; + dl2z = 0.0; + + //del4f.m[2][6] = sr375*(l2 - m2 - 1.4*l4 + 1.2*l2*m2 + m4); + dl4 = sr375*(x2 - y2 - 1.4*x4 + 1.2*x2*y2 + y4); + dl4x = sr375*(2.0 - 5.6*x2 + 2.4*y2)*x; + dl4y = sr375*(-2.0 + 2.4*x2 + 4.0*y2)*y; + dl4z = 0.0; + + MAKE_ELEMENT_7(2,6); + + + //del2f.m[2][7] = -sr06*lm; + dl2 = -sr06*xy; + dl2x = -sr06*y; + dl2y = -sr06*x; + dl2z = 0.0; + + //del4f.m[2][7] = sr96*(n2 - l2 + 0.25)*lm; + dl4 = sr96*(z2 - x2 + 0.25)*xy; + dl4x = sr96*(z2 - 3.0*x2 + 0.25)*y; + dl4y = sr96*(z2 - x2 + 0.25)*x; + dl4z = 2.0*sr96*z*xy; + + MAKE_ELEMENT_7(2,7); + + + //del2f.m[3][3] = 0.30*(1.0 - 4.0*l2 + n2); + dl2 = 0.3 - 1.2*x2 + 0.3*z2; + dl2x = -2.4*x; + dl2y = 0.0; + dl2z = 0.6*z; + + //del4f.m[3][3] = -0.4*m2 - 2.5*(l2 - 0.6*m2)*n2; + dl4 = -0.4*y2 - 2.5*(x2 - 0.6*y2)*z2; + dl4x = -5.0*x*z2; + dl4y = y*(3.0*z2 - 0.8); + dl4z = -5.0*(x2 - 0.6*y2)*z; + + MAKE_ELEMENT_7(3,3); + + + //del2f.m[3][4] = -sr09*mn; + dl2 = -sr09*yz; + dl2x = 0.0; + dl2y = -sr09*z; + dl2z = -sr09*y; + + //del4f.m[3][4] = -sr01*(6.0*n2 - 8.0*l2 - 1.0)*mn; + dl4 = -sr01*(6.0*z2 - 8.0*x2 - 1.0)*yz; + dl4x = 16.0*sr01*x*yz; + dl4y = -sr01*(6.0*z2 - 8.0*x2 - 1.0)*z; + dl4z = -sr01*(18.0*z2 - 8.0*x2 - 1.0)*y; + + MAKE_ELEMENT_7(3,4); + + + //del2f.m[3][5] = sr09*ln; + dl2 = sr09*xz; + dl2x = sr09*z; + dl2y = 0.0; + dl2z = sr09*x; + + //del4f.m[3][5] = sr01*(2.0*n2 - 8.0*l2 + 3.0)*ln; + dl4 = sr01*(2.0*z2 - 8.0*x2 + 3.0)*xz; + dl4x = sr01*(2.0*z2 - 24.0*x2 + 3.0)*z; + dl4y = 0.0; + dl4z = sr01*(6.0*z2 - 8.0*x2 + 3.0)*x; + + MAKE_ELEMENT_7(3,5); + + + //del2f.m[3][6] = sr06*lm; + dl2 = sr06*xy; + dl2x = sr06*y; + dl2y = sr06*x; + dl2z = 0.0; + + //del4f.m[3][6] = sr96*(m2 - n2 - 0.25)*lm; + dl4 = sr96*(y2 - z2 - 0.25)*xy; + dl4x = sr96*(y2 - z2 - 0.25)*y; + dl4y = sr96*(3.0*y2 - z2 - 0.25)*x; + dl4z = -2.0*sr96*z*xy; + + MAKE_ELEMENT_7(3,6); + + + //del2f.m[3][7] = -sr015*(l2 - m2); + dl2 = -sr015*(x2 - y2); + dl2x = -2.0*sr015*x; + dl2y = 2.0*sr015*y; + dl2z = 0.0; + + //del4f.m[3][7] = sr375*(l2 - m2 + 1.4*m4 - 1.2*l2*m2 - l4); + dl4 = sr375*(x2 - y2 + 1.4*y4 - 1.2*x2*y2 - x4); + dl4x = sr375*(2.0 - 2.4*y2 - 4.0*x2)*x; + dl4y = sr375*(-2.0 + 5.6*y2 - 2.4*x2)*y; + dl4z = 0.0; + + MAKE_ELEMENT_7(3,7); + + + //del2f.m[4][4] = 0.0; + dl2 = 0.0; + dl2x = 0.0; + dl2y = 0.0; + dl2z = 0.0; + + //del4f.m[4][4] = (2.0 - 3.0*n2)*n2 - 4.0*l2*m2; + dl4 = (2.0 - 3.0*z2)*z2 - 4.0*x2*y2; + dl4x = -8.0*x*y2; + dl4y = -8.0*x2*y; + dl4z = (4.0 - 12.0*z2)*z; + + MAKE_ELEMENT_7(4,4); + + //del2f.m[4][5] = 0.0; + dl2 = 0.0; + dl2x = 0.0; + dl2y = 0.0; + dl2z = 0.0; + + //del4f.m[4][5] = 2.0*(l2 - m2)*lm; + dl4 = 2.0*(x2 - y2)*xy; + dl4x = 2.0*(3.0*x2 - y2)*y; + dl4y = 2.0*(x2 - 3.0*y2)*x; + dl4z = 0.0; + + MAKE_ELEMENT_7(4,5); + + + //del2f.m[4][6] = sr15*ln; + dl2 = sr15*xz; + dl2x = sr15*z; + dl2y = 0.0; + dl2z = sr15*x; + + //del4f.m[4][6] = -sr15*(2.0*n2 - 1.0)*ln; + dl4 = -sr15*(2.0*z2 - 1.0)*xz; + dl4x = -sr15*(2.0*z2 - 1.0)*z; + dl4y = 0.0; + dl4z = -sr15*(6.0*z2 - 1.0)*x; + + MAKE_ELEMENT_7(4,6); + + + //del2f.m[4][7] = sr15*mn; + dl2 = sr15*yz; + dl2x = 0.0; + dl2y = sr15*z; + dl2z = sr15*y; + + //del4f.m[4][7] = -sr15*(2.0*n2 - 1.0)*mn; + dl4 = -sr15*(2.0*z2 - 1.0)*yz; + dl4x = 0.0; + dl4y = -sr15*(2.0*z2 - 1.0)*z; + dl4z = -sr15*(6.0*z2 - 1.0)*y; + + MAKE_ELEMENT_7(4,7); + + + //del2f.m[5][5] = 0.0; + dl2 = 0.0; + dl2x = 0.0; + dl2y = 0.0; + dl2z = 0.0; + + //del4f.m[5][5] = -pow((2.0*n2 - 1.0),2) + 4.0*l2*m2; + t1 = 2.0*z2 - 1.0; + dl4 = -t1*t1 + 4.0*x2*y2; + dl4x = 8.0*x*y2; + dl4y = 8.0*x2*y; + dl4z = -8.0*t1*z; + + MAKE_ELEMENT_7(5,5); + + + //del2f.m[5][6] = -sr15*mn; + dl2 = -sr15*yz; + dl2x = 0.0; + dl2y = -sr15*z; + dl2z = -sr15*y; + + //del4f.m[5][6] = sr15*(2.0*n2 - 1.0)*mn; + dl4 = sr15*(2.0*z2 - 1.0)*yz; + dl4x = 0.0; + dl4y = sr15*(2.0*z2 - 1.0)*z; + dl4z = sr15*(6.0*z2 - 1.0)*y; + + MAKE_ELEMENT_7(5,6); + + //del2f.m[5][7] = sr15*ln; + dl2 = sr15*xz; + dl2x = sr15*z; + dl2y = 0.0; + dl2z = sr15*x; + + //del4f.m[5][7] = -sr15*(2.0*n2 - 1.0)*ln; + dl4 = -sr15*(2.0*z2 - 1.0)*xz; + dl4x = -sr15*(2.0*z2 - 1.0)*z; + dl4y = 0.0; + dl4z = -sr15*(6.0*z2 - 1.0)*x; + + MAKE_ELEMENT_7(5,7); + + + //del2f.m[6][6] = -(3.0*n2 - 1.0)/2.0; + dl2 = 0.5 - 1.5*z2; + dl2x = 0.0; + dl2y = 0.0; + dl2z = -3.0*z; + + //del4f.m[6][6] = 1.5*(n2 - 1.0)*n2; + dl4 = (1.5*z2 - 1.5)*z2; + dl4x = 0.0; + dl4y = 0.0; + dl4z = (6.0*z2 - 3.0)*z; + + MAKE_ELEMENT_7(6,6); + + + //del2f.m[6][7] = 0.0; + dl2 = 0.0; + dl2x = 0.0; + dl2y = 0.0; + dl2z = 0.0; + + //del4f.m[6][7] = 0.0; + dl4 = 0.0; + dl4x = 0.0; + dl4y = 0.0; + dl4z = 0.0; + + MAKE_ELEMENT_7(6,7); + + + //del2f.m[7][7] = -(3.0*n2 - 1.0)/2.0; + dl2 = 0.5 - 1.5*z2; + dl2x = 0.0; + dl2y = 0.0; + dl2z = -3.0*z; + + //del4f.m[7][7] = 1.5*(n2 - 1.0)*n2; + dl4 = (1.5*z2 - 1.5)*z2; + dl4x = 0.0; + dl4y = 0.0; + dl4z = (6.0*z2 - 3.0)*z; + + MAKE_ELEMENT_7(7,7); +} + +/************************************************************************/ + +/* ---------------------------------------------------------------------- + * Fast Model Generalized Pseudopotential Theory (MGPT) interatomic + * potential routine. + * + * Copyright (2015) Lawrence Livermore National Security, LLC. + * Produced at the Lawrence Livermore National Laboratory. + * Written by Tomas Oppelstrup (oppelstrup2@llnl.gov) and John Moriarty + * (moriarty2@llnl.gov) + * LLNL-CODE-674031 All rights reserved. + * + * This program is free software; you can redistribute it and/or modify it + * under the terms of the GNU General Public License (as published by the + * Free Software Foundation) version 2, dated June 1991. + * + * This program is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF MERCHANTABILITY + * or FITNESS FOR A PARTICULAR PURPOSE. See the terms and conditions of the + * GNU General Public License for more details. + * + * LLNL Preamble Notice + * A. This notice is required to be provided under our contract with the + * U.S. Department of Energy (DOE). This work was performed under the auspices + * of the DOE by Lawrence Livermore National Laboratory under Contract No. + * DE-AC52-07NA27344. + * + * B. Neither the United States Government nor Lawrence Livermore National + * Security, LLC nor any of their employees, makes any warranty, express or + * implied, or assumes any liability or responsibility for the accuracy, + * completeness, or usefulness of any information, apparatus, product, or + * process disclosed, or represents that its use would not infringe + * privately-owned rights. + * + * C. Also, reference herein to any specific commercial products, process, + * or services by trade name, trademark, manufacturer or otherwise does not + * necessarily constitute or imply its endorsement, recommendation, or + * favoring by the United States Government or Lawrence Livermore National + * Security, LLC. The views and opinions of authors expressed herein do not + * necessarily state or reflect those of the United States Government or + * Lawrence Livermore National Security, LLC, and shall not be used for + * advertising or product endorsement purposes. +------------------------------------------------------------------------- */ diff --git a/src/USER-MGPT/pair_mgpt.h b/src/USER-MGPT/pair_mgpt.h new file mode 100644 index 0000000000..5e5740f391 --- /dev/null +++ b/src/USER-MGPT/pair_mgpt.h @@ -0,0 +1,718 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Tomas Oppelstrup, LLNL (oppelstrup2@llnl.gov) + and John Moriarty, LLNL (moriarty2@llnl.gov) + + Fast MGPT algorithm developed by Tomas Oppelstrup (2015) based on the + matrix MGPT v4.4 FORTRAN routine of John Moriarty (2006) as converted + to C++ for LAMMPS application by Jamie Marian and Alexander Stukowski + (2011). See LLNL copyright notice at bottom of this file. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(mgpt,PairMGPT) + +#else + +#ifndef LMP_PAIR_MGPT_H +#define LMP_PAIR_MGPT_H + +#include +#include +#include +#include + +#include "pair.h" +#include "domain.h" + +#include "mgpt_readpot.h" +#include "mgpt_linalg.h" + + +namespace LAMMPS_NS { + + +class PairMGPT : public Pair { + mgpt_linalg linalg; +public: + + class Doublet { + public: + int i,j; + public: + Doublet(const Doublet &t) : i(t.i),j(t.j) {} + Doublet(int ii,int jj) : i(ii < jj ? ii:jj),j(ii < jj ? jj : ii) {} + + Doublet operator=(const Doublet &t) { + i = t.i; + j = t.j; + return *this; + } + int operator==(const Doublet &b) const { + return (i == b.i) && (j == b.j); + } + int hash() const { return i*333331 + j*331; } + }; + + template class Hash { + + class Link { + public: + T data; + Link *next; + K key; + int hits; + Link(const K &k,Link *n) : next(n),key(k),hits(1) {} + + static void *operator new(std::size_t sz) { + const size_t align = 32; + size_t x = (size_t) (void *) ::operator new(sz+align); + size_t y = (x + align) - ((x+align)&(align-1)); + assert(sizeof(void *) <= align); + assert((x & (sizeof(void *)-1)) == 0); + ((void **) y)[-1] = (void *) x; + return (void *) y; + } + static void operator delete(void *ptr) { + ::operator delete(((void **) ptr)[-1]); + } + }; + + int isprime(int x) { + if(x%2 == 0) + return 0; + else { + int k = 3; + while(k*k <= x) { + if(x%k == 0) return 0; + k = k+2; + } + return 1; + } + } + + int size,used; + Link **table; + + int maxlength,nstep,nsearch; + public: + + class Iterator { + Hash &H; + int idx; + Link *p; + public: + Iterator(Hash &HH) : H(HH),idx(-1),p(0) { next(); } + Iterator(Hash &HH,int iidx,Link *pp) : H(HH),idx(iidx),p(pp) {} + void next() { + if(idx >= H.Size()) return; + if(p != 0) p = p->next; + if(p == 0) { + do { + idx = idx+1; + if(idx >= H.Size()) return; + p = H.table[idx]; + } while(p == 0); + } + } + K *key() { return &p->key; } + T *data() { return &p->data; } + Link *link() { return p; } + + int operator==(const Iterator &a) { + return idx==a.idx && p==a.p; + } + int operator!=(const Iterator &a) { + return !(*this == a); + } + }; + + Hash(int sz) { + while(!isprime(sz)) sz = sz + 1; + size = sz; + used = 0; + + + table = new Link *[size]; + for(int i = 0; inext; + delete p; + p = q; + } + } + delete[] table; + } + + Iterator begin() { return Iterator(*this); } + Iterator end() { return Iterator(*this,size,0); } + + int Size() { return size; } + int Used() { return used; } + int NSearch() { return nsearch; } + int MaxLength() { return maxlength; } + int NStep() { return nstep; } + T * Insert(const K &key) { + int idx = key.hash() % size; + if(idx < 0) idx = idx + size; + if(idx >= size || idx < 0) { + printf("(1) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); + exit(1); + } + + used = used + 1; + if(1) { + table[idx] = new Link(key,table[idx]); + return &table[idx]->data; + } else { /* This is for threading... and incomplete */ + typedef Link *LinkPtr; + LinkPtr ptr = table[idx],last = 0,dataptr = new Link(key,0); + + while(ptr != 0) { + last = ptr; + ptr = ptr->next; + } + *((volatile LinkPtr *) &(last->next)) = dataptr; + return &(dataptr->data); + } + } + void Remove(const K &key) { + int idx = key.hash() % size; + Link *p,*last = 0; + int count = 1; + if(idx < 0) idx = idx + size; + if(idx >= size || idx < 0) { + printf("(2) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); + exit(1); + } + + p = table[idx]; + while(p != 0 && !(p->key == key)) { + last = p; + p = p->next; + count = count + 1; + } + + if(p != 0) { + used = used - 1; + if(last == 0) + table[idx] = p->next; + else + last->next = p->next; + delete p; + } + + if(count > maxlength) + maxlength = count; + nsearch = nsearch + 1; + nstep = nstep + count; + } + T * Lookup(const K &key) { + int idx = key.hash() % size; + Link *p; + int count = 1; + if(idx < 0) idx = idx + size; + if(idx >= size || idx < 0) { + printf("(3) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); + exit(1); + } + + + p = table[idx]; + while(p != 0 && !(p->key == key)) { + p = p->next; + count = count + 1; + } + + if(count > maxlength) + maxlength = count; + nsearch = nsearch + 1; + nstep = nstep + count; + + if(p != 0) p->hits++; + + return (p == 0) ? 0 : &p->data; + } + }; + + public: + PairMGPT(class LAMMPS *); + ~PairMGPT(); + void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + void init_list(int, class NeighList *); + double init_one(int, int); + + private: + + void read_files(const char* parminFile, const char* potinFile, double vol); + void allocate(); + + struct Matrix { + static int sz; + + double m[8][8]; + + int align_check() { + return ((((unsigned long long int) m) & 31) > 0); + } + void zero() { + for(int i = 0; i<8; i++) + for(int j = 0; j<8; j++) + m[i][j] = 0.0; + } + + void operator=(const Matrix &A) { + for(int i = 1; i<=sz; i++) + for(int j = 1; j<=sz; j++) + m[i][j] = A.m[i][j]; + } + void operator=(double x) { + for(int i = 1; i<=sz; i++) + for(int j = 1; j<=sz; j++) + m[i][j] = x; + } + Matrix operator+(const Matrix &B) const { + Matrix s; + for(int i = 1; i<=sz; i++) + for(int j = 1; j<=sz; j++) + s.m[i][j] = m[i][j] + B.m[i][j]; + return s; + } + Matrix operator-(const Matrix &B) const { + Matrix s; + for(int i = 1; i<=sz; i++) + for(int j = 1; j<=sz; j++) + s.m[i][j] = m[i][j] - B.m[i][j]; + return s; + } + Matrix operator-() const { + Matrix s; + for(int i = 1; i<=sz; i++) + for(int j = 1; j<=sz; j++) + s.m[i][j] = -m[i][j]; + return s; + } + Matrix operator*(double x) const { + Matrix P; + for(int i = 1; i<=sz; i++) + for(int j = 0; j<=sz; j++) + P.m[i][j] = m[i][j] * x; + return P; + } + Matrix operator/(double x) const { + return (*this) * (1.0/x); + } + Matrix transpose() const { + Matrix T; + for(int i = 1; i<=sz; i++) + for(int j = 1; j<=sz; j++) + T.m[j][i] = m[i][j]; + return T; + } + }; + Matrix transpose(const Matrix &A) { return A.transpose(); } + + /* Preprocessor stuff to set alignment requirements on bonda_data + and triplet_data structures. Without alignmnt, optimized algebra + routines can fail. + */ +#ifdef __GNUC__ + #define PREALIGN struct + #define POSTALIGN __attribute__((__aligned__(32))) +#elif defined(__bgq__) + #define PREALIGN __align(32) struct + #define POSTALIGN +#elif defined(__INTEL_COMPILER) + /* This will probably not be used, since the Intel compiler also defines __GNUC__ */ + #define PREALIGN struct __declspec(align(32)) + #define POSTALIGN +#else + /* Try GNU syntax anyway... */ + #define PREALIGN struct + #define POSTALIGN __attribute__((__aligned__(32))) + /* + #define PREALIGN struct + #define POSTALIGN + */ +#endif + + PREALIGN /*struct*/ bond_data { + Matrix H,Hx,Hy,Hz; + double fl_deriv_sum; + double pad[3]; + } POSTALIGN; + PREALIGN /*struct*/ triplet_data { + Matrix H1H2; + Matrix H1xH2 , H1yH2 , H1zH2; + Matrix H1H2x , H1H2y , H1H2z; + + int align_check() { + return + (H1H2.align_check() << 0) | + (H1xH2.align_check() << 1) | + (H1yH2.align_check() << 2) | + (H1zH2.align_check() << 3) | + (H1H2x.align_check() << 4) | + (H1H2y.align_check() << 5) | + (H1H2z.align_check() << 6) ; + } + + void zero() { + H1H2.zero(); + H1xH2.zero(); H1yH2.zero(); H1zH2.zero(); + H1H2x.zero(); H1H2y.zero(); H1H2z.zero(); + } + } POSTALIGN; + +#undef PREALIGN +#undef POSTALIGN + + void make_bond(const double xx[][3],int i,int j,bond_data *bptr); + void make_triplet(bond_data *ij_bond,bond_data *ik_bond,triplet_data *triptr); + triplet_data *get_triplet(const double xx[][3],int i,int j,int k, + Hash *bhash,triplet_data *twork, + double *dvir_ij_p,double *dvir_ik_p); + + int c1_outside(const double a[3], + int triclinic,const double alpha[3]) { + const double stol = 1e-5; + + if(triclinic) { + for(int p = 0; p<3; p++) { + double cog = a[p]; + if(cog < domain->sublo_lamda[p]-0.5*rmax*alpha[p]-stol) return 1; + if(cog > domain->subhi_lamda[p]+0.5*rmax*alpha[p]+stol) return 1; + } + + } else { + double rout = 0.0; + + + for(int p = 0; p<3; p++) { + double cog = a[p]; + if(cog < domain->sublo[p]-0.5*rmax-stol) return 1; + if(cog > domain->subhi[p]+0.5*rmax+stol) return 1; + + if(cog < domain->sublo[p]-stol) { + double t = cog - (domain->sublo[p]-stol); + rout = rout + t*t; + } else if(cog > domain->subhi[p]+stol) { + double t = cog - (domain->subhi[p]+stol); + rout = rout + t*t; + } + + } + + if(rout > 0.25*rmax*rmax) + return 1; + } + + return 0; + } + int c2_outside(const double a[3],const double b[3], + int triclinic,const double alpha[3]) { + const double stol = 1e-5; + + if(triclinic) { + for(int p = 0; p<3; p++) { + double cog = 0.5*(a[p] + b[p]); + if(cog < domain->sublo_lamda[p]-0.5*rcrit*alpha[p]-stol) return 1; + if(cog > domain->subhi_lamda[p]+0.5*rcrit*alpha[p]+stol) return 1; + } + } else { + double rout = 0.0; + + for(int p = 0; p<3; p++) { + double cog = 0.5*(a[p] + b[p]); + if(cog < domain->sublo[p]-0.5*rcrit-stol) return 1; + if(cog > domain->subhi[p]+0.5*rcrit+stol) return 1; + + if(cog < domain->sublo[p]-stol) { + double t = cog - (domain->sublo[p]-stol); + rout = rout + t*t; + } else if(cog > domain->subhi[p]+stol) { + double t = cog - (domain->subhi[p]+stol); + rout = rout + t*t; + } + + } + + if(rout > 0.25*rcrit*rcrit) + return 1; + } + + return 0; + } + double get_weight(const int triclinic, + const double a[3] = 0,const double b[3] = 0, + const double c[3] = 0,const double d[3] = 0) { + const double + *s0 = triclinic ? domain->sublo_lamda : domain->sublo, + *s1 = triclinic ? domain->subhi_lamda : domain->subhi; + double weight = 1.0; + const double stol = 1e-5; + + for(int p = 0; p<3; p++) { + double cog = 0.0,q,w,n = 0.0; + if(a != 0) { cog = cog + a[p]; n = n + 1; } + if(b != 0) { cog = cog + b[p]; n = n + 1; } + if(c != 0) { cog = cog + c[p]; n = n + 1; } + if(d != 0) { cog = cog + d[p]; n = n + 1; } + cog = cog * (1.0/n); + + if(cog < 0.5*(s0[p]+s1[p])) q = cog - s0[p]; + else q = s1[p] - cog; + + w = q*(0.5/stol) + 0.5; + if(w > 1.0) w = 1.0; + if(w < 0.0) w = 0.0; + weight = weight * w; + } + return weight; + } + + void force_debug_3t(double xx[][3], + int i0,int j0,int k0, + int i ,int j ,int k , + double dfix,double dfiy,double dfiz, + double dfjx,double dfjy,double dfjz, + double dfkx,double dfky,double dfkz); + + void force_debug_3v(double xx[][3], + int i0,int j0,int k0, + int i ,int j ,int k , + double dfix,double dfiy,double dfiz, + double dfjx,double dfjy,double dfjz, + double dfkx,double dfky,double dfkz); + + void force_debug_4(double xx[][3], + int i0,int j0,int k0,int m0, + int i ,int j ,int k ,int m , + double dfix,double dfiy,double dfiz, + double dfjx,double dfjy,double dfjz, + double dfkx,double dfky,double dfkz, + double dfmx,double dfmy,double dfmz); + + double numderiv3t(double xx[][3],int i,int j,int k,int p); + double numderiv3v(double xx[][3],int i,int j,int k,int p,int ipert); + double numderiv4(double xx[][3],int i,int j,int k,int m,int p); + void compute_x(const int *nnei,const int * const *nlist, + double *e_s,double *e_p,double *e_t,double *e_q, + int evflag,int newton_pair); + + /* Reimplementation of bond matrix computation */ + void fl_deriv_new(double r,double ri,double xhat,double yhat,double zhat, + double &fl_0,double &fl_x,double &fl_y,double &fl_z, + double &fl_rp,double &fl_p1,double &fl_r0,double &fl_al); + void hamltn_5_raw(const double xin,const double yin,const double zin, + double M [8][8],double Mx[8][8], + double My[8][8],double Mz[8][8], + double *fl_deriv_sum_p); + void hamltn_7_raw(const double xin,const double yin,const double zin, + double M [8][8],double Mx[8][8], + double My[8][8],double Mz[8][8], + double *fl_deriv_sum_p); + /* * */ + // Old matrix routines, only used in force debug routines. + + /// This function calculates the matrix product of ha and hb. + inline Matrix prodmat(const Matrix& ha, const Matrix& hb) const { + Matrix h; + for(int l = 1; l <= lmax; l++) { + for(int n = 1; n <= lmax; n++) { + h.m[l][n] = 0.0; + for(int m = 1; m <= lmax; m++) + h.m[l][n] += ha.m[l][m] * hb.m[m][n]; + } + } + return h; + } + + /// This function calculates the trace of the matrix product of ha and hb. + inline double trace(const Matrix& ha, const Matrix& hb) const { + double zquan = 0.0; + for(int n = 1; n <= lmax; n++) { + double cquan = 0.0; + for(int m = 1; m <= lmax; m++) + cquan += ha.m[n][m] * hb.m[m][n]; + zquan += cquan; + } + return zquan; + } + /* * */ + + inline void transprod(const Matrix& a,const Matrix& b,Matrix &c) const + { + int i,j,k; + + if(lmax == 5) { + const int n = 5; + for(i = 1; i<=n; i++) + for(j = 1; j<=n; j++) { + double s = 0.0; + for(k = 1; k<=n; k++) + s = s + a.m[i][k]*b.m[j][k]; + c.m[i][j] = s; + } + } else if(lmax == 7) { + const int n = 7; + for(i = 1; i<=n; i++) + for(j = 1; j<=n; j++) { + double s = 0.0; + for(k = 1; k<=n; k++) + s = s + a.m[i][k]*b.m[j][k]; + c.m[i][j] = s; + } + } else { + const int n = lmax; + for(i = 1; i<=n; i++) + for(j = 1; j<=n; j++) { + double s = 0.0; + for(k = 1; k<=n; k++) + s = s + a.m[i][k]*b.m[j][k]; + c.m[i][j] = s; + } + } + } + + inline double transtrace_s(const float (*A)[8],const float (*B)[8]) const { + const int n = lmax; + double s = 0.0; + int i,j; + + for(i = 0; i Date: Thu, 22 Oct 2015 23:41:19 +0000 Subject: [PATCH 14/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14176 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/USER-MGPT/README | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/USER-MGPT/README b/src/USER-MGPT/README index 09c7b7c336..dac08c5f0e 100644 --- a/src/USER-MGPT/README +++ b/src/USER-MGPT/README @@ -13,14 +13,14 @@ the forces that move the ions are determined analytically. The mgpt pair style in this package calculates forces and energies using an optimized matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. -See the doc page for the mgpt pair style for full details on using -this package in LAMMPS. In particular, the user should note that the -MGPT potentials are explicitly volume dependent, requiring special -attention in their application. Useful example scripts are given -in the "examples/mgpt" directory. These scripts show the necessary -steps to perform constant-volume calculations and simulations. It -is strongly recommended that the user work through and understand -these examples before proceeding to more complex simulations. +See the doc page for the pair_style mgpt command for full details on +using this package in LAMMPS. In particular, the user should note that +the MGPT potentials are explicitly volume dependent, requiring special +attention in their application. Useful example scripts are given in +the "examples/USER/mgpt" directory. These scripts show the necessary +steps to perform constant-volume calculations and simulations. It is +strongly recommended that the user work through and understand these +examples before proceeding to more complex simulations. 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doc/doc2/pair_mgpt.html | 221 +++++++++++++++++++++++++++++++++ 2 files changed, 250 insertions(+) create mode 100644 doc/doc2/pair_mgpt.html diff --git a/doc/doc2/Section_packages.html b/doc/doc2/Section_packages.html index 16186a05d0..f6197d0145 100644 --- a/doc/doc2/Section_packages.html +++ b/doc/doc2/Section_packages.html @@ -216,6 +216,7 @@ serial. USER-H5MD dump output via HDF5 Pierre de Buyl (KU Leuven) dump h5md - - lib/h5md USER-INTEL Vectorized CPU and Intel(R) coprocessor styles W. Michael Brown (Intel) Section accelerate examples/intel - - USER-LB Lattice Boltzmann fluid Colin Denniston (U Western Ontario) fix lb/fluid USER/lb - - +USER-MGPT Fast MGPT multi-ion potentials Tomas Oppelstrup & John Moriarty (LLNL) pair_style mgpt USER/mgpt - - USER-MISC single-file contributions USER-MISC/README USER-MISC/README - - - USER-MOLFILE VMD molfile plug-ins Axel Kohlmeyer (Temple U) dump molfile - - VMD-MOLFILE USER-OMP OpenMP threaded styles Axel Kohlmeyer (Temple U) Section accelerate - - - @@ -597,6 +598,34 @@ Western Ontario. Contact them directly if you have questions.

+

USER-MGPT package +

+

This package contains a fast implementation for LAMMPS of +quantum-based MGPT multi-ion potentials. The MGPT or model GPT method +derives from first-principles DFT-based generalized pseudopotential +theory (GPT) through a series of systematic approximations valid for +mid-period transition metals with nearly half-filled d bands. The +MGPT method was originally developed by John Moriarty at Lawrence +Livermore National Lab (LLNL). +

+

In the general matrix representation of MGPT, which can also be +applied to f-band actinide metals, the multi-ion potentials are +evaluated on the fly during a simulation through d- or f-state matrix +multiplication, and the forces that move the ions are determined +analytically. The mgpt pair style in this package calculates forces +and energies using an optimized matrix-MGPT algorithm due to Tomas +Oppelstrup at LLNL. +

+

See this doc page to get started: +

+

pair_style mgpt +

+

The persons who created the USER-MGPT package are Tomas Oppelstrup +(oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov) +Contact them directly if you have any questions. +

+
+

USER-MISC package

The files in this package are a potpourri of (mostly) unrelated diff --git a/doc/doc2/pair_mgpt.html b/doc/doc2/pair_mgpt.html new file mode 100644 index 0000000000..11ec3c2fff --- /dev/null +++ b/doc/doc2/pair_mgpt.html @@ -0,0 +1,221 @@ + +

LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

pair_style mgpt command +

+

Syntax: +

+
pair_style mgpt 
+
+

Examples: +

+
pair_style mgpt
+pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega 
+cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin
+cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin
+pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double
+pair_coeff * * parmin potin Omega volpress yes nbody 12 
+
+

Description: +

+

Within DFT quantum mechanics, generalized pseudopotential theory (GPT) +(Moriarty1) provides a first-principles approach to +multi-ion interatomic potentials in d-band transition metals, with a +volume-dependent, real-space total-energy functional for the N-ion +elemental bulk material in the form +

+
+
+

where the prime on each summation sign indicates the exclusion of all +self-interaction terms from the summation. The leading volume term +E_vol as well as the two-ion central-force pair potential v_2 and the +three- and four-ion angular-force potentials, v_3 and v_4, depend +explicitly on the atomic volume Omega, but are structure independent +and transferable to all bulk ion configurations, either ordered or +disordered, and with of without the presence of point and line +defects. The simplified model GPT or MGPT (Moriarty2, +Moriarty3), which retains the form of E_tot and permits +more efficient large-scale atomistic simulations, derives from the GPT +through a series of systematic approximations applied to E_vol and the +potentials v_n that are valid for mid-period transition metals with +nearly half-filled d bands. +

+

Both analytic (Moriarty2) and matrix +(Moriarty3) representations of MGPT have been developed. +In the more general matrix representation, which can also be applied +to f-band actinide metals and permits both canonical and non-canonical +d/f bands, the multi-ion potentials are evaluated on the fly during a +simulation through d- or f-state matrix multiplication, and the forces +that move the ions are determined analytically. Fast matrix-MGPT +algorithms have been developed independently by Glosli +(Glosli, Moriarty3) and by Oppelstrup +(Oppelstrup) +

+

The mgpt pair style calculates forces, energies, and the total +energy per atom, E_tot/N, using the Oppelstrup matrix-MGPT algorithm. +Input potential and control data are entered through the +pair_coeff command. Each material treated requires +input parmin and potin potential files, as shown in the above +examples, as well as specification by the user of the initial atomic +volume Omega through pair_coeff. At the beginning of a time step in +any simulation, the total volume of the simulation cell V should +always be equal to Omega*N, where N is the number of metal ions +present, taking into account the presence of any vacancies and/or +interstitials in the case of a solid. In a constant-volume +simulation, which is the normal mode of operation for the mgpt pair +style, Omega, V and N all remain constant throughout the simulation +and thus are equal to their initial values. In a constant-stress +simulation, the cell volume V will change (slowly) as the simulation +proceeds. After each time step, the atomic volume should be updated +by the code as Omega = V/N. In addition, the volume term E_vol and +the potentials v_2, v_3 and v_4 have to be removed at the end of the +time step, and then respecified at the new value of Omega. In all +smulations, Omega must remain within the defined volume range for +E_vol and the potentials for the given material. +

+

The default option volpress yes in the pair_coeff +command includes all volume derivatives of E_tot required to calculate +the stress tensor and pressure correctly. The option volpress no +disregards the pressure contribution resulting from the volume term +E_vol, and can be used for testing and analysis purposes. The +additional optional variable nbody controls the specific terms in +E_tot that are calculated. The default option and the normal option +for mid-period transition and actinide metals is nbody 1234 for which +all four terms in E_tot are retained. The option nbody 12, for +example, retains only the volume term and the two-ion pair potential +term and can be used for GPT series-end transition metals that can be +well described without v_3 and v_4. The nbody option can also be used +to test or analyze the contribution of any of the four terms in E_tot +to a given calculated property. +

+

The mgpt pair style makes extensive use of matrix algebra and +includes optimized kernels for the BlueGene/Q architecture and the +Intel/AMD (x86) architectures. When compiled with the appropriate +compiler and compiler switches (-msse3 on x86, and using the IBM XL +compiler on BG/Q), these optimized routines are used automatically. +For BG/Q machines, building with the default Makefile for that +architecture (e.g., "make bgq") should enable the optimized algebra +routines. For x-86 machines, the here provided Makefile.mpi_fastmgpt +(build with "make mpi_fastmgpt") enables the fast algebra routines. +The user will be informed in the output files of the matrix kernels in +use. To further improve speed, on x86 the option precision single can +be added to the pair_coeff command line, which +improves speed (up to a factor of two) at the cost of doing matrix +calculations with 7 digit precision instead of the default 16. For +consistency the default option can be specified explicitly by the +option precision double. +

+

All remaining potential and control data are contained with the parmin +and potin files, including cutoffs, atomic mass, and other basic MGPT +variables. Specific MGPT potential data for the transition metals +tantalum (Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials), +and vanadium (V6.1 potentials) are contained in the LAMMPS potentials +directory. The stored files are, respectively, Ta4.mgpt.parmin, +Ta4.mgpt.potin, Ta6.8x.mgpt.parmin, Ta6.8x.mgpt.potin, +Mo5.2.mgpt.parmin, Mo5.2.mgpt.potin, V6.1.mgpt.parmin, and +V6.1.mgpt.potin . Useful corresponding informational "README" files +on the Ta4, Ta6.8x, Mo5.2 and V6.1 potentials are also included in the +potentials directory. These latter files indicate the volume mesh and +range for each potential and give appropriate references for the +potentials. It is expected that MGPT potentials for additional +materials will be added over time. +

+

Useful example MGPT scripts are given in the examples/USER/mgpt +directory. These scripts show the necessary steps to perform +constant-volume calculations and simulations. It is strongly +recommended that the user work through and understand these examples +before proceeding to more complex simulations. +

+
+ +

Mixing, shift, table tail correction, restart: +

+

The (mgpt) pair style does not support the +pair_modify mix, shift, table, and tail options. +

+

This pair style does not write its information to binary restart +files, since it is stored in potential files. Thus, you +needs to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. +

+

This pair style can only be used via the pair keyword of the +run_style respa command. It does not support the +inner, middle, outer keywords. +

+
+ +

Restrictions: +

+

The mgpt pair style is part of the USER-MGPT package and is only +enabled if LAMMPS is built with that package. +

+

The MGPT potentials require the newtion setting to be +"on" for pair style interactions. +

+

The stored parmin and potin potential files provided with LAMMPS in +the "potentials" directory are written in Rydberg atomic units, with +energies in Rydbergs and distances in Bohr radii. The mgpt pair +style converts Rydbergs to Hartrees to make the potential files +compatible with LAMMPS electron units. +

+

The form of E_tot used in the mgpt pair style is only appropriate +for elemental bulk solids and liquids. This includes solids with +point and extended defects such as vacancies, interstitials, grain +boundaries and dislocations. Alloys and free surfaces, however, +require significant modifications, which are not included in the +mgpt pair style. Likewise, the hybrid pair style is not allowed, +where MGPT would be used for some atoms but not for others. +

+

Electron-thermal effects are not included in the standard MGPT +potentials provided in the "potentials" directory, where the +potentials have been constructed at zero electron temperature. +Physically, electron-thermal effects may be important in 3d (e.g., V) +and 4d (e.g., Mo) transition metals at high temperatures near melt and +above. It is expected that temperature-dependent MGPT potentials for +such cases will be added over time. +

+

Related commands: +

+

pair_coeff +

+

Default: +

+

The options defaults for the pair_coeff command are +volpress yes, nbody 1234, and precision double. +

+
+ + + +

(Moriarty1) Moriarty, Physical Review B, 38, 3199 (1988). +

+ + +

(Moriarty2) Moriarty, Physical Review B, 42, 1609 (1990). +Moriarty, Physical Review B 49, 12431 (1994). +

+ + +

(Moriarty3) Moriarty, Benedict, Glosli, Hood, Orlikowski, Patel, Soderlind, Streitz, Tang, and Yang, +Journal of Materials Research, 21, 563 (2006). +

+ + +

(Glosli) Glosli, unpublished, 2005. +Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference +Series, 46, 254 (2006). +

+ + +

(Oppelstrup) Oppelstrup, unpublished, 2015. +Oppelstrup and Moriarty, to be published. +

+ From b72306641cfe456afcee15e6d8840cfb53f0ceb5 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 22 Oct 2015 23:53:49 +0000 Subject: [PATCH 17/31] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14179 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Manual.html | 19 +- doc/Section_packages.html | 98 ++++++---- doc/Section_packages.txt | 29 +++ doc/genindex.html | 8 +- doc/pair_mgpt.html | 369 ++++++++++++++++++++++++++++++++++++++ doc/pair_mgpt.txt | 211 ++++++++++++++++++++++ doc/searchindex.js | 2 +- 7 files changed, 694 insertions(+), 42 deletions(-) create mode 100644 doc/pair_mgpt.html create mode 100644 doc/pair_mgpt.txt diff --git a/doc/Manual.html b/doc/Manual.html index dd72c5f5fa..608f606624 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -244,15 +244,16 @@ it gives quick access to documentation for all LAMMPS commands.

  • 4.23. USER-H5MD package
  • 4.24. USER-INTEL package
  • 4.25. USER-LB package
    • -
  • 4.26. USER-MISC package
    • -
  • 4.27. USER-MOLFILE package
    • -
  • 4.28. USER-OMP package
    • -
  • 4.29. USER-PHONON package
    • -
  • 4.30. USER-QMMM package
    • -
  • 4.31. USER-QTB package
    • -
  • 4.32. USER-REAXC package
    • -
  • 4.33. USER-SMD package
    • -
  • 4.34. USER-SPH package
    • +
  • 4.26. USER-MGPT package
    • +
  • 4.27. USER-MISC package
    • +
  • 4.28. USER-MOLFILE package
    • +
  • 4.29. USER-OMP package
    • +
  • 4.30. USER-PHONON package
    • +
  • 4.31. USER-QMMM package
    • +
  • 4.32. USER-QTB package
    • +
  • 4.33. USER-REAXC package
    • +
  • 4.34. USER-SMD package
    • +
  • 4.35. USER-SPH package
  • 5. Accelerating LAMMPS performance
  • 5. Accelerating LAMMPS performance
    • @@ -823,7 +824,21 @@ serial.

    -USER-MISC +USER-MGPT +Fast MGPT multi-ion potentials +Tomas Oppelstrup & John Moriarty (LLNL) +pair_style mgpt +USER/mgpt +
      +
    • +
    + +
      +
    • +
    + + +USER-MISC single-file contributions USER-MISC/README USER-MISC/README @@ -840,7 +855,7 @@ serial.

    -USER-MOLFILE +USER-MOLFILE VMD molfile plug-ins Axel Kohlmeyer (Temple U) dump molfile @@ -854,7 +869,7 @@ serial.

    VMD-MOLFILE -USER-OMP +USER-OMP OpenMP threaded styles Axel Kohlmeyer (Temple U) Section accelerate @@ -871,7 +886,7 @@ serial.

    -USER-PHONON +USER-PHONON phonon dynamical matrix Ling-Ti Kong (Shanghai Jiao Tong U) fix phonon @@ -885,7 +900,7 @@ serial.

    -USER-QMMM +USER-QMMM QM/MM coupling Axel Kohlmeyer (Temple U) fix qmmm @@ -896,7 +911,7 @@ serial.

    lib/qmmm -USER-QTB +USER-QTB quantum nuclear effects Yuan Shen (Stanford) fix qtb fix_qbmsst @@ -910,7 +925,7 @@ serial.

    -USER-QUIP +USER-QUIP QUIP/libatoms interface Albert Bartok-Partay (U Cambridge) pair_style quip @@ -921,7 +936,7 @@ serial.

    lib/quip -USER-REAXC +USER-REAXC C version of ReaxFF Metin Aktulga (LBNL) pair_style reaxc @@ -935,7 +950,7 @@ serial.

    -USER-SMD +USER-SMD smoothed Mach dynamics Georg Ganzenmuller (EMI) userguide.pdf @@ -949,7 +964,7 @@ serial.

    -USER-SPH +USER-SPH smoothed particle hydrodynamics Georg Ganzenmuller (EMI) userguide.pdf @@ -960,7 +975,7 @@ serial.

    -USER-TALLY +USER-TALLY Pairwise tallied computes Axel Kohlmeyer (Temple U) compute @@ -974,7 +989,7 @@ serial.

    -  +        @@ -1275,8 +1290,31 @@ uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of Western Ontario. Contact them directly if you have questions.

    +
    +

    4.26. USER-MGPT package¶

    +

    This package contains a fast implementation for LAMMPS of +quantum-based MGPT multi-ion potentials. The MGPT or model GPT method +derives from first-principles DFT-based generalized pseudopotential +theory (GPT) through a series of systematic approximations valid for +mid-period transition metals with nearly half-filled d bands. The +MGPT method was originally developed by John Moriarty at Lawrence +Livermore National Lab (LLNL).

    +

    In the general matrix representation of MGPT, which can also be +applied to f-band actinide metals, the multi-ion potentials are +evaluated on the fly during a simulation through d- or f-state matrix +multiplication, and the forces that move the ions are determined +analytically. The mgpt pair style in this package calculates forces +and energies using an optimized matrix-MGPT algorithm due to Tomas +Oppelstrup at LLNL.

    +

    See this doc page to get started:

    +

    pair_style mgpt

    +

    The persons who created the USER-MGPT package are Tomas Oppelstrup +(oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov) +Contact them directly if you have any questions.

    +
    +
    -

    4.26. USER-MISC package¶

    +

    4.27. USER-MISC package¶

    The files in this package are a potpourri of (mostly) unrelated features contributed to LAMMPS by users. Each feature is a single pair of files (*.cpp and *.h).

    @@ -1293,7 +1331,7 @@ about the feature or its coding.

    -

    4.27. USER-MOLFILE package¶

    +

    4.28. USER-MOLFILE package¶

    This package contains a dump molfile command which uses molfile plugins that are bundled with the VMD molecular visualization and @@ -1312,7 +1350,7 @@ application itself.

    -

    4.28. USER-OMP package¶

    +

    4.29. USER-OMP package¶

    This package provides OpenMP multi-threading support and other optimizations of various LAMMPS pair styles, dihedral styles, and fix styles.

    @@ -1323,7 +1361,7 @@ styles, and fix styles.

    -

    4.29. USER-PHONON package¶

    +

    4.30. USER-PHONON package¶

    This package contains a fix phonon command that calculates dynamical matrices, which can then be used to compute phonon dispersion relations, directly from molecular dynamics simulations.

    @@ -1335,7 +1373,7 @@ if you have questions.

    -

    4.30. USER-QMMM package¶

    +

    4.31. USER-QMMM package¶

    This package provides a fix qmmm command which allows LAMMPS to be used in a QM/MM simulation, currently only in combination with pw.x code from the Quantum ESPRESSO package.

    @@ -1352,7 +1390,7 @@ without changes to LAMMPS itself.

    -

    4.31. USER-QTB package¶

    +

    4.32. USER-QTB package¶

    This package provides a self-consistent quantum treatment of the vibrational modes in a classical molecular dynamics simulation. By coupling the MD simulation to a colored thermostat, it introduces zero @@ -1374,7 +1412,7 @@ have questions.

    -

    4.32. USER-REAXC package¶

    +

    4.33. USER-REAXC package¶

    This package contains a implementation for LAMMPS of the ReaxFF force field. ReaxFF uses distance-dependent bond-order functions to represent the contributions of chemical bonding to the potential @@ -1402,7 +1440,7 @@ questions.

    -

    4.33. USER-SMD package¶

    +

    4.34. USER-SMD package¶

    This package implements smoothed Mach dynamics (SMD) in LAMMPS. Currently, the package has the following features:

      @@ -1425,7 +1463,7 @@ Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if you have questions.

    -

    4.34. USER-SPH package¶

    +

    4.35. USER-SPH package¶

    This package implements smoothed particle hydrodynamics (SPH) in LAMMPS. Currently, the package has the following features:

      diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt index 84a977e275..b53ef54c45 100644 --- a/doc/Section_packages.txt +++ b/doc/Section_packages.txt @@ -207,6 +207,7 @@ USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferra USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, - USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, - +USER-MGPT, Fast MGPT multi-ion potentials, Tomas Oppelstrup & John Moriarty (LLNL), "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -, - USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, - USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_accelerate_omp.html, -, -, - @@ -582,6 +583,34 @@ Western Ontario. Contact them directly if you have questions. :line +USER-MGPT package :h4 + +This package contains a fast implementation for LAMMPS of +quantum-based MGPT multi-ion potentials. The MGPT or model GPT method +derives from first-principles DFT-based generalized pseudopotential +theory (GPT) through a series of systematic approximations valid for +mid-period transition metals with nearly half-filled d bands. The +MGPT method was originally developed by John Moriarty at Lawrence +Livermore National Lab (LLNL). + +In the general matrix representation of MGPT, which can also be +applied to f-band actinide metals, the multi-ion potentials are +evaluated on the fly during a simulation through d- or f-state matrix +multiplication, and the forces that move the ions are determined +analytically. The {mgpt} pair style in this package calculates forces +and energies using an optimized matrix-MGPT algorithm due to Tomas +Oppelstrup at LLNL. + +See this doc page to get started: + +"pair_style mgpt"_pair_mgpt.html + +The persons who created the USER-MGPT package are Tomas Oppelstrup +(oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov) +Contact them directly if you have any questions. + +:line + USER-MISC package :h4 The files in this package are a potpourri of (mostly) unrelated diff --git a/doc/genindex.html b/doc/genindex.html index 36d13dad48..455592789c 100644 --- a/doc/genindex.html +++ b/doc/genindex.html @@ -1795,12 +1795,12 @@
      pair_style lj/smooth
      - -
      pair_style lj/smooth/linear
      +
      +
      pair_style lj96/cut
      @@ -1818,6 +1818,10 @@ +
      pair_style mgpt +
      + +
      pair_style mie/cut
      diff --git a/doc/pair_mgpt.html b/doc/pair_mgpt.html new file mode 100644 index 0000000000..950cea54d1 --- /dev/null +++ b/doc/pair_mgpt.html @@ -0,0 +1,369 @@ + + + + + + + + + + + pair_style mgpt command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      + + + + +
      + + + + + + +
      +
      +
      + +
      + +
      +
      +
      + +
      +

      pair_style mgpt command¶

      +
      +

      Syntax¶

      +
      pair_style mgpt
+
      +
      +
      +
      +

      Examples¶

      +
      pair_style mgpt
+pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega
+cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin
+cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin
+pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double
+pair_coeff * * parmin potin Omega volpress yes nbody 12
+
      +
      +
      +
      +

      Description¶

      +

      Within DFT quantum mechanics, generalized pseudopotential theory (GPT) +(Moriarty1) provides a first-principles approach to +multi-ion interatomic potentials in d-band transition metals, with a +volume-dependent, real-space total-energy functional for the N-ion +elemental bulk material in the form

      +_images/pair_mgpt.jpg +

      where the prime on each summation sign indicates the exclusion of all +self-interaction terms from the summation. The leading volume term +E_vol as well as the two-ion central-force pair potential v_2 and the +three- and four-ion angular-force potentials, v_3 and v_4, depend +explicitly on the atomic volume Omega, but are structure independent +and transferable to all bulk ion configurations, either ordered or +disordered, and with of without the presence of point and line +defects. The simplified model GPT or MGPT (Moriarty2, +Moriarty3), which retains the form of E_tot and permits +more efficient large-scale atomistic simulations, derives from the GPT +through a series of systematic approximations applied to E_vol and the +potentials v_n that are valid for mid-period transition metals with +nearly half-filled d bands.

      +

      Both analytic (Moriarty2) and matrix +(Moriarty3) representations of MGPT have been developed. +In the more general matrix representation, which can also be applied +to f-band actinide metals and permits both canonical and non-canonical +d/f bands, the multi-ion potentials are evaluated on the fly during a +simulation through d- or f-state matrix multiplication, and the forces +that move the ions are determined analytically. Fast matrix-MGPT +algorithms have been developed independently by Glosli +(Glosli, Moriarty3) and by Oppelstrup +(Oppelstrup)

      +

      The mgpt pair style calculates forces, energies, and the total +energy per atom, E_tot/N, using the Oppelstrup matrix-MGPT algorithm. +Input potential and control data are entered through the +pair_coeff command. Each material treated requires +input parmin and potin potential files, as shown in the above +examples, as well as specification by the user of the initial atomic +volume Omega through pair_coeff. At the beginning of a time step in +any simulation, the total volume of the simulation cell V should +always be equal to Omega*N, where N is the number of metal ions +present, taking into account the presence of any vacancies and/or +interstitials in the case of a solid. In a constant-volume +simulation, which is the normal mode of operation for the mgpt pair +style, Omega, V and N all remain constant throughout the simulation +and thus are equal to their initial values. In a constant-stress +simulation, the cell volume V will change (slowly) as the simulation +proceeds. After each time step, the atomic volume should be updated +by the code as Omega = V/N. In addition, the volume term E_vol and +the potentials v_2, v_3 and v_4 have to be removed at the end of the +time step, and then respecified at the new value of Omega. In all +smulations, Omega must remain within the defined volume range for +E_vol and the potentials for the given material.

      +

      The default option volpress yes in the pair_coeff +command includes all volume derivatives of E_tot required to calculate +the stress tensor and pressure correctly. The option volpress no +disregards the pressure contribution resulting from the volume term +E_vol, and can be used for testing and analysis purposes. The +additional optional variable nbody controls the specific terms in +E_tot that are calculated. The default option and the normal option +for mid-period transition and actinide metals is nbody 1234 for which +all four terms in E_tot are retained. The option nbody 12, for +example, retains only the volume term and the two-ion pair potential +term and can be used for GPT series-end transition metals that can be +well described without v_3 and v_4. The nbody option can also be used +to test or analyze the contribution of any of the four terms in E_tot +to a given calculated property.

      +

      The mgpt pair style makes extensive use of matrix algebra and +includes optimized kernels for the BlueGene/Q architecture and the +Intel/AMD (x86) architectures. When compiled with the appropriate +compiler and compiler switches (-msse3 on x86, and using the IBM XL +compiler on BG/Q), these optimized routines are used automatically. +For BG/Q machines, building with the default Makefile for that +architecture (e.g., “make bgq”) should enable the optimized algebra +routines. For x-86 machines, the here provided Makefile.mpi_fastmgpt +(build with “make mpi_fastmgpt”) enables the fast algebra routines. +The user will be informed in the output files of the matrix kernels in +use. To further improve speed, on x86 the option precision single can +be added to the pair_coeff command line, which +improves speed (up to a factor of two) at the cost of doing matrix +calculations with 7 digit precision instead of the default 16. For +consistency the default option can be specified explicitly by the +option precision double.

      +

      All remaining potential and control data are contained with the parmin +and potin files, including cutoffs, atomic mass, and other basic MGPT +variables. Specific MGPT potential data for the transition metals +tantalum (Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials), +and vanadium (V6.1 potentials) are contained in the LAMMPS potentials +directory. The stored files are, respectively, Ta4.mgpt.parmin, +Ta4.mgpt.potin, Ta6.8x.mgpt.parmin, Ta6.8x.mgpt.potin, +Mo5.2.mgpt.parmin, Mo5.2.mgpt.potin, V6.1.mgpt.parmin, and +V6.1.mgpt.potin . Useful corresponding informational “README” files +on the Ta4, Ta6.8x, Mo5.2 and V6.1 potentials are also included in the +potentials directory. These latter files indicate the volume mesh and +range for each potential and give appropriate references for the +potentials. It is expected that MGPT potentials for additional +materials will be added over time.

      +

      Useful example MGPT scripts are given in the examples/USER/mgpt +directory. These scripts show the necessary steps to perform +constant-volume calculations and simulations. It is strongly +recommended that the user work through and understand these examples +before proceeding to more complex simulations.

      +
      +

      Mixing, shift, table tail correction, restart:

      +

      The (mgpt) pair style does not support the +pair_modify mix, shift, table, and tail options.

      +

      This pair style does not write its information to binary restart files, since it is stored in potential files. Thus, you +needs to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file.

      +

      This pair style can only be used via the pair keyword of the +run_style respa command. It does not support the +inner, middle, outer keywords.

      +
      +
      +
      +

      Restrictions¶

      +

      The mgpt pair style is part of the USER-MGPT package and is only +enabled if LAMMPS is built with that package.

      +

      The MGPT potentials require the newtion setting to be +“on” for pair style interactions.

      +

      The stored parmin and potin potential files provided with LAMMPS in +the “potentials” directory are written in Rydberg atomic units, with +energies in Rydbergs and distances in Bohr radii. The mgpt pair +style converts Rydbergs to Hartrees to make the potential files +compatible with LAMMPS electron units.

      +

      The form of E_tot used in the mgpt pair style is only appropriate +for elemental bulk solids and liquids. This includes solids with +point and extended defects such as vacancies, interstitials, grain +boundaries and dislocations. Alloys and free surfaces, however, +require significant modifications, which are not included in the +mgpt pair style. Likewise, the hybrid pair style is not allowed, +where MGPT would be used for some atoms but not for others.

      +

      Electron-thermal effects are not included in the standard MGPT +potentials provided in the “potentials” directory, where the +potentials have been constructed at zero electron temperature. +Physically, electron-thermal effects may be important in 3d (e.g., V) +and 4d (e.g., Mo) transition metals at high temperatures near melt and +above. It is expected that temperature-dependent MGPT potentials for +such cases will be added over time.

      +
      + +
      +

      Default¶

      +

      The options defaults for the pair_coeff command are +volpress yes, nbody 1234, and precision double.

      +
      +

      (Moriarty1) Moriarty, Physical Review B, 38, 3199 (1988).

      +

      (Moriarty2) Moriarty, Physical Review B, 42, 1609 (1990). +Moriarty, Physical Review B 49, 12431 (1994).

      +

      (Moriarty3) Moriarty, Benedict, Glosli, Hood, Orlikowski, Patel, Soderlind, Streitz, Tang, and Yang, +Journal of Materials Research, 21, 563 (2006).

      +

      (Glosli) Glosli, unpublished, 2005. +Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference +Series, 46, 254 (2006).

      +

      (Oppelstrup) Oppelstrup, unpublished, 2015. +Oppelstrup and Moriarty, to be published.

      +
      +
      + + +
      +
      + + +
      +
      + +
      + +
      + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/pair_mgpt.txt b/doc/pair_mgpt.txt new file mode 100644 index 0000000000..69b9cbd097 --- /dev/null +++ b/doc/pair_mgpt.txt @@ -0,0 +1,211 @@ +"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 + +pair_style mgpt command :h3 + +[Syntax:] + +pair_style mgpt :pre + +[Examples:] + +pair_style mgpt +pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega +cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin +cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin +pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double +pair_coeff * * parmin potin Omega volpress yes nbody 12 :pre + +[Description:] + +Within DFT quantum mechanics, generalized pseudopotential theory (GPT) +("Moriarty1"_#Moriarty1) provides a first-principles approach to +multi-ion interatomic potentials in d-band transition metals, with a +volume-dependent, real-space total-energy functional for the N-ion +elemental bulk material in the form + +:c,image(Eqs/pair_mgpt.jpg) + +where the prime on each summation sign indicates the exclusion of all +self-interaction terms from the summation. The leading volume term +E_vol as well as the two-ion central-force pair potential v_2 and the +three- and four-ion angular-force potentials, v_3 and v_4, depend +explicitly on the atomic volume Omega, but are structure independent +and transferable to all bulk ion configurations, either ordered or +disordered, and with of without the presence of point and line +defects. The simplified model GPT or MGPT ("Moriarty2"_#Moriarty2, +"Moriarty3"_#Moriarty3), which retains the form of E_tot and permits +more efficient large-scale atomistic simulations, derives from the GPT +through a series of systematic approximations applied to E_vol and the +potentials v_n that are valid for mid-period transition metals with +nearly half-filled d bands. + +Both analytic ("Moriarty2"_#Moriarty2) and matrix +("Moriarty3"_#Moriarty3) representations of MGPT have been developed. +In the more general matrix representation, which can also be applied +to f-band actinide metals and permits both canonical and non-canonical +d/f bands, the multi-ion potentials are evaluated on the fly during a +simulation through d- or f-state matrix multiplication, and the forces +that move the ions are determined analytically. Fast matrix-MGPT +algorithms have been developed independently by Glosli +("Glosli"_#Glosi, "Moriarty3"_#Moriarty3) and by Oppelstrup +("Oppelstrup"_#Oppelstrup) + +The {mgpt} pair style calculates forces, energies, and the total +energy per atom, E_tot/N, using the Oppelstrup matrix-MGPT algorithm. +Input potential and control data are entered through the +"pair_coeff"_pair_coeff.html command. Each material treated requires +input parmin and potin potential files, as shown in the above +examples, as well as specification by the user of the initial atomic +volume Omega through pair_coeff. At the beginning of a time step in +any simulation, the total volume of the simulation cell V should +always be equal to Omega*N, where N is the number of metal ions +present, taking into account the presence of any vacancies and/or +interstitials in the case of a solid. In a constant-volume +simulation, which is the normal mode of operation for the {mgpt} pair +style, Omega, V and N all remain constant throughout the simulation +and thus are equal to their initial values. In a constant-stress +simulation, the cell volume V will change (slowly) as the simulation +proceeds. After each time step, the atomic volume should be updated +by the code as Omega = V/N. In addition, the volume term E_vol and +the potentials v_2, v_3 and v_4 have to be removed at the end of the +time step, and then respecified at the new value of Omega. In all +smulations, Omega must remain within the defined volume range for +E_vol and the potentials for the given material. + +The default option volpress yes in the "pair_coeff"_pair_coeff.html +command includes all volume derivatives of E_tot required to calculate +the stress tensor and pressure correctly. The option volpress no +disregards the pressure contribution resulting from the volume term +E_vol, and can be used for testing and analysis purposes. The +additional optional variable nbody controls the specific terms in +E_tot that are calculated. The default option and the normal option +for mid-period transition and actinide metals is nbody 1234 for which +all four terms in E_tot are retained. The option nbody 12, for +example, retains only the volume term and the two-ion pair potential +term and can be used for GPT series-end transition metals that can be +well described without v_3 and v_4. The nbody option can also be used +to test or analyze the contribution of any of the four terms in E_tot +to a given calculated property. + +The {mgpt} pair style makes extensive use of matrix algebra and +includes optimized kernels for the BlueGene/Q architecture and the +Intel/AMD (x86) architectures. When compiled with the appropriate +compiler and compiler switches (-msse3 on x86, and using the IBM XL +compiler on BG/Q), these optimized routines are used automatically. +For BG/Q machines, building with the default Makefile for that +architecture (e.g., "make bgq") should enable the optimized algebra +routines. For x-86 machines, the here provided Makefile.mpi_fastmgpt +(build with "make mpi_fastmgpt") enables the fast algebra routines. +The user will be informed in the output files of the matrix kernels in +use. To further improve speed, on x86 the option precision single can +be added to the "pair_coeff"_pair_coeff.html command line, which +improves speed (up to a factor of two) at the cost of doing matrix +calculations with 7 digit precision instead of the default 16. For +consistency the default option can be specified explicitly by the +option precision double. + +All remaining potential and control data are contained with the parmin +and potin files, including cutoffs, atomic mass, and other basic MGPT +variables. Specific MGPT potential data for the transition metals +tantalum (Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials), +and vanadium (V6.1 potentials) are contained in the LAMMPS potentials +directory. The stored files are, respectively, Ta4.mgpt.parmin, +Ta4.mgpt.potin, Ta6.8x.mgpt.parmin, Ta6.8x.mgpt.potin, +Mo5.2.mgpt.parmin, Mo5.2.mgpt.potin, V6.1.mgpt.parmin, and +V6.1.mgpt.potin . Useful corresponding informational "README" files +on the Ta4, Ta6.8x, Mo5.2 and V6.1 potentials are also included in the +potentials directory. These latter files indicate the volume mesh and +range for each potential and give appropriate references for the +potentials. It is expected that MGPT potentials for additional +materials will be added over time. + +Useful example MGPT scripts are given in the examples/USER/mgpt +directory. These scripts show the necessary steps to perform +constant-volume calculations and simulations. It is strongly +recommended that the user work through and understand these examples +before proceeding to more complex simulations. + +:line + +[Mixing, shift, table tail correction, restart]: + +The (mgpt) pair style does not support the +"pair_modify"_pair_modify.html mix, shift, table, and tail options. + +This pair style does not write its information to "binary restart +files"_restart.html, since it is stored in potential files. Thus, you +needs to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +:line + +[Restrictions:] + +The {mgpt} pair style is part of the USER-MGPT package and is only +enabled if LAMMPS is built with that package. + +The MGPT potentials require the "newtion"_newton.html setting to be +"on" for pair style interactions. + +The stored parmin and potin potential files provided with LAMMPS in +the "potentials" directory are written in Rydberg atomic units, with +energies in Rydbergs and distances in Bohr radii. The {mgpt} pair +style converts Rydbergs to Hartrees to make the potential files +compatible with LAMMPS electron "units"_units.html. + +The form of E_tot used in the {mgpt} pair style is only appropriate +for elemental bulk solids and liquids. This includes solids with +point and extended defects such as vacancies, interstitials, grain +boundaries and dislocations. Alloys and free surfaces, however, +require significant modifications, which are not included in the +{mgpt} pair style. Likewise, the {hybrid} pair style is not allowed, +where MGPT would be used for some atoms but not for others. + +Electron-thermal effects are not included in the standard MGPT +potentials provided in the "potentials" directory, where the +potentials have been constructed at zero electron temperature. +Physically, electron-thermal effects may be important in 3d (e.g., V) +and 4d (e.g., Mo) transition metals at high temperatures near melt and +above. It is expected that temperature-dependent MGPT potentials for +such cases will be added over time. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] + +The options defaults for the "pair_coeff"_pair_coeff.html command are +volpress yes, nbody 1234, and precision double. + +:line + +:link(Moriarty1) +[(Moriarty1)] Moriarty, Physical Review B, 38, 3199 (1988). + +:link(Moriarty2) +[(Moriarty2)] Moriarty, Physical Review B, 42, 1609 (1990). +Moriarty, Physical Review B 49, 12431 (1994). + +:link(Moriarty3) +[(Moriarty3)] Moriarty, Benedict, Glosli, Hood, Orlikowski, Patel, Soderlind, Streitz, Tang, and Yang, +Journal of Materials Research, 21, 563 (2006). + +:link(Glosli) +[(Glosli)] Glosli, unpublished, 2005. +Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference +Series, 46, 254 (2006). + +:link(Oppelstrup) +[(Oppelstrup)] Oppelstrup, unpublished, 2015. +Oppelstrup and Moriarty, to be published. diff --git a/doc/searchindex.js b/doc/searchindex.js index b13413c7ae..073e615520 100644 --- a/doc/searchindex.js +++ b/doc/searchindex.js @@ -1 +1 @@ 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283,291,293,296,304,309,311,312,313,315,316,317,318,319,323,325,327,331,334,335,340,347,353,354,356,357,359,361,362,363,364,365,369,376,378,385,386,387,388,394,395,396,407,408,409,410,411,412,416,420,422,423,430,440,442,443,444,447,453,455,457,458,459,460,461,463,464,466,468,470,472,475,476,479,483,484,485,486,487,488],afterrun:466,afterward:3,afterword:41,ag1:164,ag2:164,again:[6,11,12,16,17,62,140,145,151,159,188,191,217,232,279,334,347,358,408,409,453,455,456,458,460,465,472,474,484,486],against:[11,12,13,64,218,358,422,423],aggreg:[6,12,65,68,69,79,92,108,115,232,248,291,293,306,453,485],aggress:[232,472],agilio:[9,13],agre:[3,8,185,356,365,396,423],agreement:[5,7],ahd:393,ahead:327,aidan:[0,5,7,9,13,351],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:190,akohlmei:[7,9,13,192,233],aktulga:[7,9,286,423],al2o3_001:[118,294],al3:164,ala:239,alain:9,alat:[274,410],alb:[420,442,444],albeit:292,albert:9,alchem:[87,159],alcohol:323,alcu:[364,369],alcu_eam:420,alderton:382,alejandr:[252,253],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,191,200,211,214,217,239,241,242,264,276,293,296,315,316,320,323,328,354,355,356,360,363,387,409,427,429,453,455,472],alia:[12,16],alias:[1,349],aliceblu:191,align:[6,12,29,41,71,167,185,207,211,234,351,458,461,479],alkali:387,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,153,158,159,160,161,162,163,164,165,166,167,168,169,171,173,178,184,185,188,189,190,191,192,194,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,245,247,248,250,252,253,254,255,256,257,258,259,260,261,262,263,264,265,267,268,269,270,271,272,273,274,275,276,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,304,305,307,308,309,310,311,312,315,316,317,318,319,320,321,322,323,325,326,327,328,329,330,331,332,333,334,335,338,343,346,347,348,349,350,351,353,356,357,358,359,360,362,363,364,365,366,368,369,370,372,373,374,375,376,378,379,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,403,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,423,424,425,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,450,451,452,453,455,456,457,458,459,460,461,462,463,465,466,467,468,469,470,471,472,473,475,476,477,479,483,484,485,486,487,488],allen:[29,87,382,390],allentildeslei:87,allign:3,allindex:332,alloc:[3,5,6,8,9,11,12,60,226,322,357,359,363,418,423,458,466],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,142,144,145,158,163,164,165,167,173,184,185,188,190,191,192,194,195,197,199,200,201,203,204,205,206,207,208,209,211,213,214,215,216,217,218,222,223,226,228,229,230,231,233,236,239,242,243,247,249,252,253,274,278,280,281,282,283,287,293,294,296,297,299,300,304,308,315,316,317,318,320,321,322,323,324,325,331,333,335,343,348,349,351,356,357,358,359,362,363,366,369,370,371,372,373,374,379,385,387,391,392,393,394,399,403,408,409,414,420,423,424,427,429,438,448,450,453,456,458,460,461,462,463,464,465,468,470,471,472,475,476,484,485],almost:[2,3,12,60,234,283,320,349,360,363,438],alo:379,alon:[6,7,214,289,422,423,456],alond:13,along:[6,8,9,12,29,40,87,118,164,165,187,188,190,214,234,239,240,244,249,251,283,293,296,297,301,305,306,315,319,320,326,329,331,351,354,355,356,358,379,382,391,394,397,399,403,410,422,423,441,458,461,468,469,484],alonso:[411,412],alpha:[6,12,51,195,239,275,283,288,356,364,367,370,379,383,385,386,388,393,398,399,410,415,419,443,445,476,479],alpha_:445,alpha_c:407,alpha_i:[430,445],alpha_ialpha_j:445,alpha_lj:407,alphabet:[2,3,22,37,44,55,63,173,184,194,335,343,357,376,439,458],alphanumer:[3,63,194,282,290,333,357,484],alreadi:[3,7,8,9,12,16,17,18,42,165,166,168,189,199,203,207,208,211,213,217,243,281,283,308,331,357,358,383,392,394,401,409,438,448,451,454,458,459,463,468,484],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,149,151,152,153,154,155,157,158,159,160,161,162,163,165,166,167,168,169,171,173,184,185,186,188,189,190,191,192,194,195,196,197,199,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,223,226,227,228,229,230,232,233,236,237,238,239,249,250,252,253,254,255,256,257,258,263,266,267,269,270,271,272,274,275,276,278,279,280,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,301,302,305,306,308,311,312,313,314,315,319,320,321,322,324,326,329,331,333,335,340,343,346,348,349,351,352,3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,363,365,369,379,380,410,414,426,428,444,462,468,479,481],closer:[3,41,116,163,187,188,211,215,219,317,358],closest:[213,274,293,323,390,424,438,448],cloud:479,clovertown:18,clsuter:72,clump1:[278,293],clump2:[278,293],clump3:[278,293],clump:293,cluster:[],clutter:[3,9],cmap:458,cmatrix:230,cmax:410,cmd:[11,12,276,469],cmin:410,cmm:[],cn1:204,cn2:204,cna:[],cnn:204,cnr:[9,13],cnt:[394,462],co2:[40,164,296,357],coars:[7,9,29,36,40,54,177,278,293,308,392,425,470],coarser:[349,484],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,171,172,173,178,334,335,340,376,394,398,414,427,429,431,458,460],coeffcient:458,coeffici:[],coefficienct:383,coefficient0:385,coefficient1:385,coeffieci:[6,367],coeffincientn:385,coexist:[9,228,387],cohes:[6,388,410],coincid:[122,329,374,408,409,453],colberg:189,cold:[6,150,228,232,359,479],coldest:316,coleman8:9,coleman:[9,118,164,294],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,145,153,160,162,165,188,191,203,216,242,248,278,288,291,293,331,348,357,359,377,397,458,465,471,477,488],collid:[222,308,330],colliex:164,collinear:[3,278],collis:[3,239,308,326,330,384,391,451],colllis:308,colloid:[],colombo:39,colon:[192,331,459],color1:191,color2:191,color:[3,9,41,188,190,191,211,229,283,288],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,145,153,160,162,163,164,185,188,191,194,202,203,204,206,207,208,209,242,249,250,283,293,309,310,320,330,389,393,422,423,459,473,475,484],colvar:[],colvarmodul:12,com:[],comamnd:217,comand:[214,460],comannd:363,comb3:[],comb:[],comb_1:285,comb_2:285,combiant:380,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,144,158,188,190,200,206,233,242,252,276,282,312,321,329,332,334,348,349,351,355,363,377,379,380,387,388,394,406,407,430,440,442,444,447,450,461,466,471,479,484],come:[],comfort:[12,13],comm:[0,3,12,61,73,189,233,235,236,349,358,363,383,414,419,441],comm_modifi:[],comm_modift:61,comm_styl:[],command:[],comment:[2,7,11,12,38,56,171,185,188,237,293,320,357,358,364,385,386,388,398,410,416,423,430,440,441,442,443,444,447,455,456,458,479,484],commerci:7,commmand:[3,6,12,59,107,271,452,453,455,472,487],common:[],commonli:[3,6,12,17,25,57,59,105,167,188,190,192,344,392,401,430,442,444,458,461,470],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,169,190,191,211,212,213,215,216,217,233,235,239,241,242,243,252,275,282,284,285,286,293,308,320,331,346,348,359,360,361,363,384,418,455,456,460,467,468,484,486,488],communc:348,comp:[7,189,235,236,296,349,358,387,414,419,424,437,441,443],compact:[63,194,376,439],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,148,163,164,173,184,191,221,284,331,333,348,349,356,358,410,453,472,473,479,483],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,172,173,184,334,335,343,375,439],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,176,188,192,196,202,203,204,206,207,208,209,211,275,287,312,315,322,325,328,348,363,395,414,441,455,456,484],compens:[6,212,213,291,359,387],compet:319,competit:349,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,163,188,189,190,192,233,319,349,363,458,459,463,484],compl:17,complain:[12,17],complement:410,complementari:[7,379,399],complet:[3,6,9,12,15,41,59,71,191,207,211,216,242,276,279,282,308,319,321,333,347,358,363,388,427,429,446,453,458,463,466,470,472,475,479,484],complex:[6,8,11,12,13,25,40,42,62,140,142,153,165,166,239,304,329,346,358,387,441,456,458,461,484],compli:[315,319],complic:[6,7,9,12,13,201,228,456],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,160,161,162,188,190,191,197,198,202,203,204,205,206,207,208,209,210,214,215,217,218,223,226,231,235,236,239,242,244,248,249,251,252,253,256,257,258,269,270,272,273,275,276,277,280,291,293,295,296,297,301,302,305,308,311,312,313,315,322,323,328,329,330,348,351,355,356,357,358,363,383,387,391,408,409,427,429,430,458,459,468,476,484,485],componenet:6,composit:[6,201,239,385],compound:[378,387,388,447],compres:[71,114,203],compress:[3,59,71,114,168,188,190,191,203,217,250,256,280,283],compris:[40,329,397,424,446],compton:[118,164],comptu:3,compuat:349,comput:[],computation:[3,6,212,213,320,369],computational:479,compute_arrai:8,compute_fep:[196,407],compute_group_group:228,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,294],compute_scalar:8,compute_temp:8,compute_ti:196,compute_vector:8,compute_xrd:164,concaten:[2,3,487],concav:329,concentr:385,concept:[6,145,155,203,467],conceptu:[3,6,71,153,215,217,358,379,394,410,463],concern:[6,73,87,189,229],concis:[11,319],conclud:12,concret:8,concurr:[9,16,349,484],conden:[320,442,444],condens:[6,147,320,365,381,385,399,447],condit:[],conducit:6,conduct:[],cone:461,confid:[3,472],config:[12,188,455],configfil:216,configur:[1,2,6,12,15,17,38,59,122,167,185,187,188,190,194,215,216,217,218,222,228,235,236,264,276,284,319,346,356,358,365,369,386,410,440,442,444,447,453,458,460,461,472],confin:[458,472],conflict:[3,12,40,414,456],conform:[3,6,13,59,214,215,251,292,297,319,342,358,387,470],confus:[3,447],conjuct:383,conjug:[7,8,236,355,387,422,423],conjunct:[6,7,71,86,87,114,148,153,159,165,169,191,195,196,236,239,243,264,279,280,284,285,286,288,293,308,316,323,328,348,349,358,370,372,376,379,383,387,393,399,414,417,425,445,458,461,465,479,488],connect:[3,6,87,150,168,214,233,278,293,296,305,358,380,391,438,444,455,456,462,479],conput:3,consecut:[3,11,12,39,71,165,191,195,196,218,233,234,379,399,403,453,459,461],consequ:[1,6,201,320,398,472],conserv:[3,194,201,214,221,222,229,232,236,238,239,243,248,250,252,264,293,296,311,312,316,323,324,328,358,382,383,391,405,467,472],consid:[6,9,70,71,78,87,115,147,150,151,168,188,191,195,196,202,204,207,211,213,214,218,240,253,275,293,315,316,319,320,323,349,376,387,394,423,424,438,453,454,456,459,460,461,463,466,468,476,479,484],consider:[6,8,236,237,311,312,313,363,467],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,145,148,150,165,177,187,192,197,198,203,217,218,221,223,226,229,236,237,238,249,252,254,255,256,257,258,259,260,262,263,264,265,267,268,269,270,271,272,280,283,288,290,292,293,311,312,313,314,324,348,349,351,357,358,363,365,369,371,377,379,387,390,394,408,409,410,414,424,427,429,441,448,456,458,459,461,462,463,470,479,484],consistent_fe_initi:200,consit:293,constant:[],constitu:[3,6,242,293,325,329,377,424],constitut:[427,429],constrain:[3,6,8,143,144,145,146,148,151,152,153,154,155,157,158,194,203,218,228,229,234,242,246,278,279,291,293,296,306,316,323,356,357,387,463,470,479],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,118,140,164,215,252,275,292,329,359,363,382,414,438,440,441,461,462,477,484],constructor:8,consult:423,consum:[1,288,418,484],consumpt:346,contact:[],contact_stiff:[426,428],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,145,153,163,164,165,167,171,173,184,185,188,190,191,192,194,195,196,200,202,203,204,206,207,208,209,211,216,218,223,230,234,235,236,237,239,250,264,274,275,278,279,281,283,286,290,293,294,298,308,315,319,320,329,330,333,347,349,357,358,361,362,364,365,366,369,378,379,382,385,386,387,394,395,410,416,420,421,422,423,430,440,441,442,443,444,445,447,453,454,455,456,458,459,460,461,463,465,467,470,472,475,476,479,484,486,488],content:[12,18,423,474,476],context:[3,6,8,12,17,117,191,212,213,218,278,290,324,355,450,458,465,474,483,484,485],contibut:70,contigu:455,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,161,191,194,195,196,201,203,204,205,206,207,208,209,211,214,215,216,217,218,228,229,230,232,233,234,236,237,238,244,249,250,252,254,255,256,257,258,269,270,271,272,277,279,282,283,293,294,297,307,308,310,317,318,320,326,329,333,347,362,363,369,383,384,401,404,422,423,424,427,429,443,453,456,458,460,461,466,472,475,476,484,486],continuum:[6,7,9,200,320,427,429],contour_integr:200,contract:[59,215,217,252,280,293],contradictori:3,contrain:296,contraint:264,contrari:[230,237],contrast:[1,6,42,55,64,147,150,217,331,427,429,450,487],contrib:320,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,196,201,202,203,204,206,207,208,209,215,228,236,239,242,243,247,253,270,271,278,279,287,290,293,294,296,322,348,356,358,366,383,384,385,387,394,408,409,414,422,423,470,476,479],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,174,188,190,194,200,201,211,215,216,217,232,233,236,237,252,254,255,256,257,258,280,285,293,299,300,311,312,313,320,324,346,348,360,387,390,422,423,426,428,440,444,453,455,467,473,474],control_typ:200,controlfil:423,convect:91,conveni:[6,12,29,188,192,209,294,351,430,484],convent:[3,8,9,29,176,183,184,191,292,305,332,385,387,484],converg:[3,6,41,88,188,190,192,197,211,214,215,223,226,256,283,285,288,292,296,354,355,356,358,378,379,399,453,465,472],convers:[3,8,140,190,191,201,204,280,348,379,380,381,387,399,403,407,417,456,472,483],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,165,172,188,190,191,209,250,331,334,336,339,342,351,358,364,385,442,444,451,456,458,459,460,465,475,479,483,484,486,488],convex:329,convinc:[7,12],cook:9,cooki:7,cool:[7,155,232,291],cooordin:188,cooper:[5,7],coord123:114,coord1:[3,114,203,207,208],coord2:[3,114,203,207,208],coord3:[3,114,203,207,208],coord:[],coordiat:356,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,148,154,160,162,163,165,169,187,188,189,190,191,192,194,197,202,203,206,207,208,211,212,213,214,215,216,217,218,221,223,224,226,228,231,232,233,234,235,236,237,249,251,252,254,255,257,258,270,273,274,275,278,279,280,290,291,293,295,296,297,302,305,306,307,308,310,318,319,320,327,328,330,331,351,356,357,358,363,364,365,368,386,453,458,459,461,463,466,468,472,479,484,485],coordn:[114,203],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,190,320,358,376,422,456],copper:451,coproccesor:16,coprocessor:[1,4,7,9,16,17,363,471],coproprocessor:17,copy_arrai:8,copyright:[7,8,278],coral:191,core:[],core_shel:147,coreshel:[6,9,372,379,381],cornel:[6,171,470],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,190,329,330,351,446,458],cornflowerblu:191,cornsilk:191,corpor:16,corr:378,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,147,152,159,190,217,228,230,236,252,253,270,278,280,283,319,325,329,348,358,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,417,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,446,447,449,450,451,458,473,476,479],correction_max_iter:200,correctli:[3,8,9,11,17,71,81,102,103,143,144,146,148,150,151,152,153,154,157,158,161,188,191,197,218,223,226,237,246,252,253,286,293,296,305,307,326,329,358,359,363,381,409,455,456,458,468,483,485],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,143,144,152,159,164,171,172,173,174,175,176,177,179,180,182,183,185,188,190,191,195,196,197,203,205,206,207,208,210,213,215,217,224,226,227,231,236,239,240,248,249,250,252,254,255,256,257,258,259,264,267,269,270,272,275,276,280,285,293,295,296,311,313,315,324,325,326,328,329,330,332,334,335,336,337,338,339,342,344,349,353,355,357,358,364,365,367,370,371,372,373,374,375,376,377,378,379,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,414,415,416,417,419,420,422,423,424,425,430,431,440,441,442,443,444,446,447,449,450,451,453,455,456,458,459,461,471,472,473,475,476,479,484],correspondingli:[408,409,467],cosin:[],cosineshift:27,cosmo:[230,235],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,164,190,191,203,207,208,211,212,213,225,252,285,320,348,349,361,379,399,403,414,440,455,467],costheta0:[440,442,444,447],costheta:420,costli:[11,88,230,359],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,145,155,160,162,178,188,190,191,195,196,203,204,207,211,217,226,235,282,283,284,288,291,293,295,308,309,315,319,320,321,325,329,331,333,340,345,347,354,356,359,363,366,389,393,394,422,423,454,455,456,458,460,462,465,466,474,479,484,485],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,116,141,166,170,284,286,321,348,349,356,363,370,372,373,374,375,378,379,380,381,382,387,391,392,394,399,403,407,414,417,422,423,425,439,444,445,447,450,463,470,476,479,483],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,114,116,117,153,163,169,197,198,201,203,206,207,208,210,211,218,223,225,228,234,252,264,279,296,311,312,329,349,356,357,358,360,363,389,393,414,476,484],counter:[326,453,464,466,472],counteract:228,counterbal:232,counterpart:[188,293,453],counterproduct:18,coupl:[],courant:298,cours:[3,8,126,128,159,188,195,196,229,292,305,319,325,327,328,330,331,349,408,431,455,458,471,479,484,486],courtesi:351,coval:[6,29,387,410,479],covari:230,cover:[6,71,185,191,200,239,387,397,446],coverag:[71,207],cpc:235,cpp:[1,3,6,8,9,11,12,13,87,188,195,196,226,296],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,191,194,205,221,237,321,346,349,363,376,439,453,471,472,475,476,477,484],cpuremain:476,cr2:164,cr3:164,crack:[4,359],crada:[5,7],crai:[5,7,13,18,188],crash:[3,12,359,479],craympi:363,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:200,create_faceset:200,create_group:189,create_nodeset:200,createatom:[],creation:[],crimson:191,critchlei:278,criteria:[3,116,166,190,191,212,213,214,247,356,419,446,460,463,484],criterion:[12,41,121,163,165,168,201,211,214,228,264,285,298,326,331,356,358,378,387,391,463,472,473],criterioni:472,critic:[6,48,49,250,315,320,356],cross:[3,12,22,71,89,144,173,188,190,202,207,213,217,249,251,270,293,301,305,307,316,323,335,351,358,374,383,384,385,392,393,394,399,401,403,420,425,427,429,442,444,451,458,462,468,486],crossov:1,crossterm:458,crozier:[0,7,13],crucial:283,crystal:[4,6,13,73,274,275,318,351,359,462,476,479],crystallin:[6,275,351,443,479],crystallis:315,crystallogr:[118,164],crystallograph:[351,476],crystallographi:[118,164,351],cs1:164,cs_chunk:6,cs_im:[40,458],cs_re:[40,458],csanyi:[140,421,430],cscl:410,csequ:6,csh:[11,12,376],cshrc:[11,12],csic:[386,440,442,444,447],csinfo:6,csisi:[386,440,442,444,447],csld:[],cst:385,cstherm:6,cstyle:455,csvr:[],ctcm:[364,385],ctemp_cor:221,cterm:297,ctr:9,ctype:11,cu1:164,cu2:164,cu3au:410,cube:[6,41,163,168,211,221,329,351,479],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:369,cummul:[3,6,209,212,213,214,216,225,230,236,238,308,311,312,313,314,316,323,393,476],cumul:[6,201,203,206,207,208,222,228,236,250,252,256,264,293,294,358],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,145,153,155,161,163,166,169,188,189,190,191,192,195,196,200,203,207,208,209,211,212,213,214,215,216,217,218,222,223,226,228,230,233,234,236,242,249,252,253,257,258,264,269,270,272,278,284,285,287,290,291,292,293,296,297,298,299,300,301,302,304,306,307,308,311,312,313,319,320,323,324,325,326,327,328,330,331,333,346,347,348,349,352,353,355,356,357,358,363,369,376,378,382,385,387,388,391,394,395,398,408,409,410,411,412,414,420,422,423,426,427,428,429,431,442,444,445,448,453,454,455,456,458,459,460,461,462,464,465,466,468,470,472,473,475,476,484,485,486,487,488],curv:[6,165,228,275],curvatur:[390,424,451],custom:[],cut0:456,cut1:467,cut2:467,cut:[],cuthi:[274,286],cutinn:[371,408,409],cutlo:[274,286],cutmax:420,cutoff1:[375,382,399,403,407,417,425],cutoff2:[370,372,373,375,381,382,399,403,407,417,425],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,163,166,168,213,214,219,274,283,284,286,288,290,293,308,321,325,329,331,346,348,349,356,359,360,361,363,364,365,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,383,384,385,386,387,388,389,390,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,422,423,424,425,430,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,456,460,463,467,479,484],cutoffa:386,cutoffc:386,cuu3:385,cval:164,cvd:315,cvel:297,cvff:[],cwiggl:[3,249,325,328,330,484],cyan:[2,190,191],cycl:[3,228,250,252,253,256],cyclic:[3,185],cygwin:12,cylind:[3,4,190,234,279,326,329,461],cylindr:[6,234,305,326],cypress:363,cyrot:369,cyrstal:275,d3q15:239,d3q19:239,d_double_doubl:15,d_e:320,d_flag2:282,d_flag:282,d_name:[113,188,282,310,468],d_single_doubl:15,d_single_singl:15,d_sx:282,d_sy:282,d_sz:282,daan:318,dai:12,daili:12,daivi:270,damag:[],dammak:288,damp:[3,6,194,199,236,237,238,243,252,253,256,280,283,288,293,311,312,324,326,327,355,356,358,370,372,374,379,382,387,391,399,407,417,425,439,445,472,479],damp_com:237,damp_drud:237,dampen:[293,479],dampflag:[326,391],dan:17,danger:[3,12,228,331,383,476],dangl:168,daniel:9,darden:[349,382],darkblu:191,darkcyan:191,darken:190,darkgoldenrod:191,darkgrai:191,darkgreen:191,darkkhaki:191,darkmagenta:191,darkolivegreen:191,darkorang:191,darkorchid:191,darkr:191,darksalmon:191,darkseagreen:191,darkslateblu:191,darkslategrai:191,darkturquois:191,darkviolet:191,dasgupta:284,dash:[391,475],dat:[6,91,185,200,454],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,294],dataset:294,datatyp:3,date:[0,6,12,13,422,423,484],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,188,204],davi:325,david:[9,19,348,349,442,444],daw:[385,420],dbg:14,dcd:[3,6,7,188,189,190,191,192,276,459,463],ddim:187,deactiv:407,dealt:235,debug:[6,7,11,12,13,14,17,118,122,164,165,276,281,346,348,363,395,414,448,456,457,460,465,468,475,484],deby:[],decai:[379,451],decid:[3,6,12,16,71,249,282,293,321,473],decipher:351,declar:189,declin:308,decod:190,decompos:[87,430],decomposit:[3,5,7,18,62,200,276],decoupl:[6,479],decreas:[3,188,197,198,205,214,217,223,226,228,236,319,348],decrement:297,deepli:345,deeppink:191,deepskyblu:191,def:[12,13,456],defaul:61,defect:[6,70,163],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,171,172,173,174,175,176,177,179,180,182,183,184,185,186,187,188,189,190,191,194,195,196,197,198,199,200,201,202,203,204,206,207,208,209,210,211,212,213,214,215,217,218,221,222,223,226,227,228,231,234,235,236,237,238,239,247,249,251,252,253,254,255,256,257,258,260,261,262,265,267,268,269,270,271,272,274,275,276,278,279,280,282,284,286,291,293,294,295,296,298,302,306,308,310,311,312,313,314,316,317,318,320,322,323,325,326,327,328,329,330,331,333,334,335,336,337,338,339,342,343,344,346,348,349,351,353,355,356,357,358,359,360,361,362,363,365,366,367,368,370,371,372,373,374,375,376,377,379,380,382,383,384,386,387,389,390,391,392,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,413,414,415,416,417,419,420,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,455,456,458,459,461,462,463,464,467,468,469,470,472,473,475,476,479,480,481,482,483,484,485],definit:[2,3,6,8,12,13,78,80,116,140,191,203,204,205,206,207,208,209,217,234,256,294,310,322,325,328,330,332,343,346,357,366,369,377,387,397,420,427,429,430,446,456,458,460,467,469,483,484],defint:476,deform:[],deg2theta:164,deg:479,degener:[3,278],degrad:[8,18,275,349,467],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,164,165,171,172,175,176,183,185,187,190,203,214,221,228,230,231,236,237,242,252,253,256,257,258,269,270,272,276,278,292,293,296,311,312,313,318,334,336,339,342,344,356,382,385,393,468,476,479,485],degress:[145,203],del:472,delai:[3,6,12,359,384,476],deleg:394,delet:[2,3,7,8,12,54,57,60,63,163,168,169,194,203,204,206,207,208,209,212,214,225,228,252,294,311,312,331,333,347,357,359,362,414,458,459,461,469,470,475,480,482,484,485],delete_atom:[],delete_bond:[],delete_el:200,deli:187,delimit:[456,484],deloc:[253,387],delr:410,delt_lo:472,delta:[],delta_1:369,delta_3:369,delta_7:369,delta_conf:3,delta_ij:[410,420],delta_mu:3,delta_pi:369,delta_r:420,delta_sigma:369,delx:187,delz:187,demand:288,demo:11,demon:273,demonstr:[283,410],den:279,dendrim:393,denniston:[9,239,241,242,243,275],denomin:[7,170],denot:[118,221,237,275,286,288,379,392,394,423,427,429],dens:[71,214,387],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,151,163,165,195,196,200,203,207,208,211,217,226,239,242,245,246,275,279,280,284,320,325,351,353,357,364,369,385,410,411,412,420,424,433,435,436,437,458,467,468,476,483],density_continu:429,density_summ:429,depart:[0,7],departur:[250,283],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,143,148,152,153,159,165,166,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,190,191,194,195,196,197,198,201,203,205,206,207,209,210,211,213,215,217,223,224,227,230,231,232,234,236,237,239,241,242,249,252,254,255,256,257,258,259,267,269,270,272,274,285,288,290,293,295,296,302,308,311,312,313,315,317,319,320,322,324,325,328,329,330,331,333,334,335,336,337,338,339,342,344,349,351,356,357,359,360,361,363,364,365,367,368,369,370,371,372,373,374,375,376,377,378,379,380,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,413,415,416,417,419,420,422,423,424,425,430,431,439,440,441,442,443,444,445,446,447,449,450,451,453,455,458,460,461,464,468,470,472,475,476,478,484,485],dependend:6,depflag:12,dephas:[453,472],depos:218,deposit:[],deprec:[284,422],depth:[51,144,190,320,390,424],dequidt:9,der:[87,107,377,378,407,422,423,450,479],deriv:[6,7,8,9,38,56,63,87,140,159,185,204,215,217,228,236,249,252,254,255,256,257,258,274,280,284,288,317,318,320,325,326,329,355,357,365,369,377,382,387,388,392,401,405,406,410,422,423,439,441,450,479],derjagin:450,derlet:274,descend:191,descent:[7,355],descib:[40,284],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,144,145,149,150,153,156,158,159,163,164,165,167,168,177,182,185,188,189,194,195,196,203,204,205,206,207,208,209,211,214,215,216,217,218,220,221,229,230,233,234,235,236,237,238,239,241,242,243,247,251,252,253,256,263,271,274,276,281,282,283,284,285,286,293,297,305,308,309,310,311,312,313,314,315,316,317,318,323,325,326,328,333,348,349,351,354,355,356,357,358,362,365,366,368,370,371,372,374,375,376,377,378,379,382,385,387,388,390,391,392,394,399,400,401,402,403,404,405,406,407,408,409,410,413,419,420,421,422,423,424,425,430,431,438,439,440,441,442,443,444,445,447,449,450,451,453,455,456,458,459,461,462,468,471,472,475,484,485,486],descript:[],descriptor:[140,188,395],deserno:349,design:[0,3,6,7,8,9,11,13,14,15,17,118,147,150,164,200,214,220,221,252,253,274,275,294,315,320,366,367,368,371,374,379,381,387,407,408,409,411,412,420,423,441,467],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,112,117,141,147,165,178,187,203,209,215,217,226,228,229,236,237,238,242,252,270,278,279,280,281,284,288,293,296,308,311,312,313,314,319,326,340,345,348,349,351,354,356,357,358,383,385,393,408,409,440,442,444,454,455,456,458,462,467,472,473,475,476,484,485,486],desk:7,desktop:[4,6,7,10,12,190],despit:479,destabil:369,destre:342,destroi:[11,39,212,213],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,143,144,145,148,158,159,160,162,165,166,169,170,173,184,188,190,191,194,195,196,200,203,204,205,206,207,209,211,213,214,215,216,217,218,226,228,229,230,231,233,234,236,238,239,243,249,250,251,252,253,254,255,256,257,258,262,264,269,270,271,272,275,278,279,280,282,283,285,286,287,293,296,308,311,312,313,314,315,316,318,319,320,321,322,323,324,331,333,335,343,348,349,352,356,357,359,360,363,364,365,366,368,369,371,373,374,375,376,377,378,379,382,383,387,388,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,410,413,414,419,422,423,424,430,431,439,446,449,450,456,458,459,460,461,463,464,467,468,470,473,476,477,484,485,488],detect:[2,3,12,61,63,86,227,279,319,358,378,393,398,453,455,458,469,472,484],determ:363,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,153,154,163,164,165,187,188,190,191,192,193,197,198,199,202,203,204,205,206,207,208,209,210,211,215,217,218,221,223,228,231,232,234,236,237,242,247,249,250,252,257,258,269,270,272,274,276,280,283,290,291,292,293,294,295,298,300,302,308,311,312,313,315,321,322,325,326,327,328,329,330,331,343,348,349,351,357,359,360,363,365,366,373,378,382,384,385,389,391,394,395,403,410,414,423,424,438,441,445,450,455,458,459,461,463,465,468,472,474,475,477,483,484,485],detil:108,devan:[9,425],devanathan:444,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,233,256,278,283,284,287,365,369,387,412,447,460],devemi:9,deviat:[250,256,274,389],deviator:9,devic:[1,3,12,15,17,233,363],device_typ:363,devin:[285,378],devis:412,dfactor:190,dff:479,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,349],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,287],dhi:[59,187,217,279],dhug:[250,283],dhugoniot:[250,283],dia:410,diagnost:[],diagon:[3,6,83,140,141,142,215,252,280,293,323,427,429],diagonalstyl:430,diagram:[41,118,164,184,211,276],diallo:393,diam:[190,191,279,357],diamet:[3,6,40,113,165,188,190,191,195,196,236,279,293,308,324,326,357,377,390,391,397,401,424,446,450,458,459,468],diamond:[351,387,410],diamter:[40,279],dick:6,dicsuss:249,dictat:[201,250],did:[3,12,356,383,384,385,391,414,442,444,466],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,161,322,348],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,143,144,145,146,148,151,152,153,154,155,157,158,159,165,166,168,173,184,185,187,188,190,191,194,196,199,201,203,206,211,212,213,214,215,216,217,221,227,228,229,230,231,232,233,236,237,239,249,252,253,254,255,257,258,260,262,265,267,268,269,272,274,276,278,280,283,284,285,288,291,293,296,297,305,306,308,311,312,313,316,317,318,320,323,324,325,326,329,333,334,343,345,347,348,349,351,352,354,355,357,358,360,361,362,363,364,365,369,373,374,376,377,378,383,385,387,390,391,392,394,397,399,400,402,403,410,411,412,413,414,416,420,422,423,424,425,426,427,429,430,431,439,440,441,442,444,446,447,450,452,453,455,456,458,460,461,462,463,466,467,468,470,472,473,475,476,477,479,483,484,485,486],differenti:[1,3,6,29,185,348,379,420,443],difficult:[215,276,363,393,467],difficulti:[296,422],diffract:[],diffus:[],digit:[2,3,191,333],dih_table1:185,dih_table2:185,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:213,dihydrid:387,dij:296,dilat:[],dim1:3,dim2:3,dim:[3,59,71,143,146,147,148,151,152,153,154,155,157,165,187,207,217,234,326,351,410,461,483,484,485],dimdim:484,dimems:275,dimens:[],dimension:[3,39,112,118,140,143,145,146,147,148,151,152,153,154,155,157,164,186,203,207,251,275,320,351,354,358,420,458,468],dimensionless:[105,121,122,124,127,129,131,136,140,320,349,430,450],dimentionless:135,dimer:[6,293,410],dimgrai:191,dimstr:[41,211],dinola:[280,311],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,188,310,479],dir1:469,dir2:469,dir:[1,3,4,8,9,11,12,250,274,283,307,420,422,423,456,469,484],dirac:140,direc:420,direct:[],directli:[3,6,8,9,11,12,87,113,140,142,188,189,190,197,223,230,234,239,275,294,312,324,326,327,328,329,351,355,363,364,365,370,372,373,379,382,385,387,399,403,414,417,425,438,456,468,469,470,476,484],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,192,216,235,278,284,287,304,308,317,318,358,362,364,365,369,376,378,379,385,386,388,395,396,407,410,411,412,416,420,421,422,423,430,440,442,443,444,447,456,458,459,460,469,484],disabl:[3,12,16,320,398,456,471,484],disadvantag:[6,211],disallow:[188,217,252],disappear:460,discard:[2,3,41,71,205,207,211,321,329,455,460,461],discontinu:[9,185,356,405],discourag:410,discov:[13,321],discret:[6,8,40,42,190,191,236,239],discuss:[],disk:[6,84,85,158,186,218,228,279,456],disloc:70,disord:[39,70],disp:[],dispar:424,disperion:[382,403],dispers:[3,6,7,9,163,275,348,349,373,382,403,408,414,423,441,447],displac:[],displace_atom:[],displace_box:59,displacemet:461,displai:[11,13,22,37,44,55,173,184,188,190,335,343,376,439],dispters:3,dissip:[6,229,236,275,317,318,371,383,391,408,409,439],dissolut:212,dist:[6,69,91,108,117,188,276,292,384,438,453,485],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,154,160,163,165,166,167,168,172,187,188,190,191,199,203,207,208,212,213,214,215,217,218,219,222,228,234,239,249,250,251,252,256,264,274,275,279,283,284,291,292,293,296,297,301,305,306,307,308,315,316,318,319,320,323,325,326,327,328,329,330,334,348,349,351,354,356,358,359,360,363,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,38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229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,334,336,337,338,339,342,344,348,349,354,355,356,358,359,363,364,365,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,422,423,424,425,430,431,432,433,438,439,440,441,442,443,444,446,447,448,449,450,451,453,456,458,463,467,468,470,472,474,475,476,479,483,484,487],energy_update_freq:423,enforc:[6,57,58,104,187,188,189,190,192,194,201,214,217,252,273,275,285,293,296,333,348,399,455,484,485],enforce2d:[],eng:[11,65,69,108,188,226,331,333,378,412],eng_previ:333,engin:[200,217,278,297,317,385,411],engr:[422,423],enhanc:[196,200,453],enlarg:[59,190],enough:[3,40,61,86,165,166,168,211,237,279,283,288,293,321,325,326,329,359,363,379,418,458,462,463],enpub:385,enrti:[],ensembl:[],ensight:6,ensur:[3,6,140,188,201,205,215,228,229,252,298,319,349,369,384,407,440,447],enter:[57,155,388,447,472],enthalpi:[123,254,255,385,475,476,484],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,141,145,164,165,191,194,195,196,203,207,208,211,214,216,225,228,229,232,236,237,248,252,254,255,256,257,258,274,276,278,291,293,306,320,322,333,363,382,403,414,441,458,466,467],entireti:[397,446],entiti:[6,8,40,42,188,293],entri:[3,8,12,38,42,56,65,69,79,92,108,115,118,127,130,131,132,133,134,136,137,138,163,185,191,206,207,208,216,283,331,357,369,386,410,416,423,430,440,441,442,443,444,447,484],entropi:472,entry1:[38,56,191,376,441],entry2:191,entryn:191,enumer:[166,188],enumuer:6,env:363,environ:[1,3,6,11,12,16,17,18,190,230,235,274,363,364,369,376,378,386,387,420,442,455,469,484],epair:[107,191,389,393,422,423,476],epen:[422,423],epfl:[230,235],epp:382,epq:382,eps0:450,eps14:407,epsilon0:444,epsilon:[3,6,36,45,46,50,53,54,87,171,195,196,228,293,308,325,329,354,356,368,374,375,377,379,380,381,382,390,392,393,394,397,398,399,400,401,402,403,404,405,406,407,413,417,424,425,434,440,446,449,450,467,479,483],epsilon_0:451,epsilon_14:374,epsilon_:424,epsilon_d:380,epsilon_i:[390,414,424],epsilon_i_:424,epsilon_i_a:[390,424],epsilon_i_b:[390,424],epsilon_i_c:[390,424],epsilon_ij:414,epsilon_j:[390,414,424],epsilon_j_:424,epsilon_j_a:[390,424],epsilon_j_b:[390,424],epsilon_j_c:[390,424],epsilon_lj:424,epton:419,eqch:160,eqeq:[422,423],eqp:382,eqq:382,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,144,159,161,165,190,191,194,195,196,197,198,201,204,205,206,209,210,211,215,217,218,223,228,229,231,232,234,236,237,239,242,243,249,250,256,266,274,276,279,281,283,284,285,288,290,292,293,295,297,302,304,311,312,313,316,317,318,320,322,323,325,328,330,331,333,347,351,356,358,359,360,362,363,378,383,389,390,393,408,413,420,422,423,424,426,427,428,430,431,441,446,447,451,454,455,456,458,460,461,465,466,469,472,474,476,484,485],equat:[3,6,7,8,9,91,112,118,164,173,184,194,215,221,222,230,236,237,239,242,250,251,252,253,256,270,274,276,283,284,288,296,308,316,320,323,325,326,328,330,342,348,349,377,382,383,387,388,391,396,408,409,410,414,424,427,429,433,434,436,437,445,451,479],equi:253,equidist:251,equil:[3,284,352,465,488],equilater:468,equilibr:[3,4,5,6,7,9,59,91,165,194,201,204,214,215,228,250,252,253,270,271,283,284,285,286,316,317,318,323,378,379,422,423,454,468],equilibria:323,equilibribum:[212,213],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,148,149,172,174,215,217,228,229,230,237,239,252,256,270,283,288,292,296,297,305,308,315,316,318,323,334,336,339,342,378,410,416,479],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:200,equival:[6,12,13,59,61,124,125,133,138,163,167,191,206,209,215,217,228,236,252,270,280,292,293,328,383,387,442,444,458,461,466,467,476,479],equlibrium:6,equliibr:[284,286],er3:164,eradiu:[40,113,387,458],eras:[295,317],erat:[217,409],erc:379,erfc:[379,399,414],erforc:113,erg:483,erhart:[201,385,442,444],ermscal:366,ernst:9,eror:3,eros:410,erose_form:410,erot:[],errata:[442,444],erratum:325,erron:3,error:[],erta:391,ervel:[113,458],escap:[218,479],especi:[8,11,16,153,165,194,201,211,228,283,288,291,292,363,455],espresso:[9,287],essenti:[8,11,12,27,88,128,146,147,148,151,152,153,154,155,157,174,204,256,275,324,349,365,379,399,444,463,476],essex:29,establish:[87,232],estim:[1,3,6,10,12,38,41,56,91,141,200,211,222,250,308,315,348,349,354,414,423,441,472,476],esu:483,esub:410,eta:[6,239,252,283,284,286,324,386,388,390,420,443,447,483],eta_dot:252,eta_ij:420,eta_ji:388,etag:[40,458],etail:476,etap:252,etap_dot:252,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,143,145,146,147,148,149,151,152,153,154,155,157,159,165,167,168,169,178,188,190,191,194,195,200,201,202,203,206,207,208,209,212,213,217,218,226,228,229,236,252,279,290,294,320,321,329,333,347,348,356,357,358,359,361,385,386,394,407,409,418,422,423,440,442,444,447,453,456,458,459,460,465,467,468,472,474,475,476,477,479,483,484,486,488],ethernet:18,etol:[356,358,453,472],etot0:283,etot:[6,94,96,97,110,141,151,191,221,237,250,283,475,476],eu2:164,eu3:164,euler:[356,358],eulerian:200,euqat:432,europhi:239,ev_tal:8,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,140,142,145,155,163,165,188,190,191,195,196,197,198,200,202,203,204,205,206,207,208,209,210,217,223,229,231,232,234,235,236,237,275,281,284,295,298,302,311,312,313,322,325,328,330,331,333,348,349,354,356,363,414,420,426,428,441,453,454,456,460,461,463,465,466,467,468,472,474,476,484,485],evalut:[333,456],evan:[153,270],evanseck:[6,20,171,374,470],evapor:[],evaul:[8,356],evdwl:[107,422,423,476],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,119,166,167,181,185,188,191,194,195,196,201,202,203,206,207,208,209,211,212,213,215,217,218,221,234,237,250,252,253,275,288,290,293,294,304,308,316,320,323,325,329,331,341,348,354,356,358,363,368,387,388,391,394,414,424,447,448,458,459,461,463,464,465,467,468,470,473,475,476,477,479,488],evenli:[3,41,141,185,211,239,397,448,458],event:[],eventu:[3,6,12,15,167,284,472],ever:[54,56,235,308],evera:[377,390,424,439],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,113,119,128,153,168,188,189,190,191,192,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,222,225,226,228,230,232,233,234,239,240,248,252,253,256,273,274,275,279,280,281,282,283,284,285,286,288,290,291,293,294,296,297,308,310,311,312,313,314,315,316,319,320,321,322,323,331,333,347,349,358,359,360,363,383,384,394,407,422,423,435,452,453,454,458,460,462,463,465,466,467,472,473,474,476,484,488],everyth:[8,107],everywher:[116,401],eviri:387,evolut:[230,239,276,453],evolv:[239,276,321],ewald:[2,3,5,6,7,8,12,88,110,118,141,321,348,349,356,370,372,373,379,382,387,399,403,417,425,439,441,460],ewald_disp:382,ewalddisp:3,exact:[22,41,44,71,122,159,168,173,211,214,229,230,236,237,238,279,288,289,308,320,335,348,376,460,465,472,484,486,488],exactli:[3,6,12,14,17,38,41,56,59,71,91,116,144,149,156,165,185,195,196,206,211,217,222,229,236,237,238,253,263,264,271,275,283,308,313,314,327,363,376,383,385,391,394,397,408,414,441,460,461,468,472,484],exager:479,examin:[6,8,9,17,214,275],examp:[456,484],exampl:[],exce:[3,6,16,17,18,41,58,71,167,203,207,208,211,215,217,222,225,252,275,299,300,308,356,363,458,484],exceed:[3,41,59,211,217,252,308,466],excel:387,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,191,194,197,203,204,206,210,211,215,217,224,227,228,231,234,236,238,252,253,254,255,256,257,258,259,263,264,267,269,270,271,272,276,285,286,293,295,296,305,308,311,313,314,320,324,328,331,333,334,335,336,337,338,339,342,343,344,348,349,351,353,357,358,359,361,362,363,364,365,367,370,371,372,373,374,375,376,377,378,379,381,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,411,415,416,417,419,422,423,424,425,431,439,440,441,442,443,444,446,447,449,450,451,453,455,456,458,460,461,463,466,467,468,469,470,472,476,479,483,484,485,487],excess:[205,387],exchang:[2,3,6,8,9,61,62,194,200,201,228,236,285,293,316,320,323,348,363,387,473],exchange:348,excit:[9,387],exclud:[3,6,9,12,16,17,63,71,112,140,145,152,153,169,188,203,207,212,213,240,248,278,291,293,315,326,331,356,357,359,371,391,394,408,409,414,438,470],exclus:[1,3,9,12,16,87,363,378,414,467,477],excurs:453,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,166,190,233,287,333,347,350,362,454,456,466,469,472,484],exemplari:229,exemplifi:387,exert:[6,234,237,288,327,328,329,349],exhaust:[200,362,484],exhibit:[252,355,387,467],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,122,165,166,184,189,190,191,194,199,210,213,215,218,228,278,279,281,331,334,336,337,339,343,352,357,363,394,422,448,454,456,458,459,460,469,470,471,484,485,486],exit:[2,3,11,12,41,57,188,211,347,362,456,457,466,475,484],exlanatori:3,exp:[],expand:[],expans:[12,140,188,469,484],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,146,157,163,185,211,223,228,230,249,274,280,282,283,288,293,331,349,359,376,410,414,453,456,458,460,463,467,472,484],expens:[6,10,71,191,274,278,293,320,331,348,349,359,363,456],experi:[6,13,15,17,210,218,233,242,251,280,292,293,354,358,383,414,467,472],experienc:[6,12,241,242],experiment:[228,348,363,472],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,145,153,185,188,190,191,194,203,204,209,211,213,215,217,252,274,282,293,305,331,333,347,348,351,357,358,362,368,385,397,431,446,456,459,460,463,465,468,479,484,488],explan:[3,6,59,113,140,188,203,251,274,394,452,455,456,458,467],explanatori:[3,8,117,188,202,203,206,207,208,293,357,455,484],explantori:[3,289],explic:413,explicit:[6,9,11,22,44,77,87,113,116,159,173,195,196,217,299,300,335,353,365,366,369,374,376,385,387,398,408,445,452,455,459,462],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,143,152,155,163,165,171,172,174,175,176,177,179,180,182,183,185,188,191,197,207,210,217,224,227,229,231,236,252,254,255,256,257,258,259,267,269,270,272,282,283,285,293,295,296,311,313,314,320,324,328,334,336,337,338,339,342,344,357,363,364,365,367,370,371,372,373,374,375,376,377,378,379,380,382,383,384,385,386,388,389,390,391,392,393,394,397,398,399,400,401,402,403,404,405,406,407,408,411,414,415,416,417,419,424,425,431,432,433,434,435,436,437,439,440,441,442,443,444,445,446,447,449,450,451,458,460,467,468,470,471,477,479],explictli:[16,471],exploit:[9,15,17,276],explor:[118,164],expon:[3,284,286,385,390,393,407,413,425],exponenti:[87,420,440,447,451,472,484],expos:11,exposit:[200,383,384],express:[6,140,151,165,195,196,215,249,274,284,320,326,333,369,385,387,401,410,430,439,484],expressiont:369,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,194,197,198,201,209,210,216,219,223,226,227,228,230,231,232,234,236,238,250,252,256,264,274,275,291,292,293,295,297,302,305,307,311,312,313,314,315,317,318,320,322,325,329,330,390,410,423,424,430,475,476],extent:[1,3,41,45,57,71,163,167,188,199,207,211,234,327,330,348,351,365,426,428,441,455,458,461],exterior:[3,6,329],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,143,144,146,148,151,152,153,154,155,157,158,164,165,166,167,171,191,206,211,213,252,281,282,283,293,308,356,357,360,361,382,391,394,397,410,414,455,456,458,461,470,479,484],extract:[3,6,11,13,36,63,87,107,115,117,119,195,196,286,358,379,388,410,430,456,463,475],extract_atom:11,extract_comput:[11,456],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,190,205,215,217,252,318,387,443,479],extrema:407,extrins:200,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[161,322],f_a:[442,443,444],f_ave:117,f_c:443,f_f:444,f_fix_id:283,f_harm:318,f_i:420,f_id:[6,71,117,119,188,194,202,203,204,205,206,207,208,209,247,310,322,476,484],f_ij:420,f_indent:209,f_int:317,f_jj:91,f_k:420,f_langevin:320,f_max:[283,288],f_msst:250,f_r:[237,442,443,444],f_sigma:369,f_solid:318,f_ss:6,f_temp:237,face:[3,6,57,59,71,153,163,167,199,207,208,325,327,328,329,330,351,390,410,424,458,461],face_threshold:163,facet:163,facil:[0,12],facilit:[6,13],fact:[6,8,16,230,308,318,391,470],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,116,118,140,159,164,167,171,182,188,190,191,195,196,204,211,215,217,218,228,233,236,238,239,250,252,253,256,276,280,292,296,298,300,308,312,316,323,324,325,329,339,349,351,357,363,365,366,369,370,372,374,379,380,381,383,387,391,394,398,399,410,414,416,417,423,425,431,440,445,455,458,461,462,467,470,472,473,476,479,483,484],factori:[3,456],factoriz:348,fail:[3,11,12,59,169,215,218,348,356,358,381,423,456],failur:[121,427,457,484],fairli:[11,414,467,472],faken:73,falcon:233,fall:[3,6,191,206,279,456,484],fals:[86,331,333,484],fame:8,famili:[447,455],familiar:[0,11],fan:420,far:[3,6,12,17,57,59,61,86,188,191,192,211,212,213,215,218,252,274,292,293,308,325,336,339,354,358,359,446,456,458,463,476],farago:236,farrel:[442,444],farther:188,fashion:[6,8,41,71,165,191,194,195,196,201,207,211,213,218,228,230,234,249,250,252,254,255,256,257,258,266,269,270,271,272,282,283,285,293,297,301,307,310,318,320,324,325,326,328,330,358,394,408,461,470,484,487],fasolino:396,fast:[6,7,9,12,13,17,39,188,261,283,321,348,349,371,408,409,439,441,460,465,467,476,485,488],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,143,152,171,172,174,175,176,177,179,180,182,183,185,188,191,194,197,210,211,217,224,227,231,235,236,252,254,255,256,257,258,259,267,269,270,272,280,284,285,293,295,296,308,311,313,315,317,320,324,328,334,336,337,338,339,342,344,348,349,360,361,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,382,383,385,386,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,411,415,416,417,419,424,425,431,439,440,441,442,443,444,446,447,449,450,451,453,467,471,479],fastest:[1,6,14,17,153,207,320,321,363,455],fatal:[3,475],fault:[70,423],faulti:12,fava:390,favor:214,favorit:7,fbmc:315,fcc:[],fcm:[266,484],fdirect:221,fdotr:395,fdti:87,fe2:164,fe3:164,fe_md_boundari:200,featu:8,featur:[],fecr:385,feedback:[7,233],feel:[7,233,234,242,274,329,331,358,414],felling:412,felt:329,femtosecond:483,fene:[],fennel:[379,399],fep:[],ferguson:[6,171,470],fermi:[1,12,15,151,363,444],fermion:[9,387],ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,192,202,203,204,206,207,208,209,237,252,279,282,284,296,322,348,356,357,358,365,455,458,463,467,469,477,484,486],fewer:[1,3,11,15,16,61,242,467],fewest:3,fextern:226,feynman:276,fff:456,ffield:[378,388,422,423],ffmpeg:[3,12,190],ffplai:190,fft:[1,3,7,12,14,15,88,109,110,141,275,348,349,467],fft_inc:[12,349],fft_lib:12,fft_path:12,fftbench:[348,477],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:438,fictiti:[6,197,198,223,226,230,276,292,379,399,403,438],field1:[459,463],field2:459,field:[],fifth:[305,416],figur:[1,3,8,11,12,283,455,456],fij:382,file0:274,file1:[11,13,274,319,333,357,463,465,469],file2:[11,13,319,333,357,463,465,469],file:[],file_from:189,filen:357,filenam:[3,12,13,38,41,56,185,188,190,191,192,200,203,204,205,206,207,208,209,211,216,274,278,281,284,285,286,289,290,293,294,319,320,345,346,347,357,358,364,365,369,379,385,386,388,396,410,411,412,416,420,421,422,423,430,440,441,442,443,444,447,454,455,456,459,460,465,469,476,484,486,487,488],filennam:465,filep:[3,188,191,460,465,488],filepo:290,fill:[7,165,190,279,320,351,359,369,423,461],filter:[191,200],final_integr:8,final_integrate_respa:8,finchham:[6,147,381],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,168,185,192,201,214,215,225,228,251,274,280,288,292,354,356,358,359,379,394,399,403,410,439,441,479,484],find_custom:8,fine:[16,17,169,197,223,318,359,363,484],finer:[140,165,484],finest:348,finger:[165,187,249,461],finish:[6,11,41,211,333,345,347,348,360,362,363,446,463,484,485],finit:[],finni:[7,385,439],finvers:221,fiorin:[9,216],fire:[354,355,356,358,472],firebrick:191,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,150,153,159,161,163,164,166,167,168,172,185,188,189,190,191,192,194,195,203,204,206,207,208,209,211,214,217,228,229,234,239,249,250,251,252,274,276,281,282,283,285,290,293,296,297,305,306,308,309,310,317,318,319,320,322,326,331,333,334,340,351,356,357,358,359,362,363,364,365,368,369,370,372,374,376,378,379,385,387,388,391,392,394,395,396,398,399,403,408,409,410,412,414,416,420,422,423,430,438,440,441,442,443,444,447,451,453,454,455,456,458,459,460,463,465,467,470,471,472,475,476,479,484,485,486,488],fischer:[6,9,19,20,171,374,470],fit:[3,6,9,12,38,56,185,292,308,365,369,396,410,414,434,441,443,466,484],five:[73,151,283,357,369,411,458,472],fix:[],fix_adapt:[159,196,407],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,201,279],fix_evapor:201,fix_flux:200,fix_gcmc:[201,357],fix_gl:230,fix_gld:230,fix_grav:279,fix_id:[3,215,250,252,254,255,256,257,258,280,283],fix_modifi:[],fix_mov:[187,326],fix_nh:8,fix_npt:230,fix_nvt:[201,228],fix_poem:[3,6],fix_pour:[3,218],fix_qbmsst:9,fix_qeq:[3,378],fix_rattl:296,fix_reax_bond:422,fix_rigid:[242,368],fix_saed_vtk:294,fix_setforc:8,fix_shak:296,fix_srd:3,fix_styl:256,fix_temp_rescal:314,fixedpoint:[215,252],fixextern:226,fixid:200,fji:382,flag1:[220,361],flag2:[220,361],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,93,103,104,106,118,160,164,168,188,190,191,192,209,214,216,220,233,236,240,242,248,249,275,282,293,305,307,308,315,319,328,331,346,349,357,361,362,363,365,393,398,410,438,453,455,456,458,459,460,462,463,464,468,484],flag_buck:373,flag_coul:[373,382,403],flag_lj:[382,403],flagfld:[371,408,409],flaghi:[3,371,408,409],flaglog:[371,408,409],flagn:220,flagvf:[371,408,409],flat:[6,320,325,326,330],flavor:[2,7,12],fld:[9,325,371,408,409],flen:366,flex_press:366,flexibl:[3,6,8,166,190,203,207,216,230,253,316,323,387,443,476],flip:[3,6,217,252,327,328],floor:484,flop:12,floralwhit:191,flow:[],fluctuat:[6,64,87,215,228,229,236,239,252,256,274,275,318,320,342],fluid:[],fluid_veloc:243,flush:[3,191,475],flux:[],flv:190,fly:[7,9,12,41,190,194,200,205,218,221,293,296,321,369,476,479],fmackai:9,fmag:219,fmass:276,fmax:[356,476],fmomentum:221,fmsec:[2,191,236,237,249,252,280,293,311,312,467,478,483,485],fname:347,fno:[12,16],fnorm:[356,476],fnpt:221,fnvt:221,foce:394,fock:366,focu:296,fogarti:[9,286,423],foil:[140,274,430],fold:[306,467],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,144,145,151,153,158,161,163,165,166,171,174,175,176,177,179,180,182,183,185,188,189,190,191,194,200,201,202,203,204,205,206,207,208,209,211,216,217,218,221,222,226,228,229,230,233,235,236,237,239,242,250,252,256,257,258,269,270,272,275,276,278,281,282,283,284,286,288,290,292,293,294,296,310,311,312,313,316,317,318,319,320,322,323,331,332,336,337,338,339,342,344,346,351,353,356,357,358,363,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,423,424,425,427,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,447,449,450,451,453,455,456,458,459,460,461,463,465,466,467,470,472,473,474,479,484,485,487],foo:[4,8,11,12,188,1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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":212,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,145,153,154,158,164,165,168,170,184,186,187,188,190,191,192,193,195,196,197,199,200,201,203,207,208,209,212,213,215,216,217,218,222,225,228,229,234,236,237,238,239,240,242,247,250,252,253,256,270,271,275,276,279,280,281,282,283,285,288,290,291,293,294,308,310,315,316,317,318,321,323,325,327,331,343,346,348,349,351,352,354,355,357,359,360,361,363,366,369,371,387,408,409,414,422,423,438,439,453,454,455,458,459,461,463,465,466,467,470,472,474,475,476,477,478,483,485,486,487],"function":484,"long":[205,370,372,373,374,375,379,381,382,399,403,407,417,425],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[195,196],addforc:197,addit:[12,13],addtorqu:198,adiabat:6,adjust_dt:298,adp:364,airebo:365,alloi:385,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:199,arrai:6,aspher:[6,82,144,254,257,260,261,269],atc:[9,200],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,163,199,201,202,282,484],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:210,awpmd:[9,366],balanc:[41,211],barostat:6,basal:67,beck:367,berendsen:[280,311],between:6,binary2txt:13,bodi:[6,8,42,68,262,368],bond:[8,13,69,212,213,214,289],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:369,born:[370,381],boundari:[7,57],box:[6,58,215],brownian:371,buck:[372,373,381],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,171,374,407],chunk:[6,66,71,75,90,93,104,106,114,145,160,162,203],citat:7,class2:[21,43,172,334,375],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[325,377,450],colvar:[9,13,216],com:[74,75,146],comb3:378,comb:[285,378],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,484],compute_modifi:102,condit:7,conduct:[6,316],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:[204,205],cosin:[23,24,25,26,27,28,174],cossq:336,coul:[370,372,373,374,375,379,380,381,392,399,403,407,417,425],coupl:6,creat:213,create_atom:165,create_bond:166,create_box:167,createatom:13,creation:7,csld:312,csvr:312,cubic:401,cuda:[9,14,109,112,143,152,197,210,224,227,231,252,259,295,296,311,313,324,370,372,374,375,385,391,392,399,400,402,405,415,440,442],custom:8,cut:[49,366,372,375,379,382,387,389,399,400,407,413,417],cvff:337,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[379,399],deform:[148,149,217],delete_atom:168,delete_bond:169,delta:24,deposit:218,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488],diagnost:7,diel:380,dielectr:170,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:173,dihedral_styl:[2,171,172,174,175,176,177,178,179,180,181,182,183,184,185],dilat:80,dimens:186,dipol:[6,29,382],direct:221,discuss:6,disp:6,displac:[81,86],displace_atom:187,distribut:[7,12],document:0,dpd:383,drag:219,dreid:[6,393],drude:[6,9,150,220,221,237],dsf:[379,399],dsmc:384,dump:[6,8,188,189,190,192],dump_modifi:191,dynam:284,eam:[13,385],echo:193,edip:386,eff:[9,13,96,97,149,151,156,238,253,263,271,314,387],efield:223,eim:388,elast:6,emac:13,enforce2d:224,ensembl:7,erot:[82,83,84,85],error:3,evapor:225,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488],exp:[27,174],expand:[46,402],extend:[8,11],extern:226,fcc:274,featur:[7,8,484],fene:[45,46],fep:[9,13,87,196],field:[6,7],file:6,finit:6,fix:[2,6,8,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,484],fix_modifi:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330],flow:6,fluid:239,flux:[91,142],forc:[6,7,142,309],fourier:[30,31,175,338],freez:227,from:[6,11],futur:5,gauss:389,gaybern:390,gcmc:228,gener:[1,6,7,13],get:12,gld:229,gle:230,global:6,gpu:[9,15,367,370,372,374,375,377,379,382,383,385,389,390,392,399,400,401,402,413,415,424,425,431,440,441,442,449,450,451],gran:[326,391],granular:6,graviti:231,gromac:392,group2ndx:332,group:[88,331,484],gyrat:[89,90],h5md:[9,188,189],harmon:[32,47,48,49,176,179,325,339,416],hbond:393,heat:[91,142,232],heatconduct:432,helix:177,hertz:[391,426],histo:206,histori:[5,391],hook:391,hourglass_error:122,how:6,hybrid:[33,50,178,340,394],idealga:433,imag:[188,190],imd:233,implicit:374,improp:[8,92],improper_coeff:335,improper_styl:[2,334,336,337,338,339,340,341,342,343,344],includ:345,inclus:8,indent:234,indic:0,individu:2,induc:6,inertia:93,info:[0,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,346],input:[2,6,8],instal:11,instruct:9,integr:[6,7],integrate_tlsph:299,integrate_ulsph:300,intel:[9,16,374,390,399,440],interfac:[6,11],internal_energi:123,introduct:7,invers:221,ipi:235,ipp:13,jul:[],jump:347,kate:13,keyword:414,kim:[9,395],kokko:[9,17],kspace:[2,8,9,321],kspace_modifi:348,kspace_styl:[6,349],label:350,lammp:[0,1,2,6,7,8,11,12],langevin:[236,237,238],lattic:351,lcbop:396,librari:[6,11,12],limit:[264,313],line:[12,265,397],linear:406,lineforc:244,list:[2,398],lj1043:325,lj126:325,lj93:325,lj96:400,lmp2arc:13,lmp2cfg:13,lmp2vmd:13,local:[6,65,68,69,79,92,108,115],log:352,lubric:408,lubricateu:409,make:12,mass:353,math:484,matlab:13,meam:[9,410,411,412],measur:1,meso:[245,246],meso_:99,meso_rho:100,meso_t:101,messag:3,micelle2d:13,mie:413,min_modifi:354,min_styl:355,minim:[8,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,356],misc:9,mod:[320,443],model:[6,7],modifi:8,molecul:357,molfil:[9,188,192],moltempl:13,momentum:[240,248],morri:437,mors:[51,393,415],move:249,move_tri_surf:301,movi:[188,190],mpi:11,msd:[103,104,105],msi2lmp:13,msm:[370,372,374,379,399],msst:250,multi:[6,7,179],multipl:6,nb3b:416,neb:[251,358],neigh_modifi:359,neighbor:360,nemd:6,newton:361,next:362,nharmon:180,noforc:[261,266],non:[6,7],none:[34,52,181,341,418],nongauss:105,nonlinear:53,nph:[252,253,254,255,293],nphug:256,npt:[252,253,257,258,293],nve:[259,260,261,262,263,264,265,266,267,268,293],nvt:[252,253,269,270,271,272,293],omega:106,omp:[9,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,43,45,46,47,48,49,51,53,54,56,171,172,174,175,176,177,179,180,182,183,185,231,252,254,255,256,257,258,259,267,269,270,272,285,334,336,337,338,339,342,344,364,365,367,370,371,372,373,374,375,377,378,379,380,382,383,385,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,411,412,415,416,417,419,424,425,431,440,441,442,443,444,446,447,449,450,451],onewai:273,open:7,oper:484,opl:182,opt:[19,374,385,399,403,415],optim:1,option:[6,8,12],orient:274,orthogon:6,other:6,output:[6,7,8,12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330],overlai:394,overview:11,packag:[1,9,12,14,15,16,17,18,19,363],pair:[6,107,108],pair_coeff:376,pair_modifi:414,pair_styl:[2,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,450,451],pair_writ:448,pairwis:8,parallel:11,paramet:6,pars:2,partial:152,particl:[6,7,42],partit:452,past:5,per:6,perform:[1,10],peri:419,period:25,phonon:[9,13,275],pimd:276,piston:327,planeforc:277,plastic:111,plastic_strain:124,plastic_strain_r:125,pmb:419,poem:[9,278],point:284,polariz:6,poli:[371,408,409],polym:13,polymorph:420,post:7,potenti:[2,6,8],pour:279,pppm:6,prd:453,pre:7,press:280,pressur:112,previou:12,print:[281,454],problem:[3,4],process:[6,7],processor:455,profil:153,properti:[6,113,114,115,282],pymol_aspher:13,python:[9,11,13,456],qbmsst:283,qeq:[284,285,286],qmmm:[9,287],qtb:[9,288],quadrat:183,quantiti:6,quartic:[35,54],quip:421,quit:457,ramp:154,rattl:296,rdf:116,read_data:458,read_dump:459,read_restart:460,reax:[9,13,286,289,290,422,423],reaxc:9,rebo:365,recent:291,reduc:117,refer:484,reflect:328,region:[8,117,155,156,329,461,484],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,182,183,184,185,186,187,188,189,190,191,192,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,227,228,229,230,231,232,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,288,289,290,291,293,294,295,297,298,299,300,301,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,342,343,344,345,346,347,348,349,351,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,463,464,465,466,467,468,470,471,472,473,474,475,476,477,478,480,481,482,484,485,486,487,488],relax:215,replic:462,replica:[6,7],report:3,requir:12,rerun:463,rescal:[313,314],reset:222,reset_timestep:464,resquar:424,restart2data:13,restart:[6,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,465],restrain:292,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488],rho:126,rhosum:435,rigid:[6,83,98,242,293],ring:342,rotat:157,rule:2,run:[6,11,12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,466],run_styl:467,scalabl:10,scalar:6,screen:12,script:[2,6,8,11],sdk:[36,425],self:307,serial:11,set:[6,468],setforc:295,setvel:302,shake:296,share:[11,12],shell:[6,469],shield:284,shift:[26,27,48,49,174],simpl:31,simul:6,size:6,slater:284,slice:119,sllod:[270,271],small:293,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,297,298,299,300,301,302,304,426,427,428,429],smooth:[405,406],sna:140,snad:140,snap:430,snapshot:6,snav:140,soft:[407,431],solver:2,sourc:7,spatial:[207,208],spc:6,speci:290,special:[7,414,484],special_bond:470,sph:[9,432,433,434,435,436,437],sphere:[84,85,158,208,242,255,258,267,272],spheric:6,spline:[411,412],spring:[305,306,307,318],squar:28,srd:[308,330],srp:438,standard:9,start:[12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330],state:310,stationari:246,stop:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330],store:[309,310],strategi:1,streitz:379,stress:[141,142],structur:2,style:[1,2,6,8],submit:8,suffix:471,summari:6,swap:[201,214],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488],system:6,tabl:[0,6,38,56,185,441,442],tad:472,taitwat:[436,437],talli:142,temp:[143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,311,312,313,314],temper:473,temperatur:6,tersoff:[442,443,444],test:11,tfmc:315,thermal:[6,316],thermo:[6,474],thermo_modifi:475,thermo_styl:476,thermodynam:[6,8],thermostat:6,thole:445,time:[6,209],timer:477,timestep:478,tip3p:6,tip4p:[6,379,399,403,407],tip:12,tlsph:427,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:319,tool:[12,13],torqu:160,transform:221,tri:[268,446],tri_surfac:428,triangle_mesh_vertic:134,tric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\ No newline at end of file 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248,249,250,252,257,258,264,269,270,272,275,279,283,291,293,296,304,309,311,312,313,315,316,317,318,319,323,325,327,331,334,335,340,347,353,354,356,357,359,361,362,363,364,365,369,376,378,385,386,387,388,394,395,396,407,408,409,410,411,412,413,417,421,423,424,431,441,443,444,445,448,454,456,458,459,460,461,462,464,465,467,469,471,473,476,477,480,484,485,486,487,488,489],afterrun:467,afterward:3,afterword:41,ag1:164,ag2:164,again:[6,11,12,16,17,62,140,145,151,159,188,191,217,232,279,334,347,358,408,409,454,456,457,459,461,466,473,475,485,487],against:[11,12,13,64,218,358,423,424],aggreg:[6,12,65,68,69,79,92,108,115,232,248,291,293,306,454,486],aggress:[232,473],agilio:[9,13],agre:[3,8,185,356,365,396,424],agreement:[5,7],ahd:393,ahead:327,aidan:[0,5,7,9,13,351],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:190,akohlmei:[7,9,13,192,233],aktulga:[7,9,286,424],al2o3_001:[118,294],al3:164,ala:239,alain:9,alat:[274,410],alb:[421,443,445],albeit:292,albert:9,alchem:[87,159],alcohol:323,alcu:[364,369],alcu_eam:421,alderton:382,alejandr:[252,253],alessandro:13,algebra:413,algorithm:[0,1,6,7,8,9,41,61,191,200,211,214,217,239,241,242,264,276,293,296,315,316,320,323,328,354,355,356,360,363,387,409,413,428,430,454,456,473],alia:[12,16],alias:[1,349],aliceblu:191,align:[6,12,29,41,71,167,185,207,211,234,351,459,462,480],alkali:387,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,153,158,159,160,161,162,163,164,165,166,167,168,169,171,173,178,184,185,188,189,190,191,192,194,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,245,247,248,250,252,253,254,255,256,257,258,259,260,261,262,263,264,265,267,268,269,270,271,272,273,274,275,276,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,304,305,307,308,309,310,311,312,315,316,317,318,319,320,321,322,323,325,326,327,328,329,330,331,332,333,334,335,338,343,346,347,348,349,350,351,353,356,357,358,359,360,362,363,364,365,366,368,369,370,372,373,374,375,376,378,379,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,403,407,408,409,410,411,412,413,414,415,416,417,418,420,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,452,453,454,456,457,458,459,460,461,462,463,464,466,467,468,469,470,471,472,473,474,476,477,478,480,484,485,486,487,488,489],allen:[29,87,382,390],allentildeslei:87,allign:3,allindex:332,alloc:[3,5,6,8,9,11,12,60,226,322,357,359,363,419,424,459,467],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,142,144,145,158,163,164,165,167,173,184,185,188,190,191,192,194,195,197,199,200,201,203,204,205,206,207,208,209,211,213,214,215,216,217,218,222,223,226,228,229,230,231,233,236,239,242,243,247,249,252,253,274,278,280,281,282,283,287,293,294,296,297,299,300,304,308,315,316,317,318,320,321,322,323,324,325,331,333,335,343,348,349,351,356,357,358,359,362,363,366,369,370,371,372,373,374,379,385,387,391,392,393,394,399,403,408,409,413,415,421,424,425,428,430,439,449,451,454,457,459,461,462,463,464,465,466,469,471,472,473,476,477,485,486],almost:[2,3,12,60,234,283,320,349,360,363,439],alo:379,alon:[6,7,214,289,423,424,457],alond:13,along:[6,8,9,12,29,40,87,118,164,165,187,188,190,214,234,239,240,244,249,251,283,293,296,297,301,305,306,315,319,320,326,329,331,351,354,355,356,358,379,382,391,394,397,399,403,410,423,424,442,459,462,469,470,485],alonso:[411,412],alpha:[6,12,51,195,239,275,283,288,356,364,367,370,379,383,385,386,388,393,398,399,410,416,420,444,446,477,480],alpha_:446,alpha_c:407,alpha_i:[431,446],alpha_ialpha_j:446,alpha_lj:407,alphabet:[2,3,22,37,44,55,63,173,184,194,335,343,357,376,440,459],alphanumer:[3,63,194,282,290,333,357,485],alreadi:[3,7,8,9,12,16,17,18,42,165,166,168,189,199,203,207,208,211,213,217,243,281,283,308,331,357,358,383,392,394,401,409,439,449,452,455,459,460,464,469,485],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,149,151,152,153,154,155,157,158,159,160,161,162,163,165,166,167,168,169,171,173,184,185,186,188,189,190,191,192,194,195,196,197,199,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,223,226,227,228,229,230,232,233,236,237,238,239,249,250,252,253,254,255,256,257,258,263,266,267,269,270,271,272,274,275,276,278,279,280,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,301,302,305,306,308,311,312,313,3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335,343,358,376,440],client:[233,235],climb:[251,358,473],clinic:[7,13],clo:[154,187,486],clock:[12,454,473],clockwis:326,close:[3,6,11,12,13,39,41,67,141,168,188,213,214,215,230,237,239,252,270,293,296,326,329,347,349,352,354,355,358,363,365,369,379,380,410,415,427,429,445,463,469,480,482],closer:[3,41,116,163,187,188,211,215,219,317,358],closest:[213,274,293,323,390,425,439,449],cloud:480,clovertown:18,clsuter:72,clump1:[278,293],clump2:[278,293],clump3:[278,293],clump:293,cluster:[],clutter:[3,9],cmap:459,cmatrix:230,cmax:410,cmd:[11,12,276,470],cmin:410,cmm:[],cn1:204,cn2:204,cna:[],cnn:204,cnr:[9,13],cnt:[394,463],co2:[40,164,296,357],coars:[7,9,29,36,40,54,177,278,293,308,392,426,471],coarser:[349,485],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,171,172,173,178,334,335,340,376,394,398,415,428,430,432,459,461],coeffcient:459,coeffici:[],coefficienct:383,coefficient0:385,coefficient1:385,coeffieci:[6,367],coeffincientn:385,coexist:[9,228,387],cohes:[6,388,410],coincid:[122,329,374,408,409,454],colberg:189,cold:[6,150,228,232,359,480],coldest:316,coleman8:9,coleman:[9,118,164,294],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,145,153,160,162,165,188,191,203,216,242,248,278,288,291,293,331,348,357,359,377,397,459,466,472,478,489],collid:[222,308,330],colliex:164,collinear:[3,278],collis:[3,239,308,326,330,384,391,452],colllis:308,colloid:[],colombo:39,colon:[192,331,460],color1:191,color2:191,color:[3,9,41,188,190,191,211,229,283,288],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,145,153,160,162,163,164,185,188,191,194,202,203,204,206,207,208,209,242,249,250,283,293,309,310,320,330,389,393,423,424,460,474,476,485],colvar:[],colvarmodul:12,com:[],comamnd:217,comand:[214,461],comannd:363,comb3:[],comb:[],comb_1:285,comb_2:285,combiant:380,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,144,158,188,190,200,206,233,242,252,276,282,312,321,329,332,334,348,349,351,355,363,377,379,380,387,388,394,406,407,431,441,443,445,448,451,462,467,472,480,485],come:[],comfort:[12,13],comm:[0,3,12,61,73,189,233,235,236,349,358,363,383,415,420,442],comm_modifi:[],comm_modift:61,comm_styl:[],command:[],comment:[2,7,11,12,38,56,171,185,188,237,293,320,357,358,364,385,386,388,398,410,417,424,431,441,442,443,444,445,448,456,457,459,480,485],commerci:7,commmand:[3,6,12,59,107,271,453,454,456,473,488],common:[],commonli:[3,6,12,17,25,57,59,105,167,188,190,192,344,392,401,431,443,445,459,462,471],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,169,190,191,211,212,213,215,216,217,233,235,239,241,242,243,252,275,282,284,285,286,293,308,320,331,346,348,359,360,361,363,384,419,456,457,461,468,469,485,487,489],communc:348,comp:[7,189,235,236,296,349,358,387,415,420,425,438,442,444],compact:[63,194,376,440],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,148,163,164,173,184,191,221,284,331,333,348,349,356,358,410,454,473,474,480,484],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,172,173,184,334,335,343,375,440],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,176,188,192,196,202,203,204,206,207,208,209,211,275,287,312,315,322,325,328,348,363,395,413,415,442,456,457,485],compens:[6,212,213,291,359,387],compet:319,competit:349,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,163,188,189,190,192,233,319,349,363,413,459,460,464,485],compl:17,complain:[12,17],complement:410,complementari:[7,379,399],complet:[3,6,9,12,15,41,59,71,191,207,211,216,242,276,279,282,308,319,321,333,347,358,363,388,428,430,447,454,459,464,467,471,473,476,480,485],complex:[6,8,11,12,13,25,40,42,62,140,142,153,165,166,239,304,329,346,358,387,413,442,457,459,462,485],compli:[315,319],complic:[6,7,9,12,13,201,228,457],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,160,161,162,188,190,191,197,198,202,203,204,205,206,207,208,209,210,214,215,217,218,223,226,231,235,236,239,242,244,248,249,251,252,253,256,257,258,269,270,272,273,275,276,277,280,291,293,295,296,297,301,302,305,308,311,312,313,315,322,323,328,329,330,348,351,355,356,357,358,363,383,387,391,408,409,428,430,431,459,460,469,477,485,486],componenet:6,composit:[6,201,239,385],compound:[378,387,388,448],compres:[71,114,203],compress:[3,59,71,114,168,188,190,191,203,217,250,256,280,283],compris:[40,329,397,425,447],compton:[118,164],comptu:3,compuat:349,comput:[],computation:[3,6,212,213,320,369],computational:480,compute_arrai:8,compute_fep:[196,407],compute_group_group:228,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,294],compute_scalar:8,compute_temp:8,compute_ti:196,compute_vector:8,compute_xrd:164,concaten:[2,3,488],concav:329,concentr:385,concept:[6,145,155,203,468],conceptu:[3,6,71,153,215,217,358,379,394,410,464],concern:[6,73,87,189,229],concis:[11,319],conclud:12,concret:8,concurr:[9,16,349,485],conden:[320,443,445],condens:[6,147,320,365,381,385,399,448],condit:[],conducit:6,conduct:[],cone:462,confer:413,confid:[3,473],config:[12,188,456],configfil:216,configur:[1,2,6,12,15,17,38,59,122,167,185,187,188,190,194,215,216,217,218,222,228,235,236,264,276,284,319,346,356,358,365,369,386,410,413,441,443,445,448,454,459,461,462,473],confin:[459,473],conflict:[3,12,40,415,457],conform:[3,6,13,59,214,215,251,292,297,319,342,358,387,471],confus:[3,448],conjuct:383,conjug:[7,8,236,355,387,423,424],conjunct:[6,7,71,86,87,114,148,153,159,165,169,191,195,196,236,239,243,264,279,280,284,285,286,288,293,308,316,323,328,348,349,358,370,372,376,379,383,387,393,399,415,418,426,446,459,462,466,480,489],connect:[3,6,87,150,168,214,233,278,293,296,305,358,380,391,439,445,456,457,463,480],conput:3,consecut:[3,11,12,39,71,165,191,195,196,218,233,234,379,399,403,454,460,462],consequ:[1,6,201,320,398,473],conserv:[3,194,201,214,221,222,229,232,236,238,239,243,248,250,252,264,293,296,311,312,316,323,324,328,358,382,383,391,405,468,473],consid:[6,9,70,71,78,87,115,147,150,151,168,188,191,195,196,202,204,207,211,213,214,218,240,253,275,293,315,316,319,320,323,349,376,387,394,424,425,439,454,455,457,460,461,462,464,467,469,477,480,485],consider:[6,8,236,237,311,312,313,363,468],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,145,148,150,165,177,187,192,197,198,203,217,218,221,223,226,229,236,237,238,249,252,254,255,256,257,258,259,260,262,263,264,265,267,268,269,270,271,272,280,283,288,290,292,293,311,312,313,314,324,348,349,351,357,358,363,365,369,371,377,379,387,390,394,408,409,410,413,415,425,428,430,442,449,457,459,460,462,463,464,471,480,485],consistent_fe_initi:200,consit:293,constant:[],constitu:[3,6,242,293,325,329,377,425],constitut:[428,430],constrain:[3,6,8,143,144,145,146,148,151,152,153,154,155,157,158,194,203,218,228,229,234,242,246,278,279,291,293,296,306,316,323,356,357,387,464,471,480],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,118,140,164,215,252,275,292,329,359,363,382,413,415,439,441,442,462,463,478,485],constructor:8,consult:424,consum:[1,288,419,485],consumpt:346,contact:[],contact_stiff:[427,429],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,145,153,163,164,165,167,171,173,184,185,188,190,191,192,194,195,196,200,202,203,204,206,207,208,209,211,216,218,223,230,234,235,236,237,239,250,264,274,275,278,279,281,283,286,290,293,294,298,308,315,319,320,329,330,333,347,349,357,358,361,362,364,365,366,369,378,379,382,385,386,387,394,395,410,413,417,421,422,423,424,431,441,442,443,444,445,446,448,454,455,456,457,459,460,461,462,464,466,468,471,473,476,477,480,485,487,489],content:[12,18,424,475,477],context:[3,6,8,12,17,117,191,212,213,218,278,290,324,355,451,459,466,475,484,485,486],contibut:70,contigu:456,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,161,191,194,195,196,201,203,204,205,206,207,208,209,211,214,215,216,217,218,228,229,230,232,233,234,236,237,238,244,249,250,252,254,255,256,257,258,269,270,271,272,277,279,282,283,293,294,297,307,308,310,317,318,320,326,329,333,347,362,363,369,383,384,401,404,423,424,425,428,430,444,454,457,459,461,462,467,473,476,477,485,487],continuum:[6,7,9,200,320,428,430],contour_integr:200,contract:[59,215,217,252,280,293],contradictori:3,contrain:296,contraint:264,contrari:[230,237],contrast:[1,6,42,55,64,147,150,217,331,428,430,451,488],contrib:320,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,196,201,202,203,204,206,207,208,209,215,228,236,239,242,243,247,253,270,271,278,279,287,290,293,294,296,322,348,356,358,366,383,384,385,387,394,408,409,413,415,423,424,471,477,480],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,174,188,190,194,200,201,211,215,216,217,232,233,236,237,252,254,255,256,257,258,280,285,293,299,300,311,312,313,320,324,346,348,360,387,390,413,423,424,427,429,441,445,454,456,468,474,475],control_typ:200,controlfil:424,convect:91,conveni:[6,12,29,188,192,209,294,351,431,485],convent:[3,8,9,29,176,183,184,191,292,305,332,385,387,485],converg:[3,6,41,88,188,190,192,197,211,214,215,223,226,256,283,285,288,292,296,354,355,356,358,378,379,399,454,466,473],convers:[3,8,140,190,191,201,204,280,348,379,380,381,387,399,403,407,418,457,473,484],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,165,172,188,190,191,209,250,331,334,336,339,342,351,358,364,385,413,443,445,452,457,459,460,461,466,476,480,484,485,487,489],convex:329,convinc:[7,12],cook:9,cooki:7,cool:[7,155,232,291],cooordin:188,cooper:[5,7],coord123:114,coord1:[3,114,203,207,208],coord2:[3,114,203,207,208],coord3:[3,114,203,207,208],coord:[],coordiat:356,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,148,154,160,162,163,165,169,187,188,189,190,191,192,194,197,202,203,206,207,208,211,212,213,214,215,216,217,218,221,223,224,226,228,231,232,233,234,235,236,237,249,251,252,254,255,257,258,270,273,274,275,278,279,280,290,291,293,295,296,297,302,305,306,307,308,310,318,319,320,327,328,330,331,351,356,357,358,363,364,365,368,386,454,459,460,462,464,467,469,473,480,485,486],coordn:[114,203],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,190,320,358,376,423,457],copper:452,coproccesor:16,coprocessor:[1,4,7,9,16,17,363,472],coproprocessor:17,copy_arrai:8,copyright:[7,8,278],coral:191,core:[],core_shel:147,coreshel:[6,9,372,379,381],cornel:[6,171,471],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,190,329,330,351,447,459],cornflowerblu:191,cornsilk:191,corpor:16,corr:378,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,147,152,159,190,217,228,230,236,252,253,270,278,280,283,319,325,329,348,358,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,448,450,451,452,459,474,477,480],correction_max_iter:200,correctli:[3,8,9,11,17,71,81,102,103,143,144,146,148,150,151,152,153,154,157,158,161,188,191,197,218,223,226,237,246,252,253,286,293,296,305,307,326,329,358,359,363,381,409,413,456,457,459,469,484,486],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,143,144,152,159,164,171,172,173,174,175,176,177,179,180,182,183,185,188,190,191,195,196,197,203,205,206,207,208,210,213,215,217,224,226,227,231,236,239,240,248,249,250,252,254,255,256,257,258,259,264,267,269,270,272,275,276,280,285,293,295,296,311,313,315,324,325,326,328,329,330,332,334,335,336,337,338,339,342,344,349,353,355,357,358,364,365,367,370,371,372,373,374,375,376,377,378,379,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,413,415,416,417,418,420,421,423,424,425,426,431,432,441,442,443,444,445,447,448,450,451,452,454,456,457,459,460,462,472,473,474,476,477,480,485],correspondingli:[408,409,468],cosin:[],cosineshift:27,cosmo:[230,235],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,164,190,191,203,207,208,211,212,213,225,252,285,320,348,349,361,379,399,403,413,415,441,456,468],costheta0:[441,443,445,448],costheta:421,costli:[11,88,230,359],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,145,155,160,162,178,188,190,191,195,196,203,204,207,211,217,226,235,282,283,284,288,291,293,295,308,309,315,319,320,321,325,329,331,333,340,345,347,354,356,359,363,366,389,393,394,423,424,455,456,457,459,461,463,466,467,475,480,485,486],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,116,141,166,170,284,286,321,348,349,356,363,370,372,373,374,375,378,379,380,381,382,387,391,392,394,399,403,407,415,418,423,424,426,440,445,446,448,451,464,471,477,480,484],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,114,116,117,153,163,169,197,198,201,203,206,207,208,210,211,218,223,225,228,234,252,264,279,296,311,312,329,349,356,357,358,360,363,389,393,415,477,485],counter:[326,454,465,467,473],counteract:228,counterbal:232,counterpart:[188,293,454],counterproduct:18,coupl:[],courant:298,cours:[3,8,126,128,159,188,195,196,229,292,305,319,325,327,328,330,331,349,408,432,456,459,472,480,485,487],courtesi:351,coval:[6,29,387,410,480],covari:230,cover:[6,71,185,191,200,239,387,397,447],coverag:[71,207],cpc:235,cpp:[1,3,6,8,9,11,12,13,87,188,195,196,226,296],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,191,194,205,221,237,321,346,349,363,376,440,454,472,473,476,477,478,485],cpuremain:477,cr2:164,cr3:164,crack:[4,359],crada:[5,7],crai:[5,7,13,18,188],crash:[3,12,359,480],craympi:363,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:200,create_faceset:200,create_group:189,create_nodeset:200,createatom:[],creation:[],crimson:191,critchlei:278,criteria:[3,116,166,190,191,212,213,214,247,356,420,447,461,464,485],criterion:[12,41,121,163,165,168,201,211,214,228,264,285,298,326,331,356,358,378,387,391,464,473,474],criterioni:473,critic:[6,48,49,250,315,320,356],cross:[3,12,22,71,89,144,173,188,190,202,207,213,217,249,251,270,293,301,305,307,316,323,335,351,358,374,383,384,385,392,393,394,399,401,403,421,426,428,430,443,445,452,459,463,469,487],crossov:1,crossterm:459,crozier:[0,7,13],crucial:283,crystal:[4,6,13,73,274,275,318,351,359,463,477,480],crystallin:[6,275,351,444,480],crystallis:315,crystallogr:[118,164],crystallograph:[351,477],crystallographi:[118,164,351],cs1:164,cs_chunk:6,cs_im:[40,459],cs_re:[40,459],csanyi:[140,422,431],cscl:410,csequ:6,csh:[11,12,376],cshrc:[11,12],csic:[386,441,443,445,448],csinfo:6,csisi:[386,441,443,445,448],csld:[],cst:385,cstherm:6,cstyle:456,csvr:[],ctcm:[364,385],ctemp_cor:221,cterm:297,ctr:9,ctype:11,cu1:164,cu2:164,cu3au:410,cube:[6,41,163,168,211,221,329,351,480],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:369,cummul:[3,6,209,212,213,214,216,225,230,236,238,308,311,312,313,314,316,323,393,477],cumul:[6,201,203,206,207,208,222,228,236,250,252,256,264,293,294,358],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,145,153,155,161,163,166,169,188,189,190,191,192,195,196,200,203,207,208,209,211,212,213,214,215,216,217,218,222,223,226,228,230,233,234,236,242,249,252,253,257,258,264,269,270,272,278,284,285,287,290,291,292,293,296,297,298,299,300,301,302,304,306,307,308,311,312,313,319,320,323,324,325,326,327,328,330,331,333,346,347,348,349,352,353,355,356,357,358,363,369,376,378,382,385,387,388,391,394,395,398,408,409,410,411,412,415,421,423,424,427,428,429,430,432,443,445,446,449,454,455,456,457,459,460,461,462,463,465,466,467,469,471,473,474,476,477,485,486,487,488,489],curv:[6,165,228,275],curvatur:[390,425,452],custom:[],cut0:457,cut1:468,cut2:468,cut:[],cuthi:[274,286],cutinn:[371,408,409],cutlo:[274,286],cutmax:421,cutoff1:[375,382,399,403,407,418,426],cutoff2:[370,372,373,375,381,382,399,403,407,418,426],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,163,166,168,213,214,219,274,283,284,286,288,290,293,308,321,325,329,331,346,348,349,356,359,360,361,363,364,365,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,383,384,385,386,387,388,389,390,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,431,432,433,434,435,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,457,461,464,468,480,485],cutoffa:386,cutoffc:386,cuu3:385,cval:164,cvd:315,cvel:297,cvff:[],cwiggl:[3,249,325,328,330,485],cyan:[2,190,191],cycl:[3,228,250,252,253,256],cyclic:[3,185],cygwin:12,cylind:[3,4,190,234,279,326,329,462],cylindr:[6,234,305,326],cypress:363,cyrot:369,cyrstal:275,d3q15:239,d3q19:239,d_double_doubl:15,d_e:320,d_flag2:282,d_flag:282,d_name:[113,188,282,310,469],d_single_doubl:15,d_single_singl:15,d_sx:282,d_sy:282,d_sz:282,daan:318,dai:12,daili:12,daivi:270,damag:[],dammak:288,damp:[3,6,194,199,236,237,238,243,252,253,256,280,283,288,293,311,312,324,326,327,355,356,358,370,372,374,379,382,387,391,399,407,418,426,440,446,473,480],damp_com:237,damp_drud:237,dampen:[293,480],dampflag:[326,391],dan:17,danger:[3,12,228,331,383,477],dangl:168,daniel:9,darden:[349,382],darkblu:191,darkcyan:191,darken:190,darkgoldenrod:191,darkgrai:191,darkgreen:191,darkkhaki:191,darkmagenta:191,darkolivegreen:191,darkorang:191,darkorchid:191,darkr:191,darksalmon:191,darkseagreen:191,darkslateblu:191,darkslategrai:191,darkturquois:191,darkviolet:191,dasgupta:284,dash:[391,476],dat:[6,91,185,200,455],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,294],dataset:294,datatyp:3,date:[0,6,12,13,423,424,485],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,188,204],davi:325,david:[9,19,348,349,443,445],daw:[385,421],dbg:14,dcd:[3,6,7,188,189,190,191,192,276,460,464],ddim:187,deactiv:407,dealt:235,debug:[6,7,11,12,13,14,17,118,122,164,165,276,281,346,348,363,395,415,449,457,458,461,466,469,476,485],deby:[],decai:[379,452],decid:[3,6,12,16,71,249,282,293,321,474],decipher:351,declar:189,declin:308,decod:190,decompos:[87,431],decomposit:[3,5,7,18,62,200,276],decoupl:[6,480],decreas:[3,188,197,198,205,214,217,223,226,228,236,319,348],decrement:297,deepli:345,deeppink:191,deepskyblu:191,def:[12,13,457],defaul:61,defect:[6,70,163,413],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,171,172,173,174,175,176,177,179,180,182,183,184,185,186,187,188,189,190,191,194,195,196,197,198,199,200,201,202,203,204,206,207,208,209,210,211,212,213,214,215,217,218,221,222,223,226,227,228,231,234,235,236,237,238,239,247,249,251,252,253,254,255,256,257,258,260,261,262,265,267,268,269,270,271,272,274,275,276,278,279,280,282,284,286,291,293,294,295,296,298,302,306,308,310,311,312,313,314,316,317,318,320,322,323,325,326,327,328,329,330,331,333,334,335,336,337,338,339,342,343,344,346,348,349,351,353,355,356,357,358,359,360,361,362,363,365,366,367,368,370,371,372,373,374,375,376,377,379,380,382,383,384,386,387,389,390,391,392,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,413,414,415,416,417,418,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,456,457,459,460,462,463,464,465,468,469,470,471,473,474,476,477,480,481,482,483,484,485,486],definit:[2,3,6,8,12,13,78,80,116,140,191,203,204,205,206,207,208,209,217,234,256,294,310,322,325,328,330,332,343,346,357,366,369,377,387,397,421,428,430,431,447,457,459,461,468,470,484,485],defint:477,deform:[],deg2theta:164,deg:480,degener:[3,278],degrad:[8,18,275,349,468],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,164,165,171,172,175,176,183,185,187,190,203,214,221,228,230,231,236,237,242,252,253,256,257,258,269,270,272,276,278,292,293,296,311,312,313,318,334,336,339,342,344,356,382,385,393,469,477,480,486],degress:[145,203],del:473,delai:[3,6,12,359,384,477],deleg:394,delet:[2,3,7,8,12,54,57,60,63,163,168,169,194,203,204,206,207,208,209,212,214,225,228,252,294,311,312,331,333,347,357,359,362,415,459,460,462,470,471,476,481,483,485,486],delete_atom:[],delete_bond:[],delete_el:200,deli:187,delimit:[457,485],deloc:[253,387],delr:410,delt_lo:473,delta:[],delta_1:369,delta_3:369,delta_7:369,delta_conf:3,delta_ij:[410,421],delta_mu:3,delta_pi:369,delta_r:421,delta_sigma:369,delx:187,delz:187,demand:288,demo:11,demon:273,demonstr:[283,410],den:279,dendrim:393,denniston:[9,239,241,242,243,275],denomin:[7,170],denot:[118,221,237,275,286,288,379,392,394,424,428,430],dens:[71,214,387],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,151,163,165,195,196,200,203,207,208,211,217,226,239,242,245,246,275,279,280,284,320,325,351,353,357,364,369,385,410,411,412,421,425,434,436,437,438,459,468,469,477,484],density_continu:430,density_summ:430,depart:[0,7],departur:[250,283],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,143,148,152,153,159,165,166,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,190,191,194,195,196,197,198,201,203,205,206,207,209,210,211,213,215,217,223,224,227,230,231,232,234,236,237,239,241,242,249,252,254,255,256,257,258,259,267,269,270,272,274,285,288,290,293,295,296,302,308,311,312,313,315,317,319,320,322,324,325,328,329,330,331,333,334,335,336,337,338,339,342,344,349,351,356,357,359,360,361,363,364,365,367,368,369,370,371,372,373,374,375,376,377,378,379,380,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,413,414,416,417,418,420,421,423,424,425,426,431,432,440,441,442,443,444,445,446,447,448,450,451,452,454,456,459,461,462,465,469,471,473,476,477,479,485,486],dependend:6,depflag:12,dephas:[454,473],depos:218,deposit:[],deprec:[284,423],depth:[51,144,190,320,390,425],dequidt:9,der:[87,107,377,378,407,423,424,451,480],deriv:[6,7,8,9,38,56,63,87,140,159,185,204,215,217,228,236,249,252,254,255,256,257,258,274,280,284,288,317,318,320,325,326,329,355,357,365,369,377,382,387,388,392,401,405,406,410,413,423,424,440,442,451,480],derjagin:451,derlet:274,descend:191,descent:[7,355],descib:[40,284],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,144,145,149,150,153,156,158,159,163,164,165,167,168,177,182,185,188,189,194,195,196,203,204,205,206,207,208,209,211,214,215,216,217,218,220,221,229,230,233,234,235,236,237,238,239,241,242,243,247,251,252,253,256,263,271,274,276,281,282,283,284,285,286,293,297,305,308,309,310,311,312,313,314,315,316,317,318,323,325,326,328,333,348,349,351,354,355,356,357,358,362,365,366,368,370,371,372,374,375,376,377,378,379,382,385,387,388,390,391,392,394,399,400,401,402,403,404,405,406,407,408,409,410,413,414,420,421,422,423,424,425,426,431,432,439,440,441,442,443,444,445,446,448,450,451,452,454,456,457,459,460,462,463,469,472,473,476,485,486,487],descript:[],descriptor:[140,188,395],deserno:349,design:[0,3,6,7,8,9,11,13,14,15,17,118,147,150,164,200,214,220,221,252,253,274,275,294,315,320,366,367,368,371,374,379,381,387,407,408,409,411,412,421,424,442,468],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,112,117,141,147,165,178,187,203,209,215,217,226,228,229,236,237,238,242,252,270,278,279,280,281,284,288,293,296,308,311,312,313,314,319,326,340,345,348,349,351,354,356,357,358,383,385,393,408,409,441,443,445,455,456,457,459,463,468,473,474,476,477,485,486,487],desk:7,desktop:[4,6,7,10,12,190],despit:480,destabil:369,destre:342,destroi:[11,39,212,213],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,143,144,145,148,158,159,160,162,165,166,169,170,173,184,188,190,191,194,195,196,200,203,204,205,206,207,209,211,213,214,215,216,217,218,226,228,229,230,231,233,234,236,238,239,243,249,250,251,252,253,254,255,256,257,258,262,264,269,270,271,272,275,278,279,280,282,283,285,286,287,293,296,308,311,312,313,314,315,316,318,319,320,321,322,323,324,331,333,335,343,348,349,352,356,357,359,360,363,364,365,366,368,369,371,373,374,375,376,377,378,379,382,383,387,388,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,410,414,415,420,423,424,425,431,432,440,447,450,451,457,459,460,461,462,464,465,468,469,471,474,477,478,485,486,489],detect:[2,3,12,61,63,86,227,279,319,358,378,393,398,454,456,459,470,473,485],determ:363,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,153,154,163,164,165,187,188,190,191,192,193,197,198,199,202,203,204,205,206,207,208,209,210,211,215,217,218,221,223,228,231,232,234,236,237,242,247,249,250,252,257,258,269,270,272,274,276,280,283,290,291,292,293,294,295,298,300,302,308,311,312,313,315,321,322,325,326,327,328,329,330,331,343,348,349,351,357,359,360,363,365,366,373,378,382,384,385,389,391,394,395,403,410,413,415,424,425,439,442,446,451,456,459,460,462,464,466,469,473,475,476,478,484,485,486],detil:108,devan:[9,426],devanathan:445,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,233,256,278,283,284,287,365,369,387,412,413,448,461],devemi:9,deviat:[250,256,274,389],deviator:9,devic:[1,3,12,15,17,233,363],device_typ:363,devin:[285,378],devis:412,dfactor:190,dff:480,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,349],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,287,413],dhi:[59,187,217,279],dhug:[250,283],dhugoniot:[250,283],dia:410,diagnost:[],diagon:[3,6,83,140,141,142,215,252,280,293,323,428,430],diagonalstyl:431,diagram:[41,118,164,184,211,276],diallo:393,diam:[190,191,279,357],diamet:[3,6,40,113,165,188,190,191,195,196,236,279,293,308,324,326,357,377,390,391,397,401,425,447,451,459,460,469],diamond:[351,387,410],diamter:[40,279],dick:6,dicsuss:249,dictat:[201,250],did:[3,12,356,383,384,385,391,415,443,445,467],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,161,322,348],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,143,144,145,146,148,151,152,153,154,155,157,158,159,165,166,168,173,184,185,187,188,190,191,194,196,199,201,203,206,211,212,213,214,215,216,217,221,227,228,229,230,231,232,233,236,237,239,249,252,253,254,255,257,258,260,262,265,267,268,269,272,274,276,278,280,283,284,285,288,291,293,296,297,305,306,308,311,312,313,316,317,318,320,323,324,325,326,329,333,334,343,345,347,348,349,351,352,354,355,357,358,360,361,362,363,364,365,369,373,374,376,377,378,383,385,387,390,391,392,394,397,399,400,402,403,410,411,412,414,415,417,421,423,424,425,426,427,428,430,431,432,440,441,442,443,445,447,448,451,453,454,456,457,459,461,462,463,464,467,468,469,471,473,474,476,477,478,480,484,485,486,487],differenti:[1,3,6,29,185,348,379,421,444],difficult:[215,276,363,393,468],difficulti:[296,423],diffract:[],diffus:[],digit:[2,3,191,333,413],dih_table1:185,dih_table2:185,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:213,dihydrid:387,dij:296,dilat:[],dim1:3,dim2:3,dim:[3,59,71,143,146,147,148,151,152,153,154,155,157,165,187,207,217,234,326,351,410,462,484,485,486],dimdim:485,dimems:275,dimens:[],dimension:[3,39,112,118,140,143,145,146,147,148,151,152,153,154,155,157,164,186,203,207,251,275,320,351,354,358,421,459,469],dimensionless:[105,121,122,124,127,129,131,136,140,320,349,431,451],dimentionless:135,dimer:[6,293,410],dimgrai:191,dimstr:[41,211],dinola:[280,311],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,188,310,480],dir1:470,dir2:470,dir:[1,3,4,8,9,11,12,250,274,283,307,421,423,424,457,470,485],dirac:140,direc:421,direct:[],directli:[3,6,8,9,11,12,87,113,140,142,188,189,190,197,223,230,234,239,275,294,312,324,326,327,328,329,351,355,363,364,365,370,372,373,379,382,385,387,399,403,415,418,426,439,457,469,470,471,477,485],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,192,216,235,278,284,287,304,308,317,318,358,362,364,365,369,376,378,379,385,386,388,395,396,407,410,411,412,413,417,421,422,423,424,431,441,443,444,445,448,457,459,460,461,470,485],disabl:[3,12,16,320,398,457,472,485],disadvantag:[6,211],disallow:[188,217,252],disappear:461,discard:[2,3,41,71,205,207,211,321,329,456,461,462],discontinu:[9,185,356,405],discourag:410,discov:[13,321],discret:[6,8,40,42,190,191,236,239],discuss:[],disk:[6,84,85,158,186,218,228,279,457],disloc:[70,413],disord:[39,70,413],disp:[],dispar:425,disperion:[382,403],dispers:[3,6,7,9,163,275,348,349,373,382,403,408,415,424,442,448],displac:[],displace_atom:[],displace_box:59,displacemet:462,displai:[11,13,22,37,44,55,173,184,188,190,335,343,376,440],dispters:3,disregard:413,dissip:[6,229,236,275,317,318,371,383,391,408,409,440],dissolut:212,dist:[6,69,91,108,117,188,276,292,384,439,454,486],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,154,160,163,165,166,167,168,172,187,188,190,191,199,203,207,208,212,213,214,215,217,218,219,222,228,234,239,249,250,251,252,256,264,274,275,279,283,284,291,292,293,296,297,301,305,306,307,308,315,316,318,319,320,323,325,326,327,328,329,330,334,348,349,351,354,356,358,359,360,363,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,383,384,385,386,387,389,390,391,392,393,397,398,399,400,401,402,403,404,405,406,407,408,409,410,413,414,415,416,417,418,419,420,421,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,454,457,459,462,468,469,473,477,480,484,486],distinct:[6,221,290,348,425],distinguish:[6,86,140,242,387,458],distort:364,distrbut:364,distribut:[],distro:[111,376,420,421],ditto:[8,11,12,14,15,16,17,18,115,213,452,457],div:8,divd:117,diverg:[3,12,39,293,318,461,480,487],divid:[3,6,16,41,91,112,117,126,128,141,162,163,173,184,191,203,204,206,211,217,274,316,323,328,348,356,358,388,424,448,468,476,485],divis:[6,239,369,397,407,456,459,477,485],dl_poli:[6,7],dlambda:159,dlammps_async_imd:233,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,190],dlammps_gzip:[3,12,188,190,319,459,460,464],dlammps_jpeg:[3,12,190],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,190],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,188],dlen:469,dlmp_intel_offload:[12,16],dlo:[59,187,217,279],dlopen:6,dlvo:[7,377,451],dm_lb:239,dmax:[308,354],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,141,144,145,158,160,162,165,166,167,173,184,188,189,190,191,192,194,195,196,201,202,203,204,205,206,207,208,209,218,228,236,237,247,252,253,257,258,262,269,270,271,272,279,282,293,305,308,311,312,313,322,326,329,331,333,335,343,347,356,357,358,363,364,365,368,376,378,379,385,386,388,393,394,396,397,410,411,412,415,417,420,421,422,431,440,441,443,445,447,448,457,459,460,461,462,464,467,468,469,476,477,485,486,487,488],docuement:425,dodgerblu:191,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,116,117,118,142,144,145,147,148,153,155,159,164,165,166,167,169,171,173,178,184,185,187,188,189,190,191,194,200,201,203,207,210,211,213,214,215,217,221,223,225,228,229,232,234,236,237,239,242,248,252,253,254,255,257,258,269,270,271,272,280,281,282,286,288,291,293,308,311,313,315,316,320,323,324,325,328,329,330,331,336,337,339,340,342,347,348,349,350,351,357,358,359,364,365,366,367,368,369,371,373,374,375,377,378,379,380,382,383,384,385,386,387,389,390,391,392,394,395,396,397,398,401,402,404,405,406,408,409,410,411,412,413,415,421,422,423,424,425,427,428,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,450,451,452,454,455,456,457,459,460,461,462,463,466,467,469,470,471,472,473,476,477,480,485,489],doegenomestolif:7,doesn:[3,7,8,12,165,188,201,207,208,305,357,359,363,365,378,386,396,423,424,441,443,444,445,448,459,461],dof:[3,8,112,144,145,158,203,293,486],dof_per_atom:[145,203],dof_per_chunk:[145,203],doff:[357,459],doi:[6,216],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,154,164,167,187,189,190,191,194,201,211,215,217,218,232,235,239,252,253,276,288,293,320,325,326,348,349,358,363,384,415,454,456,459,463,476],domin:[1,387,473],don:[0,8,11,12,13,116,168,197,223,237,282,329,410,457,459],donadio:312,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,159,162,165,168,185,188,190,191,200,201,203,205,206,207,208,209,211,212,213,214,215,217,218,226,228,233,234,236,237,244,252,257,258,269,270,272,273,275,276,277,282,290,293,294,296,308,311,312,313,315,317,318,331,333,347,348,349,356,358,359,362,363,365,373,385,394,395,396,403,409,410,415,423,439,442,447,454,455,456,457,460,463,464,467,477,478,480,485,486],donor:393,dot:[141,161,197,223,231,251],doti:[369,421],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,217,226,281,329,333,347,349,362,363,369,388,392,413,423,424,455,459,463,467,472,485,486],dover:200,down:[3,6,7,8,11,39,71,215,228,236,308,324,363,387,415,458,478],downhil:[354,355],download:[5,7,8,9,11,12,13,17,233,395,422],downsid:6,downward:290,dozen:[8,12,107,194,423,424],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:245,dproduct:366,dr_ewald:[118,294],drag:[],dragforc:239,drai:[250,283],drain:[232,324,356],dramat:[59,187,212,213,214,215,217,252,308,311,312,349,363,415,456],drautz:369,draw:190,drawback:282,drawn:[188,190,191,229,454],drayleigh:[250,283],dreid:[],drfourth:105,drho:[113,364,385],drift:[6,103,105,229,230,236,237,248,291,308,468,476,480],drive:[11,12,198,215,217,231,252,274,280,293,327,358],driven:[6,177],driver:[6,12,14,15,194,226,233],drop:[3,191,383],droplet:394,drsquar:105,drude:[],dry:225,dsecriptor:395,dsf:[],dsmc:[],dstyle:279,dt_collis:239,dt_lb:239,dt_md:239,dt_srd:308,dtilt:[59,217],dtneb:473,dtqm:283,dtype:[115,213],dual:[16,17,308,363],dudarev:164,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,93,102,103,104,1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,21,23,24,25,26,27,28,29,30,31,32,35,36,38,40,43,45,46,47,48,49,51,53,54,56,63,65,69,82,83,84,85,86,87,88,91,94,95,96,97,98,99,101,102,107,108,109,110,112,123,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,188,191,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,334,336,337,338,339,342,344,348,349,354,355,356,358,359,363,364,365,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,423,424,425,426,431,432,433,434,439,440,441,442,443,444,445,447,448,449,450,451,452,454,457,459,464,468,469,471,473,475,476,477,480,484,485,488],energy_update_freq:424,enforc:[6,57,58,104,187,188,189,190,192,194,201,214,217,252,273,275,285,293,296,333,348,399,456,485,486],enforce2d:[],eng:[11,65,69,108,188,226,331,333,378,412],eng_previ:333,engin:[200,217,278,297,317,385,411],engr:[423,424],enhanc:[196,200,454],enlarg:[59,190],enough:[3,40,61,86,165,166,168,211,237,279,283,288,293,321,325,326,329,359,363,379,419,459,463,464],enpub:385,enrti:[],ensembl:[],ensight:6,ensur:[3,6,140,188,201,205,215,228,229,252,298,319,349,369,384,407,441,448],enter:[57,155,388,413,448,473],enthalpi:[123,254,255,385,476,477,485],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,141,145,164,165,191,194,195,196,203,207,208,211,214,216,225,228,229,232,236,237,248,252,254,255,256,257,258,274,276,278,291,293,306,320,322,333,363,382,403,415,442,459,467,468],entireti:[397,447],entiti:[6,8,40,42,188,293],entri:[3,8,12,38,42,56,65,69,79,92,108,115,118,127,130,131,132,133,134,136,137,138,163,185,191,206,207,208,216,283,331,357,369,386,410,417,424,431,441,442,443,444,445,448,485],entropi:473,entry1:[38,56,191,376,442],entry2:191,entryn:191,enumer:[166,188],enumuer:6,env:363,environ:[1,3,6,11,12,16,17,18,190,230,235,274,363,364,369,376,378,386,387,421,443,456,470,485],epair:[107,191,389,393,423,424,477],epen:[423,424],epfl:[230,235],epp:382,epq:382,eps0:451,eps14:407,epsilon0:445,epsilon:[3,6,36,45,46,50,53,54,87,171,195,196,228,293,308,325,329,354,356,368,374,375,377,379,380,381,382,390,392,393,394,397,398,399,400,401,402,403,404,405,406,407,414,418,425,426,435,441,447,450,451,468,480,484],epsilon_0:452,epsilon_14:374,epsilon_:425,epsilon_d:380,epsilon_i:[390,415,425],epsilon_i_:425,epsilon_i_a:[390,425],epsilon_i_b:[390,425],epsilon_i_c:[390,425],epsilon_ij:415,epsilon_j:[390,415,425],epsilon_j_:425,epsilon_j_a:[390,425],epsilon_j_b:[390,425],epsilon_j_c:[390,425],epsilon_lj:425,epton:420,eqch:160,eqeq:[423,424],eqp:382,eqq:382,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,144,159,161,165,190,191,194,195,196,197,198,201,204,205,206,209,210,211,215,217,218,223,228,229,231,232,234,236,237,239,242,243,249,250,256,266,274,276,279,281,283,284,285,288,290,292,293,295,297,302,304,311,312,313,316,317,318,320,322,323,325,328,330,331,333,347,351,356,358,359,360,362,363,378,383,389,390,393,408,413,414,421,423,424,425,427,428,429,431,432,442,447,448,452,455,456,457,459,461,462,466,467,470,473,475,477,485,486],equat:[3,6,7,8,9,91,112,118,164,173,184,194,215,221,222,230,236,237,239,242,250,251,252,253,256,270,274,276,283,284,288,296,308,316,320,323,325,326,328,330,342,348,349,377,382,383,387,388,391,396,408,409,410,415,425,428,430,434,435,437,438,446,452,480],equi:253,equidist:251,equil:[3,284,352,466,489],equilater:469,equilibr:[3,4,5,6,7,9,59,91,165,194,201,204,214,215,228,250,252,253,270,271,283,284,285,286,316,317,318,323,378,379,423,424,455,469],equilibria:323,equilibribum:[212,213],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,148,149,172,174,215,217,228,229,230,237,239,252,256,270,283,288,292,296,297,305,308,315,316,318,323,334,336,339,342,378,410,417,480],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:200,equival:[6,12,13,59,61,124,125,133,138,163,167,191,206,209,215,217,228,236,252,270,280,292,293,328,383,387,443,445,459,462,467,468,477,480],equlibrium:6,equliibr:[284,286],er3:164,eradiu:[40,113,387,459],eras:[295,317],erat:[217,409],erc:379,erfc:[379,399,415],erforc:113,erg:484,erhart:[201,385,443,445],ermscal:366,ernst:9,eror:3,eros:410,erose_form:410,erot:[],errata:[443,445],erratum:325,erron:3,error:[],erta:391,ervel:[113,459],escap:[218,480],especi:[8,11,16,153,165,194,201,211,228,283,288,291,292,363,456],espresso:[9,287],essenti:[8,11,12,27,88,128,146,147,148,151,152,153,154,155,157,174,204,256,275,324,349,365,379,399,445,464,477],essex:29,establish:[87,232],estim:[1,3,6,10,12,38,41,56,91,141,200,211,222,250,308,315,348,349,354,415,424,442,473,477],esu:484,esub:410,eta:[6,239,252,283,284,286,324,386,388,390,421,444,448,484],eta_dot:252,eta_ij:421,eta_ji:388,etag:[40,459],etail:477,etap:252,etap_dot:252,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,143,145,146,147,148,149,151,152,153,154,155,157,159,165,167,168,169,178,188,190,191,194,195,200,201,202,203,206,207,208,209,212,213,217,218,226,228,229,236,252,279,290,294,320,321,329,333,347,348,356,357,358,359,361,385,386,394,407,409,419,423,424,441,443,445,448,454,457,459,460,461,466,468,469,473,475,476,477,478,480,484,485,487,489],ethernet:18,etol:[356,358,454,473],etot0:283,etot:[6,94,96,97,110,141,151,191,221,237,250,283,476,477],eu2:164,eu3:164,euler:[356,358],eulerian:200,euqat:433,europhi:239,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,87,88,91,107,117,140,142,145,155,163,165,188,190,191,195,196,197,198,200,202,203,204,205,206,207,208,209,210,217,223,229,231,232,234,235,236,237,275,281,284,295,298,302,311,312,313,322,325,328,330,331,333,348,349,354,356,363,413,415,421,427,429,442,454,455,457,461,462,464,466,467,468,469,473,475,477,485,486],evalut:[333,457],evan:[153,270],evanseck:[6,20,171,374,471],evapor:[],evaul:[8,356],evdwl:[107,423,424,477],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,119,166,167,181,185,188,191,194,195,196,201,202,203,206,207,208,209,211,212,213,215,217,218,221,234,237,250,252,253,275,288,290,293,294,304,308,316,320,323,325,329,331,341,348,354,356,358,363,368,387,388,391,394,415,425,448,449,459,460,462,464,465,466,468,469,471,474,476,477,478,480,489],evenli:[3,41,141,185,211,239,397,449,459],event:[],eventu:[3,6,12,15,167,284,473],ever:[54,56,235,308],evera:[377,390,425,440],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,113,119,128,153,168,188,189,190,191,192,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,222,225,226,228,230,232,233,234,239,240,248,252,253,256,273,274,275,279,280,281,282,283,284,285,286,288,290,291,293,294,296,297,308,310,311,312,313,314,315,316,319,320,321,322,323,331,333,347,349,358,359,360,363,383,384,394,407,423,424,436,453,454,455,459,461,463,464,466,467,468,473,474,475,477,485,489],everyth:[8,107],everywher:[116,401],eviri:387,evolut:[230,239,276,454],evolv:[239,276,321],ewald:[2,3,5,6,7,8,12,88,110,118,141,321,348,349,356,370,372,373,379,382,387,399,403,418,426,440,442,461],ewald_disp:382,ewalddisp:3,exact:[22,41,44,71,122,159,168,173,211,214,229,230,236,237,238,279,288,289,308,320,335,348,376,461,466,473,485,487,489],exactli:[3,6,12,14,17,38,41,56,59,71,91,116,144,149,156,165,185,195,196,206,211,217,222,229,236,237,238,253,263,264,271,275,283,308,313,314,327,363,376,383,385,391,394,397,408,415,442,461,462,469,473,485],exager:480,examin:[6,8,9,17,214,275],examp:[457,485],exampl:[],exce:[3,6,16,17,18,41,58,71,167,203,207,208,211,215,217,222,225,252,275,299,300,308,356,363,459,485],exceed:[3,41,59,211,217,252,308,467],excel:387,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,191,194,197,203,204,206,210,211,215,217,224,227,228,231,234,236,238,252,253,254,255,256,257,258,259,263,264,267,269,270,271,272,276,285,286,293,295,296,305,308,311,313,314,320,324,328,331,333,334,335,336,337,338,339,342,343,344,348,349,351,353,357,358,359,361,362,363,364,365,367,370,371,372,373,374,375,376,377,378,379,381,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,411,416,417,418,420,423,424,425,426,432,440,441,442,443,444,445,447,448,450,451,452,454,456,457,459,461,462,464,467,468,469,470,471,473,477,480,484,485,486,488],excess:[205,387],exchang:[2,3,6,8,9,61,62,194,200,201,228,236,285,293,316,320,323,348,363,387,474],exchange:348,excit:[9,387],exclud:[3,6,9,12,16,17,63,71,112,140,145,152,153,169,188,203,207,212,213,240,248,278,291,293,315,326,331,356,357,359,371,391,394,408,409,415,439,471],exclus:[1,3,9,12,16,87,363,378,413,415,468,478],excurs:454,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,166,190,233,287,333,347,350,362,455,457,467,470,473,485],exemplari:229,exemplifi:387,exert:[6,234,237,288,327,328,329,349],exhaust:[200,362,485],exhibit:[252,355,387,468],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,122,165,166,184,189,190,191,194,199,210,213,215,218,228,278,279,281,331,334,336,337,339,343,352,357,363,394,423,449,455,457,459,460,461,470,471,472,485,486,487],exit:[2,3,11,12,41,57,188,211,347,362,457,458,467,476,485],exlanatori:3,exp:[],expand:[],expans:[12,140,188,470,485],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,146,157,163,185,211,223,228,230,249,274,280,282,283,288,293,331,349,359,376,410,413,415,454,457,459,461,464,468,473,485],expens:[6,10,71,191,274,278,293,320,331,348,349,359,363,457],experi:[6,13,15,17,210,218,233,242,251,280,292,293,354,358,383,415,468,473],experienc:[6,12,241,242],experiment:[228,348,363,473],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,145,153,185,188,190,191,194,203,204,209,211,213,215,217,252,274,282,293,305,331,333,347,348,351,357,358,362,368,385,397,432,447,457,460,461,464,466,469,480,485,489],explan:[3,6,59,113,140,188,203,251,274,394,453,456,457,459,468],explanatori:[3,8,117,188,202,203,206,207,208,293,357,456,485],explantori:[3,289],explic:414,explicit:[6,9,11,22,44,77,87,113,116,159,173,195,196,217,299,300,335,353,365,366,369,374,376,385,387,398,408,446,453,456,460,463],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,143,152,155,163,165,171,172,174,175,176,177,179,180,182,183,185,188,191,197,207,210,217,224,227,229,231,236,252,254,255,256,257,258,259,267,269,270,272,282,283,285,293,295,296,311,313,314,320,324,328,334,336,337,338,339,342,344,357,363,364,365,367,370,371,372,373,374,375,376,377,378,379,380,382,383,384,385,386,388,389,390,391,392,393,394,397,398,399,400,401,402,403,404,405,406,407,408,411,413,415,416,417,418,420,425,426,432,433,434,435,436,437,438,440,441,442,443,444,445,446,447,448,450,451,452,459,461,468,469,471,472,478,480],explictli:[16,472],exploit:[9,15,17,276],explor:[118,164],expon:[3,284,286,385,390,393,407,414,426],exponenti:[87,421,441,448,452,473,485],expos:11,exposit:[200,383,384],express:[6,140,151,165,195,196,215,249,274,284,320,326,333,369,385,387,401,410,431,440,485],expressiont:369,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,194,197,198,201,209,210,216,219,223,226,227,228,230,231,232,234,236,238,250,252,256,264,274,275,291,292,293,295,297,302,305,307,311,312,313,314,315,317,318,320,322,325,329,330,390,410,413,424,425,431,476,477],extent:[1,3,41,45,57,71,163,167,188,199,207,211,234,327,330,348,351,365,427,429,442,456,459,462],exterior:[3,6,329],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,143,144,146,148,151,152,153,154,155,157,158,164,165,166,167,171,191,206,211,213,252,281,282,283,293,308,356,357,360,361,382,391,394,397,410,415,456,457,459,462,471,480,485],extract:[3,6,11,13,36,63,87,107,115,117,119,195,196,286,358,379,388,410,431,457,464,476],extract_atom:11,extract_comput:[11,457],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,190,205,215,217,252,318,387,444,480],extrema:407,extrins:200,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[161,322],f_a:[443,444,445],f_ave:117,f_c:444,f_f:445,f_fix_id:283,f_harm:318,f_i:421,f_id:[6,71,117,119,188,194,202,203,204,205,206,207,208,209,247,310,322,477,485],f_ij:421,f_indent:209,f_int:317,f_jj:91,f_k:421,f_langevin:320,f_max:[283,288],f_msst:250,f_r:[237,443,444,445],f_sigma:369,f_solid:318,f_ss:6,f_temp:237,face:[3,6,57,59,71,153,163,167,199,207,208,325,327,328,329,330,351,390,410,425,459,462],face_threshold:163,facet:163,facil:[0,12],facilit:[6,13],fact:[6,8,16,230,308,318,391,471],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,116,118,140,159,164,167,171,182,188,190,191,195,196,204,211,215,217,218,228,233,236,238,239,250,252,253,256,276,280,292,296,298,300,308,312,316,323,324,325,329,339,349,351,357,363,365,366,369,370,372,374,379,380,381,383,387,391,394,398,399,410,413,415,417,418,424,426,432,441,446,456,459,462,463,468,471,473,474,477,480,484,485],factori:[3,457],factoriz:348,fail:[3,11,12,59,169,215,218,348,356,358,381,424,457],failur:[121,428,458,485],fairli:[11,415,468,473],faken:73,falcon:233,fall:[3,6,191,206,279,457,485],fals:[86,331,333,485],fame:8,famili:[448,456],familiar:[0,11],fan:421,far:[3,6,12,17,57,59,61,86,188,191,192,211,212,213,215,218,252,274,292,293,308,325,336,339,354,358,359,447,457,459,464,477],farago:236,farrel:[443,445],farther:188,fashion:[6,8,41,71,165,191,194,195,196,201,207,211,213,218,228,230,234,249,250,252,254,255,256,257,258,266,269,270,271,272,282,283,285,293,297,301,307,310,318,320,324,325,326,328,330,358,394,408,462,471,485,488],fasolino:396,fast:[6,7,9,12,13,17,39,188,261,283,321,348,349,371,408,409,413,440,442,461,466,468,477,486,489],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,143,152,171,172,174,175,176,177,179,180,182,183,185,188,191,194,197,210,211,217,224,227,231,235,236,252,254,255,256,257,258,259,267,269,270,272,280,284,285,293,295,296,308,311,313,315,317,320,324,328,334,336,337,338,339,342,344,348,349,360,361,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,382,383,385,386,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,411,416,417,418,420,425,426,432,440,441,442,443,444,445,447,448,450,451,452,454,468,472,480],fastest:[1,6,14,17,153,207,320,321,363,456],fatal:[3,476],fault:[70,424],faulti:12,fava:390,favor:214,favorit:7,fbmc:315,fcc:[],fcm:[266,485],fdirect:221,fdotr:395,fdti:87,fe2:164,fe3:164,fe_md_boundari:200,featu:8,featur:[],fecr:385,feedback:[7,233],feel:[7,233,234,242,274,329,331,358,415],felling:412,felt:329,femtosecond:484,fene:[],fennel:[379,399],fep:[],ferguson:[6,171,471],fermi:[1,12,15,151,363,445],fermion:[9,387],ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,192,202,203,204,206,207,208,209,237,252,279,282,284,296,322,348,356,357,358,365,456,459,464,468,470,478,485,487],fewer:[1,3,11,15,16,61,242,468],fewest:3,fextern:226,feynman:276,fff:457,ffield:[378,388,423,424],ffmpeg:[3,12,190],ffplai:190,fft:[1,3,7,12,14,15,88,109,110,141,275,348,349,468],fft_inc:[12,349],fft_lib:12,fft_path:12,fftbench:[348,478],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:439,fictiti:[6,197,198,223,226,230,276,292,379,399,403,439],field1:[460,464],field2:460,field:[],fifth:[305,417],figur:[1,3,8,11,12,283,456,457],fij:382,file0:274,file1:[11,13,274,319,333,357,464,466,470],file2:[11,13,319,333,357,464,466,470],file:[],file_from:189,filen:357,filenam:[3,12,13,38,41,56,185,188,190,191,192,200,203,204,205,206,207,208,209,211,216,274,278,281,284,285,286,289,290,293,294,319,320,345,346,347,357,358,364,365,369,379,385,386,388,396,410,411,412,417,421,422,423,424,431,441,442,443,444,445,448,455,456,457,460,461,466,470,477,485,487,488,489],filennam:466,filep:[3,188,191,461,466,489],filepo:290,fill:[7,9,165,190,279,320,351,359,369,413,424,462],filter:[191,200],final_integr:8,final_integrate_respa:8,finchham:[6,147,381],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,168,185,192,201,214,215,225,228,251,274,280,288,292,354,356,358,359,379,394,399,403,410,440,442,480,485],find_custom:8,fine:[16,17,169,197,223,318,359,363,485],finer:[140,165,485],finest:348,finger:[165,187,249,462],finish:[6,11,41,211,333,345,347,348,360,362,363,447,464,485,486],finit:[],finni:[7,385,440],finvers:221,fiorin:[9,216],fire:[354,355,356,358,473],firebrick:191,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,150,153,159,161,163,164,166,167,168,172,185,188,189,190,191,192,194,195,203,204,206,207,208,209,211,214,217,228,229,234,239,249,250,251,252,274,276,281,282,283,285,290,293,296,297,305,306,308,309,310,317,318,319,320,322,326,331,333,334,340,351,356,357,358,359,362,363,364,365,368,369,370,372,374,376,378,379,385,387,388,391,392,394,395,396,398,399,403,408,409,410,412,413,415,417,421,423,424,431,439,441,442,443,444,445,448,452,454,455,456,457,459,460,461,464,466,468,471,472,473,476,477,480,485,486,487,489],fischer:[6,9,19,20,171,374,471],fit:[3,6,9,12,38,56,185,292,308,365,369,396,410,415,435,442,444,467,485],five:[73,151,283,357,369,411,459,473],fix:[],fix_adapt:[159,196,407],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,201,279],fix_evapor:201,fix_flux:200,fix_gcmc:[201,357],fix_gl:230,fix_gld:230,fix_grav:279,fix_id:[3,215,250,252,254,255,256,257,258,280,283],fix_modifi:[],fix_mov:[187,326],fix_nh:8,fix_npt:230,fix_nvt:[201,228],fix_poem:[3,6],fix_pour:[3,218],fix_qbmsst:9,fix_qeq:[3,378],fix_rattl:296,fix_reax_bond:423,fix_rigid:[242,368],fix_saed_vtk:294,fix_setforc:8,fix_shak:296,fix_srd:3,fix_styl:256,fix_temp_rescal:314,fixedpoint:[215,252],fixextern:226,fixid:200,fji:382,flag1:[220,361],flag2:[220,361],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,93,103,104,106,118,160,164,168,188,190,191,192,209,214,216,220,233,236,240,242,248,249,275,282,293,305,307,308,315,319,328,331,346,349,357,361,362,363,365,393,398,410,439,454,456,457,459,460,461,463,464,465,469,485],flag_buck:373,flag_coul:[373,382,403],flag_lj:[382,403],flagfld:[371,408,409],flaghi:[3,371,408,409],flaglog:[371,408,409],flagn:220,flagvf:[371,408,409],flat:[6,320,325,326,330],flavor:[2,7,12],fld:[9,325,371,408,409],flen:366,flex_press:366,flexibl:[3,6,8,166,190,203,207,216,230,253,316,323,387,444,477],flip:[3,6,217,252,327,328],floor:485,flop:12,floralwhit:191,flow:[],fluctuat:[6,64,87,215,228,229,236,239,252,256,274,275,318,320,342],fluid:[],fluid_veloc:243,flush:[3,191,476],flux:[],flv:190,fly:[7,9,12,41,190,194,200,205,218,221,293,296,321,369,413,477,480],fmackai:9,fmag:219,fmass:276,fmax:[356,477],fmomentum:221,fmsec:[2,191,236,237,249,252,280,293,311,312,468,479,484,486],fname:347,fno:[12,16],fnorm:[356,477],fnpt:221,fnvt:221,foce:394,fock:366,focu:296,fogarti:[9,286,424],foil:[140,274,431],fold:[306,468],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,144,145,151,153,158,161,163,165,166,171,174,175,176,177,179,180,182,183,185,188,189,190,191,194,200,201,202,203,204,205,206,207,208,209,211,216,217,218,221,222,226,228,229,230,233,235,236,237,239,242,250,252,256,257,258,269,270,272,275,276,278,281,282,283,284,286,288,290,292,293,294,296,310,311,312,313,316,317,318,31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:[275,283,288,378,480],supercomput:[12,18,457],superpos:[394,440],superposit:7,supinski:413,supplement:[230,423,424],supplementari:[216,390,425],suppli:[12,185,228,250,320],support:[1,3,6,7,8,9,11,12,13,14,15,16,17,18,19,40,41,42,61,87,88,102,107,188,189,190,191,192,195,196,197,198,203,211,214,215,216,223,226,230,231,234,236,237,238,239,247,250,252,254,255,256,257,258,269,270,271,272,274,275,280,283,285,287,292,293,298,299,300,301,302,304,305,307,311,312,313,314,318,323,325,329,346,347,348,349,355,356,357,363,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,450,451,452,456,460,461,466,468,469,470,472,473,480,484,485,488,489],suppos:[3,8,388,485],suppress:[6,12,163],sure:[6,8,11,13,14,185,195,196,215,293,296,330,385,442],surf:166,surfac:[2,3,4,6,8,9,40,42,57,70,118,140,163,165,168,190,194,218,225,234,239,242,274,285,292,301,304,305,308,315,320,325,329,330,358,369,394,408,409,413,429,447,451,456,462],surface_mov:320,surfact:[380,389],surpris:387,surrog:9,surround:[38,56,70,165,185,191,215,252,254,255,257,258,274,280,293,442,480],suspect:3,suspens:[408,409],sustain:[188,215,391],suzuki:[252,293],svg:6,svn:[7,11,12],sw_exampl:422,swamp:293,swap:[],swegat:319,swiggl:[3,249,325,328,330,462,485],swiler:[140,431],switch7_section_start:389,switchflag:[140,431],swm4:480,swol:53,swope:6,sxx:191,sy0302:9,symbol:[6,12,118,164,290,369,387,431],symmetr:[6,70,87,93,112,131,132,133,136,137,138,141,195,196,215,252,253,316,323,364,376,382,385,443,445,485],symmetri:[3,5,6,7,8,63,64,70,167,188,250,274,334,349,364,459,480],sync:[3,6,478],synchron:[1,230,358,478],synechococcu:7,syntax:[],sysdim:275,sysmt:17,sysstem:369,system:[],system_:276,systemat:[6,9,205,228,236,413],systemx:3,t10:474,t11:474,t12:474,t13:474,t14:474,t15:474,t3e:12,t_chain:3,t_corr:3,t_correl:454,t_dephas:454,t_e:320,t_e_min:320,t_equil:[317,318],t_event:[3,454,473],t_hi:473,t_infil:320,t_init:[283,320],t_iter:3,t_lb:239,t_lo:473,t_order:3,t_oufil:320,t_out:320,t_outfil:320,t_qm:283,t_switch:[317,318],t_target:371,ta06a:431,ta4:413,ta5:164,ta6:413,tab:[2,459],tabbernor:118,tabinn:415,tabul:[3,7,13,22,37,38,44,55,56,65,71,79,92,185,308,348,364,369,370,372,373,374,375,376,379,385,387,399,403,418,421,424,426,440,442,443,449,461],tabular:421,tabulate_long_rang:424,tad:[],tadmor:9,tag:[200,220,480],tagint:3,tail:[3,87,110,159,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,448,450,451,452,461,477,485],tailor:[71,321],tait:[9,437,438],taitwat:[],take:[1,2,3,6,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,56,59,77,87,89,91,109,112,113,116,117,141,143,152,159,163,169,171,172,173,174,175,176,177,179,180,182,183,185,188,190,191,195,196,197,210,211,215,217,224,227,231,235,236,237,252,254,255,256,257,258,259,267,269,270,272,285,293,295,296,305,306,307,308,310,311,312,313,321,324,328,331,334,335,336,337,338,339,342,344,348,349,353,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,382,383,385,386,388,389,390,391,392,393,397,399,400,401,402,403,404,405,406,407,408,411,413,416,417,418,420,423,424,425,426,432,439,441,442,443,444,445,446,447,448,450,451,452,453,457,460,467,468,469,476,477,478,485],taken:[6,59,147,165,187,214,218,228,229,230,236,237,238,239,279,283,286,320,338,385,387,390,441,448,454,468,469],talk:[6,7],talli:[8,41,107,113,203,206,207,208,211,213,236,238,253,308,316,323,387,389,393,424],tan:[191,485],tandem:[4,16,293],tang:413,tangent:251,tangenti:[6,108,308,326,330,391],tanh:320,tantalum:[4,413,431],taper:[3,286],tar:12,tarbal:[0,8,11,12],target:[3,6,7,8,9,11,12,17,39,41,191,199,211,215,216,218,228,229,230,236,237,238,252,253,254,255,256,257,258,269,270,271,272,276,280,283,288,293,297,306,311,312,313,314,319,320,323,324,327,346,349,371,383,454,465,467,486],target_fil:319,task:[1,6,7,12,13,14,15,16,17,18,54,191,233,276,321,363,457,478],taskset:16,tatb:[4,289],tatom:480,tau:[3,154,205,236,237,239,252,280,293,311,312,317,318,320,479,484],tau_1:229,tau_k:229,tau_n_k:229,tb3:164,tbead:157,tbp:369,tchain:[252,253,256,270,271,293],tcl:288,tcom:237,tcsh:[11,12,376],tdamp:[236,252,253,256,293,311,312],tdephas:454,tdrude:[150,221,237,480],teal:191,tech:[7,9,13],technic:[6,7,9,239,286,308,424],techniqu:[6,7,9,87,194,215,250,283,293,324,327,349,415,442,480],technolgi:9,technolog:[9,14,19,233],tell:[2,6,11,12,37,55,184,194,275,343,359,423,424,440,457,461,480],telsa:17,temeperatur:11,temp:[],temp_drud:480,temp_eff:97,tempcom:[144,158],temper:[],temperar:276,temperatur:[],temperature_definit:200,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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":212,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,145,153,154,158,164,165,168,170,184,186,187,188,190,191,192,193,195,196,197,199,200,201,203,207,208,209,212,213,215,216,217,218,222,225,228,229,234,236,237,238,239,240,242,247,250,252,253,256,270,271,275,276,279,280,281,282,283,285,288,290,291,293,294,308,310,315,316,317,318,321,323,325,327,331,343,346,348,349,351,352,354,355,357,359,360,361,363,366,369,371,387,408,409,413,415,423,424,439,440,454,455,456,459,460,462,464,466,467,468,471,473,475,476,477,478,479,484,486,487,488],"function":485,"long":[205,370,372,373,374,375,379,381,382,399,403,407,418,426],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[195,196],addforc:197,addit:[12,13],addtorqu:198,adiabat:6,adjust_dt:298,adp:364,airebo:365,alloi:385,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:199,arrai:6,aspher:[6,82,144,254,257,260,261,269],atc:[9,200],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,163,199,201,202,282,485],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:210,awpmd:[9,366],balanc:[41,211],barostat:6,basal:67,beck:367,berendsen:[280,311],between:6,binary2txt:13,bodi:[6,8,42,68,262,368],bond:[8,13,69,212,213,214,289],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:369,born:[370,381],boundari:[7,57],box:[6,58,215],brownian:371,buck:[372,373,381],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,171,374,407],chunk:[6,66,71,75,90,93,104,106,114,145,160,162,203],citat:7,class2:[21,43,172,334,375],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[325,377,451],colvar:[9,13,216],com:[74,75,146],comb3:378,comb:[285,378],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,481,482,483,484,485,486,487,488,489],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,485],compute_modifi:102,condit:7,conduct:[6,316],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:[204,205],cosin:[23,24,25,26,27,28,174],cossq:336,coul:[370,372,373,374,375,379,380,381,392,399,403,407,418,426],coupl:6,creat:213,create_atom:165,create_bond:166,create_box:167,createatom:13,creation:7,csld:312,csvr:312,cubic:401,cuda:[9,14,109,112,143,152,197,210,224,227,231,252,259,295,296,311,313,324,370,372,374,375,385,391,392,399,400,402,405,416,441,443],custom:8,cut:[49,366,372,375,379,382,387,389,399,400,407,414,418],cvff:337,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[379,399],deform:[148,149,217],delete_atom:168,delete_bond:169,delta:24,deposit:218,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,481,482,483,484,485,486,487,488,489],diagnost:7,diel:380,dielectr:170,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:173,dihedral_styl:[2,171,172,174,175,176,177,178,179,180,181,182,183,184,185],dilat:80,dimens:186,dipol:[6,29,382],direct:221,discuss:6,disp:6,displac:[81,86],displace_atom:187,distribut:[7,12],document:0,dpd:383,drag:219,dreid:[6,393],drude:[6,9,150,220,221,237],dsf:[379,399],dsmc:384,dump:[6,8,188,189,190,192],dump_modifi:191,dynam:284,eam:[13,385],echo:193,edip:386,eff:[9,13,96,97,149,151,156,238,253,263,271,314,387],efield:223,eim:388,elast:6,emac:13,enforce2d:224,ensembl:7,erot:[82,83,84,85],error:3,evapor:225,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,472,473,474,475,476,477,478,479,481,482,483,484,485,486,487,488,489],exp:[27,174],expand:[46,402],extend:[8,11],extern:226,fcc:274,featur:[7,8,485],fene:[45,46],fep:[9,13,87,196],field:[6,7],file:6,finit:6,fix:[2,6,8,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,485],fix_modifi:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,26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\ No newline at end of file From b45a8bb7e3d9326a8a075de1fcad5b72f8a00fe7 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 23 Oct 2015 00:04:22 +0000 Subject: [PATCH 18/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14180 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/USER-SMTBQ/README | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/USER-SMTBQ/README b/src/USER-SMTBQ/README index 19fac74388..c94ad47324 100644 --- a/src/USER-SMTBQ/README +++ b/src/USER-SMTBQ/README @@ -1,9 +1,9 @@ This package implements the Second Moment Tight Binding - QEq (SMTB-Q) potential for the description of the ionocovalent bond in oxides. -Authors: Nicolas Salles, Emile Maras, Olivier Politano, Robert T\'e9tot +Authors: Nicolas Salles, Emile Maras, Olivier Politano, Robert Tetot -Contact email: lammps@u-bourgogne.fr +Contact emails: lammps@u-bourgogne.fr, nsalles@laas.fr See the doc page for the pair_style smtbq command to get started. From 336aa4093e41475031a8ee3eec56b746f0980b3f Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 23 Oct 2015 00:06:46 +0000 Subject: [PATCH 19/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14181 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- examples/USER/smtbq/data.Alpha | 1811 ++++++++++++++++++++++++ examples/USER/smtbq/ffield.smtbq.Al | 34 + examples/USER/smtbq/ffield.smtbq.Al2O3 | 56 + examples/USER/smtbq/ffield.smtbq.TiO2 | 53 + examples/USER/smtbq/in.smtbq.Al | 77 + examples/USER/smtbq/in.smtbq.Al2O3 | 55 + examples/USER/smtbq/in.smtbq.TiO2 | 97 ++ examples/USER/smtbq/log.smtbq.Al | 279 ++++ examples/USER/smtbq/log.smtbq.Al2O3 | 210 +++ examples/USER/smtbq/log.smtbq.TiO2 | 255 ++++ 10 files changed, 2927 insertions(+) create mode 100755 examples/USER/smtbq/data.Alpha create mode 100755 examples/USER/smtbq/ffield.smtbq.Al create mode 100755 examples/USER/smtbq/ffield.smtbq.Al2O3 create mode 100755 examples/USER/smtbq/ffield.smtbq.TiO2 create mode 100755 examples/USER/smtbq/in.smtbq.Al create mode 100755 examples/USER/smtbq/in.smtbq.Al2O3 create mode 100755 examples/USER/smtbq/in.smtbq.TiO2 create mode 100644 examples/USER/smtbq/log.smtbq.Al create mode 100644 examples/USER/smtbq/log.smtbq.Al2O3 create mode 100644 examples/USER/smtbq/log.smtbq.TiO2 diff --git a/examples/USER/smtbq/data.Alpha b/examples/USER/smtbq/data.Alpha new file mode 100755 index 0000000000..735f33c36c --- /dev/null +++ b/examples/USER/smtbq/data.Alpha @@ -0,0 +1,1811 @@ + + 1800 atoms + 2 atom types + + 0.00 0.237690E+02 xlo xhi + 0.00 0.247015E+02 ylo yhi + 0.00 0.259564E+02 zlo zhi + 0.0 0.0 0.0 xy xz yz + + Atoms + + 1 2 2.70 -9.0322200000 -10.2922789113 12.7351615747 + 2 2 2.70 -11.4091200000 -6.1753673468 12.7351615747 + 3 1 -1.80 -9.9540293580 -8.9199750564 11.8966833333 + 4 1 -1.80 11.4380706420 -4.8030634919 11.8966833333 + 5 1 -1.80 -9.7597653210 -11.7767411602 11.8966833333 + 6 1 -1.80 11.6323346790 -7.6598295957 11.8966833333 + 7 1 -1.80 11.6323346790 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-1.0815166667 +1684 1 -1.80 1.9304706420 11.6645827661 -1.0815166667 +1685 1 -1.80 4.5016346790 4.6909050979 -1.0815166667 +1686 1 -1.80 2.1247346790 8.8078166624 -1.0815166667 +1687 1 -1.80 2.1247346790 6.2875257408 -1.0815166667 +1688 1 -1.80 -0.2521653210 10.4044373053 -1.0815166667 +1689 2 2.70 2.8522800000 4.8030634919 -1.9199949080 +1690 2 2.70 0.4753800000 8.9199750564 -1.9199949080 +1691 2 2.70 2.8522800000 7.5476712016 -2.4060717587 +1692 2 2.70 0.4753800000 11.6645827661 -2.4060717587 +1693 1 -1.80 3.5798253210 6.0632089527 -3.2445500000 +1694 1 -1.80 1.2029253210 10.1801205172 -3.2445500000 +1695 1 -1.80 6.1509893580 4.8030634919 -3.2445500000 +1696 1 -1.80 3.7740893580 8.9199750564 -3.2445500000 +1697 1 -1.80 1.2029253210 7.6598295957 -3.2445500000 +1698 1 -1.80 -1.1739746790 11.7767411602 -3.2445500000 +1699 2 2.70 5.2291800000 6.1753673468 -4.0830282413 +1700 2 2.70 2.8522800000 10.2922789113 -4.0830282413 +1701 2 2.70 2.8522800000 4.8030634919 -4.5691050920 +1702 2 2.70 0.4753800000 8.9199750564 -4.5691050920 +1703 1 -1.80 4.5016346790 4.9152218860 -5.4075833333 +1704 1 -1.80 2.1247346790 9.0321334505 -5.4075833333 +1705 1 -1.80 4.5016346790 7.4355128075 -5.4075833333 +1706 1 -1.80 2.1247346790 11.5524243721 -5.4075833333 +1707 1 -1.80 1.9304706420 6.1753673468 -5.4075833333 +1708 1 -1.80 -0.4464293580 10.2922789113 -5.4075833333 +1709 2 2.70 2.8522800000 7.5476712016 -6.2460615747 +1710 2 2.70 0.4753800000 11.6645827661 -6.2460615747 +1711 2 2.70 5.2291800000 6.1753673468 -6.7321384253 +1712 2 2.70 2.8522800000 10.2922789113 -6.7321384253 +1713 1 -1.80 1.3971893580 7.5476712016 -7.5706166667 +1714 1 -1.80 -0.9797106420 11.6645827661 -7.5706166667 +1715 1 -1.80 5.9567253210 4.6909050979 -7.5706166667 +1716 1 -1.80 3.5798253210 8.8078166624 -7.5706166667 +1717 1 -1.80 3.5798253210 6.2875257408 -7.5706166667 +1718 1 -1.80 1.2029253210 10.4044373053 -7.5706166667 +1719 2 2.70 2.8522800000 4.8030634919 -8.4090949080 +1720 2 2.70 0.4753800000 8.9199750564 -8.4090949080 +1721 2 2.70 2.8522800000 7.5476712016 -8.8951717587 +1722 2 2.70 0.4753800000 11.6645827661 -8.8951717587 +1723 1 -1.80 4.3073706420 4.8030634919 -9.7336500000 +1724 1 -1.80 1.9304706420 8.9199750564 -9.7336500000 +1725 1 -1.80 2.1247346790 6.0632089527 -9.7336500000 +1726 1 -1.80 -0.2521653210 10.1801205172 -9.7336500000 +1727 1 -1.80 4.5016346790 7.6598295957 -9.7336500000 +1728 1 -1.80 2.1247346790 11.7767411602 -9.7336500000 +1729 2 2.70 5.2291800000 6.1753673468 -10.5721282413 +1730 2 2.70 2.8522800000 10.2922789113 -10.5721282413 +1731 2 2.70 2.8522800000 4.8030634919 -11.0582050920 +1732 2 2.70 0.4753800000 8.9199750564 -11.0582050920 +1733 1 -1.80 1.2029253210 7.4355128075 -11.8966833333 +1734 1 -1.80 -1.1739746790 11.5524243721 -11.8966833333 +1735 1 -1.80 5.9567253210 4.9152218860 -11.8966833333 +1736 1 -1.80 3.5798253210 9.0321334505 -11.8966833333 +1737 1 -1.80 3.7740893580 6.1753673468 -11.8966833333 +1738 1 -1.80 1.3971893580 10.2922789113 -11.8966833333 +1739 2 2.70 2.8522800000 7.5476712016 -12.7351615747 +1740 2 2.70 0.4753800000 11.6645827661 -12.7351615747 +1741 2 2.70 9.9829800000 6.1753673468 -0.2430384253 +1742 2 2.70 7.6060800000 10.2922789113 -0.2430384253 +1743 1 -1.80 9.0611706420 7.5476712016 -1.0815166667 +1744 1 -1.80 6.6842706420 11.6645827661 -1.0815166667 +1745 1 -1.80 9.2554346790 4.6909050979 -1.0815166667 +1746 1 -1.80 6.8785346790 8.8078166624 -1.0815166667 +1747 1 -1.80 6.8785346790 6.2875257408 -1.0815166667 +1748 1 -1.80 4.5016346790 10.4044373053 -1.0815166667 +1749 2 2.70 7.6060800000 4.8030634919 -1.9199949080 +1750 2 2.70 5.2291800000 8.9199750564 -1.9199949080 +1751 2 2.70 7.6060800000 7.5476712016 -2.4060717587 +1752 2 2.70 5.2291800000 11.6645827661 -2.4060717587 +1753 1 -1.80 8.3336253210 6.0632089527 -3.2445500000 +1754 1 -1.80 5.9567253210 10.1801205172 -3.2445500000 +1755 1 -1.80 10.9047893580 4.8030634919 -3.2445500000 +1756 1 -1.80 8.5278893580 8.9199750564 -3.2445500000 +1757 1 -1.80 5.9567253210 7.6598295957 -3.2445500000 +1758 1 -1.80 3.5798253210 11.7767411602 -3.2445500000 +1759 2 2.70 9.9829800000 6.1753673468 -4.0830282413 +1760 2 2.70 7.6060800000 10.2922789113 -4.0830282413 +1761 2 2.70 7.6060800000 4.8030634919 -4.5691050920 +1762 2 2.70 5.2291800000 8.9199750564 -4.5691050920 +1763 1 -1.80 9.2554346790 4.9152218860 -5.4075833333 +1764 1 -1.80 6.8785346790 9.0321334505 -5.4075833333 +1765 1 -1.80 9.2554346790 7.4355128075 -5.4075833333 +1766 1 -1.80 6.8785346790 11.5524243721 -5.4075833333 +1767 1 -1.80 6.6842706420 6.1753673468 -5.4075833333 +1768 1 -1.80 4.3073706420 10.2922789113 -5.4075833333 +1769 2 2.70 7.6060800000 7.5476712016 -6.2460615747 +1770 2 2.70 5.2291800000 11.6645827661 -6.2460615747 +1771 2 2.70 9.9829800000 6.1753673468 -6.7321384253 +1772 2 2.70 7.6060800000 10.2922789113 -6.7321384253 +1773 1 -1.80 6.1509893580 7.5476712016 -7.5706166667 +1774 1 -1.80 3.7740893580 11.6645827661 -7.5706166667 +1775 1 -1.80 10.7105253210 4.6909050979 -7.5706166667 +1776 1 -1.80 8.3336253210 8.8078166624 -7.5706166667 +1777 1 -1.80 8.3336253210 6.2875257408 -7.5706166667 +1778 1 -1.80 5.9567253210 10.4044373053 -7.5706166667 +1779 2 2.70 7.6060800000 4.8030634919 -8.4090949080 +1780 2 2.70 5.2291800000 8.9199750564 -8.4090949080 +1781 2 2.70 7.6060800000 7.5476712016 -8.8951717587 +1782 2 2.70 5.2291800000 11.6645827661 -8.8951717587 +1783 1 -1.80 9.0611706420 4.8030634919 -9.7336500000 +1784 1 -1.80 6.6842706420 8.9199750564 -9.7336500000 +1785 1 -1.80 6.8785346790 6.0632089527 -9.7336500000 +1786 1 -1.80 4.5016346790 10.1801205172 -9.7336500000 +1787 1 -1.80 9.2554346790 7.6598295957 -9.7336500000 +1788 1 -1.80 6.8785346790 11.7767411602 -9.7336500000 +1789 2 2.70 9.9829800000 6.1753673468 -10.5721282413 +1790 2 2.70 7.6060800000 10.2922789113 -10.5721282413 +1791 2 2.70 7.6060800000 4.8030634919 -11.0582050920 +1792 2 2.70 5.2291800000 8.9199750564 -11.0582050920 +1793 1 -1.80 5.9567253210 7.4355128075 -11.8966833333 +1794 1 -1.80 3.5798253210 11.5524243721 -11.8966833333 +1795 1 -1.80 10.7105253210 4.9152218860 -11.8966833333 +1796 1 -1.80 8.3336253210 9.0321334505 -11.8966833333 +1797 1 -1.80 8.5278893580 6.1753673468 -11.8966833333 +1798 1 -1.80 6.1509893580 10.2922789113 -11.8966833333 +1799 2 2.70 7.6060800000 7.5476712016 -12.7351615747 +1800 2 2.70 5.2291800000 11.6645827661 -12.7351615747 diff --git a/examples/USER/smtbq/ffield.smtbq.Al b/examples/USER/smtbq/ffield.smtbq.Al new file mode 100755 index 0000000000..f63b6c43ba --- /dev/null +++ b/examples/USER/smtbq/ffield.smtbq.Al @@ -0,0 +1,34 @@ +# DATE: 2015-10-22 CONTRIBUTOR: Nicolas Salles, nsalles@laas.fr CITATION: N. Salles, O. Politano, E. Amzallag and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189 +# SMTBQ parameter for Al-Al interaction. +# Edited by N. Salles Univ. Bourgogne and E. Maras from Aalto Univ. +# year: 2014 +# ========================================================================= +' Nombre.de.type.d.atome..........:' 1 +' ====== atomic parameters ======= ' +' Cation.de.l.oxyde..Stoechio.....:' 'Al' 1 +' Qform.....masse.................:' 3.0 26.98 +' Param.QEq.(ne,.Chi,.J,.R_eff)...:' 3 1.19258 11.05345 0.57701 +' Nbre.d.etats.partage.par.cation.:' 3 +' ===== potential Parameter ======' +' Atom1..atom2..potential..mode....' 'Al' 'Al' 'second_moment' 'metal' +' Potentiel.Cat-Ox.(A,.p,.Ksi,.q).:' 0.1221 8.612 1.316 2.516 +' Pot..Cat-Ox.(rc1,.rc2,.r0).Iota.:' 5.6 7.0 2.863 2.0 +' ======== Parametre tab ========= ' +' Rcoul...........................:' 11.1714 +' rmin...dr.......................:' 1.18845 0.001 +' ======== IFQM Parameter ======== ' +' Frenquency.Q.resolution..........' 0 +' loopmax.-.precision..............' 5000 0.0002 +' ==== Coordination parameters ====' +' .r1n................r2n..........' 2.5 3.2 +' ========== QInitMode ========= ' +' QInitMode....QInit(if.needed)....' 'false' 0.0 +' ======== Mode for QEq ======== ' +' mode(see.end.of.this.file.)......' 'QEqAllParallel' +' parameters.for.mode..............' +' ========== Verbose ============ ' +' Verbose(true.or.false)...........' 'false' +' Print.Energy.components..........' 'false' 300.0 +' Print.electroneg...components....' 'false' 300.0 +# =========================== END's parameters ========================= + diff --git a/examples/USER/smtbq/ffield.smtbq.Al2O3 b/examples/USER/smtbq/ffield.smtbq.Al2O3 new file mode 100755 index 0000000000..9c26ade9ec --- /dev/null +++ b/examples/USER/smtbq/ffield.smtbq.Al2O3 @@ -0,0 +1,56 @@ +# DATE: 2015-10-22 CONTRIBUTOR: Nicolas Salles, nsalles@laas.fr CITATION: N. Salles, O. Politano, E. Amzallag and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189 +# SMTBQ parameter for AlO interaction with a limit length 'rc2sm=dc2**2'. +# Edited by N. Salles from Univ Bourgogne and E. Maras from Aalto Univ. +# +# Presentation atom : nature +# q, qmin, qmax, masse +# parameter QEq : Chi, J, R_eff +# Parameter SM : A, p, Ksi, q +# CutOff SM : dc1, dc2, r0 +# ========================================================================= +# -------------------------- Begin's parameters --------------------------- +' Number.of.atoms.type............:' 2 +' ====== atomic parameters ======= ' +' 1st.element.(Oxygen).Stoechio...:' 'O' 3 +' Qform.....mass..................:' -2.0 16.00 +' Param.QEq.(ne,.Chi0,.JiO).......:' 2 6.57 10.22 +' coordBB.coordB.coordS.rBB.rB.rS.:' 6. 4. 3.00 0.529 0.529 0.529 +' Number.of.shared.state.by.ions..:' 3 +' -------------------------------- ' +' 2nd.element.(metal).Stoechio....:' 'Al' 2 +' Qform.....mass..................:' 3.0 26.98 +' Param.QEq.(ne,.Chi0,.Ji0,.R_eff):' 3 1.19009 11.1903 0.56619 +' Number.of.shared.state.by.ions..:' 4 +' ===== potential Parameter ======' +' Atom1..atom2..potential..mode....' 'Al' 'O' 'second_moment' 'oxide' +' Pot.CatOx.(A,.p,.Ksi(ref=O),.q).:' 0.18176 8.80041 0.26044 1.58851 +' Pot..Cat-Ox.(rc1,.rc2,.r0)......:' 4. 5.6 1.91 +' -------------------------------- ' +' atom1..atom2..potential..........' 'O' 'O' 'buck' +' Potentiel.O-O...(C,.Rho)........:' 580.440 0.3540 +' ======== Parametre tab ========= ' +' Rcoul=a*rc(SMASH)...............:' 11.1714 +' rmin...dr.......................:' 1.18845 0.001 +' ======== IFQM Parameter ======== ' +' Nevery.charge.calculation........' 1 +' loopmax....precision.............' 7000 0.000001 +' ==== Coordination parameters ====' +' .r1n................r2n..........' 2.5 3.2 +' ========== QInitMode ========= ' +' QInitMode....QInit(if.needed)....' 'false' -1.8 +' ======== Mode for QEq ======== ' +' mode(see.end.of.this.file.)......' 'QEqAll' +' parameters.for.mode..............' +' ========== Verbose ============ ' +' Verbose(true.or.false)...........' 'false' +' Print.Energy.components..........' 'false' 300.0 +' Print.electroneg...components....' 'false' 300.0 +# =========================== FIN des parametres ========================= + +#Possible QInit modes +# true (then initialize all the oxygen charges to QOxInit and set the cation charge in order to keep the charge balance (neutrality of the box) +#any other name would lead to either 0 charges or charge read from the lammps atomic position file +#Possible QEq modes | parameters +# QEqAll | no parameters +# QEqAllParallel | no parameters +# Surface | zlim (QEq only for z>zlim) diff --git a/examples/USER/smtbq/ffield.smtbq.TiO2 b/examples/USER/smtbq/ffield.smtbq.TiO2 new file mode 100755 index 0000000000..4c8d9df535 --- /dev/null +++ b/examples/USER/smtbq/ffield.smtbq.TiO2 @@ -0,0 +1,53 @@ +# DATE: 2015-10-22 CONTRIBUTOR: Nicolas Salles, nsalles@laas.fr CITATION: N. Salles, O. Politano, E. Amzallag and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189 +# ======================================================================== +# SMTBQ parameter for Ti-O interaction with a limit length 'rc2sm=dc2**2'. +# Edited by N. Salles from Univ Bourgogne and E. Maras from Aalto Univ +# september 2014 +# ======================================================================== +' Number.of.atoms.type............:' 2 +' ====== atomic parameters ======= ' +' 1st.element.(Oxygen).Stoechio...:' 'O' 2 +' Qform.....mass..................:' -2.0 16.00 +' Param.QEq.(ne,.Chi0,.JiO).......:' 2 6.57 10.22 +' coordBB.coordB.coordS.rBB.rB.rS.:' 6. 3. 2.00 0.52 0.54348 0.58 +' Number.of.shared.state.by.ions..:' 3 +' -------------------------------- ' +' 2nd.element.(metal).Stoechio....:' 'Ti' 1 +' Qform.....mass..................:' 4.0 26.98 +' Param.QEq.(nq,.Chi0,.Ji0,.R_eff):' 3 0.00 10.572 0.734 +' Number.of.shared.state.by.ions..:' 5 +' ===== potential Parameter ======' +' Atom1..atom2..potential..mode....' 'Ti' 'O' 'second_moment' 'oxide' +' Pot.CatOx.(A,.p,.Ksi(ref=O),.q).:' 0.134 12.609 0.5434 2.0965 +' Pot..Cat-Ox.(rc1,.rc2,.r0)......:' 3.6 6.0 1.95 +' -------------------------------- ' +' atom1..atom2..potential..........' 'O' 'O' 'buckPlusAttr' +' Potential.O-O...(C,.Rho)........:' 580.440 0.3540 +' Potential.O-O...(D.B.r1OO.r2OO).:' -20.86 -0.916 1.4 1.8 +' ======== Tab Parameter ========= ' +' Rcoul=a*rc(SMASH)...............:' 12.1744 +' rmin...dr.......................:' 1.0675 0.001 +' ======== IFQM Parameter ======== ' +' Nevery.charge.calculation........' 1 +' loopmax....precision.............' 7000 0.000001 +' ==== Coordination parameters ====' +' .r1n................r2n..........' 2.0 3.5 +' ========== QInitMode ========= ' +' QInitMode....QInit(if.needed)....' 'false' -1.0 +' ======== Mode for QEq ======== ' +' mode(see.end.of.this.file.)......' 'QEqAll' +' parameters.for.mode..............' +' ========== Verbose ============ ' +' Verbose(true.or.false)...........' 'false' +' Print.Energy.components..........' 'false' 300.0 +' Print.electroneg...components....' 'false' 300.0 +# =========================== END's parameters ========================= + +#Possible QInit modes +# true (then initialize all the oxygen charges to QOxInit and set the cation charge in order to keep the charge balance (neutrality of the box) +#any other name would lead to either 0 charges or charge read from the lammps atomic position file +#Possible QEq modes | parameters +# QEqAll | no parameters +# QEqAllParallel | no parameters +# Surface | zlim (QEq only for z>zlim) +# BulkFromSlab | zlim1 zlim2 (QEq only for zlim1 bins = 5 6 5 +Memory usage per processor = 4.52298 Mbytes +Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume + 0 300 729.26605 -5600.8541 65.108335 -5535.7458 28.637825 34.721517 28.059223 27900.653 + 1 299.98323 729.90439 -5600.8505 65.104695 -5535.7458 28.637825 34.721517 28.059223 27900.653 + 2 299.93288 731.82072 -5600.8395 65.093767 -5535.7458 28.637825 34.721517 28.059223 27900.653 + 3 299.84896 735.01448 -5600.8213 65.075556 -5535.7458 28.637825 34.721517 28.059223 27900.653 + 4 299.7315 739.48472 -5600.7958 65.050064 -5535.7458 28.637825 34.721517 28.059223 27900.653 + 5 299.58053 745.23012 -5600.7631 65.017299 -5535.7458 28.637825 34.721517 28.059223 27900.653 + 6 299.39609 752.24896 -5600.723 64.977269 -5535.7458 28.637825 34.721517 28.059223 27900.653 + 7 299.17822 760.5391 -5600.6757 64.929985 -5535.7458 28.637825 34.721517 28.059223 27900.653 + 8 298.92698 770.098 -5600.6212 64.875459 -5535.7458 28.637825 34.721517 28.059223 27900.653 + 9 298.64244 780.92261 -5600.5595 64.813707 -5535.7458 28.637825 34.721517 28.059223 27900.653 + 10 298.32468 793.00943 -5600.4905 64.744743 -5535.7458 28.637825 34.721517 28.059223 27900.653 +Loop time of 5.10336 on 1 procs for 10 steps with 1680 atoms + +Performance: 0.034 ns/day, 708.800 hours/ns, 1.959 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.1023 | 5.1023 | 5.1023 | 0.0 | 99.98 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00045538 | 0.00045538 | 0.00045538 | 0.0 | 0.01 +Output | 0.00024509 | 0.00024509 | 0.00024509 | 0.0 | 0.00 +Modify | 0.00026131 | 0.00026131 | 0.00026131 | 0.0 | 0.01 +Other | | 0.0001056 | | | 0.00 + +Nlocal: 1680 ave 1680 max 1680 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7518 ave 7518 max 7518 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 638400 ave 638400 max 638400 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 638400 +Ave neighs/atom = 380 +Neighbor list builds = 0 +Dangerous builds = 0 + +unfix 3 +#thermo 15 +fix 1 all box/relax tri 0.0 vmax 0.001 +minimize 1.0e-8 1.0e-10 1000 10000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.6714 + ghost atom cutoff = 11.6714 + binsize = 5.8357 -> bins = 5 6 5 +Memory usage per processor = 5.64798 Mbytes +Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume + 10 298.32468 793.00943 -5600.4905 64.744743 -5535.7458 28.637825 34.721517 28.059223 27900.653 + 11 298.32468 2483.3228 -5600.5212 64.744743 -5535.7764 28.617938 34.697425 28.039771 27842.617 + 12 298.32468 3102.6624 -5600.6242 64.744743 -5535.8795 28.594201 34.68783 28.048729 27820.715 + 13 298.32468 1681.0688 -5600.6477 64.744743 -5535.903 28.619779 34.708131 28.055945 27869.065 + 14 298.32468 949.90841 -5600.6635 64.744743 -5535.9187 28.648416 34.718691 28.044409 27893.966 + 15 298.32468 2009.1662 -5600.7072 64.744743 -5535.9625 28.652241 34.703261 28.01635 27857.391 + 16 298.32468 2867.1434 -5600.7192 64.744743 -5535.9744 28.626861 34.69005 28.022309 27828.038 + 17 298.32468 2480.3207 -5600.7238 64.744743 -5535.9791 28.618046 34.695106 28.040113 27841.2 + 18 298.32468 2482.4906 -5600.7249 64.744743 -5535.9802 28.614169 34.704237 28.036452 27841.119 + 19 298.32468 2495.6209 -5600.7261 64.744743 -5535.9813 28.616207 34.697481 28.039453 27840.662 + 20 298.32468 2210.2897 -5600.7271 64.744743 -5535.9823 28.620852 34.699678 28.042926 27850.393 + 21 298.32468 2464.137 -5600.734 64.744743 -5535.9893 28.625239 34.687085 28.040022 27841.67 + 22 298.32468 3091.7034 -5600.7471 64.744743 -5536.0024 28.623565 34.674943 28.02983 27820.181 + 23 298.32468 2334.9443 -5600.7598 64.744743 -5536.0151 28.634413 34.684598 28.037298 27845.891 + 24 298.32468 2462.2836 -5600.7767 64.744743 -5536.032 28.615834 34.692433 28.044664 27841.422 + 25 298.32468 2652.08 -5600.7914 64.744743 -5536.0466 28.61528 34.695645 28.035991 27834.85 + 26 298.32468 2365.4126 -5600.7923 64.744743 -5536.0476 28.618526 34.699347 28.039662 27844.623 + 27 298.32468 2334.9429 -5600.7934 64.744743 -5536.0486 28.61826 34.698136 28.041941 27845.656 + 28 298.32468 2501.1598 -5600.7937 64.744743 -5536.0489 28.616356 34.695993 28.039825 27839.982 + 29 298.32468 2506.0962 -5600.794 64.744743 -5536.0493 28.617255 34.699031 28.036317 27839.811 + 30 298.32468 2400.7588 -5600.7942 64.744743 -5536.0495 28.618372 34.698464 28.039299 27843.404 + 31 298.32468 2499.8528 -5600.7945 64.744743 -5536.0497 28.61702 34.69385 28.040945 27840.021 + 32 298.32468 2629.5393 -5600.7967 64.744743 -5536.0519 28.619399 34.691546 28.036003 27835.58 + 33 298.32468 2397.5939 -5600.7973 64.744743 -5536.0526 28.621863 34.69535 28.03848 27843.488 + 34 298.32468 2222.7714 -5600.8007 64.744743 -5536.056 28.609815 34.705091 28.048395 27849.426 + 35 298.32468 2748.5871 -5600.8042 64.744743 -5536.0594 28.600322 34.6998 28.043876 27831.457 + 36 298.32468 2661.1018 -5600.8166 64.744743 -5536.0719 28.615123 34.696499 28.034947 27834.344 + 37 298.32468 2255.4994 -5600.8185 64.744743 -5536.0737 28.618919 34.702261 28.040497 27848.173 + 38 298.32468 2260.815 -5600.8239 64.744743 -5536.0791 28.614993 34.70246 28.043972 27847.962 + 39 298.32468 2549.2876 -5600.8248 64.744743 -5536.0801 28.612892 34.697988 28.039725 27838.113 + 40 298.32468 2488.3825 -5600.8266 64.744743 -5536.0819 28.623347 34.695524 28.033557 27840.182 + 41 298.32468 2400.9714 -5600.8283 64.744743 -5536.0835 28.619176 34.695733 28.040468 27843.155 + 42 298.32468 2496.6566 -5600.8284 64.744743 -5536.0837 28.617629 34.694692 28.039536 27839.89 + 43 298.32468 2486.2773 -5600.8285 64.744743 -5536.0838 28.617585 34.697413 28.037736 27840.243 + 44 298.32468 2446.3916 -5600.8287 64.744743 -5536.0839 28.617115 34.696389 28.040393 27841.603 + 45 298.32468 2547.2311 -5600.8288 64.744743 -5536.0841 28.615267 34.694882 28.039956 27838.161 + 46 298.32468 2479.9982 -5600.8321 64.744743 -5536.0874 28.603008 34.71581 28.037344 27840.427 + 47 298.32468 2449.645 -5600.8444 64.744743 -5536.0997 28.612743 34.683541 28.054837 27841.375 + 48 298.32468 2682.7109 -5600.8695 64.744743 -5536.1248 28.617414 34.683477 28.042139 27833.265 + 49 298.32468 2350.1707 -5600.8711 64.744743 -5536.1263 28.619236 34.694213 28.043092 27844.6 + 50 298.32468 2486.1481 -5600.8719 64.744743 -5536.1271 28.615167 34.699435 28.038181 27839.955 + 51 298.32468 2498.3384 -5600.8721 64.744743 -5536.1274 28.616069 34.696071 28.039596 27839.537 + 52 298.32468 2443.1247 -5600.8722 64.744743 -5536.1274 28.617616 34.696737 28.039439 27841.421 +Loop time of 36.9389 on 1 procs for 42 steps with 1680 atoms + +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -5600.49050006 -5600.87213771 -5600.87218615 + Force two-norm initial, final = 50.879 1.39888 + Force max component initial, final = 29.3783 0.749036 + Final line search alpha, max atom move = 0.0013373 0.00100168 + Iterations, force evaluations = 42 71 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 36.918 | 36.918 | 36.918 | 0.0 | 99.94 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0033035 | 0.0033035 | 0.0033035 | 0.0 | 0.01 +Output | 0.0011785 | 0.0011785 | 0.0011785 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.01603 | | | 0.04 + +Nlocal: 1680 ave 1680 max 1680 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7518 ave 7518 max 7518 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 638400 ave 638400 max 638400 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 638400 +Ave neighs/atom = 380 +Neighbor list builds = 0 +Dangerous builds = 0 + +unfix 1 +thermo 1 +fix 3 all nve +run 10 +Neighbor list info ... + 1 neighbor list requests + update every 20 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.6714 + ghost atom cutoff = 11.6714 + binsize = 5.8357 -> bins = 5 6 5 +Memory usage per processor = 4.52298 Mbytes +Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume + 52 298.32468 2443.1247 -5600.8722 64.744743 -5536.1274 28.617616 34.696737 28.039439 27841.421 + 53 298.28341 2444.4342 -5600.8632 64.735788 -5536.1274 28.617616 34.696737 28.039439 27841.421 + 54 298.20852 2447.019 -5600.847 64.719534 -5536.1274 28.617616 34.696737 28.039439 27841.421 + 55 298.1 2450.8786 -5600.8234 64.695982 -5536.1274 28.617616 34.696737 28.039439 27841.421 + 56 297.95788 2456.0119 -5600.7926 64.665139 -5536.1274 28.617616 34.696737 28.039439 27841.421 + 57 297.7822 2462.4173 -5600.7545 64.62701 -5536.1274 28.617616 34.696737 28.039439 27841.421 + 58 297.57298 2470.0928 -5600.709 64.581604 -5536.1274 28.617616 34.696737 28.039439 27841.421 + 59 297.33028 2479.0363 -5600.6564 64.528932 -5536.1274 28.617616 34.696737 28.039439 27841.421 + 60 297.05416 2489.245 -5600.5964 64.469006 -5536.1274 28.617616 34.696737 28.039439 27841.421 + 61 296.74469 2500.7159 -5600.5293 64.401842 -5536.1274 28.617616 34.696737 28.039439 27841.421 + 62 296.40194 2513.4457 -5600.4549 64.327455 -5536.1274 28.617616 34.696737 28.039439 27841.421 +Loop time of 5.13028 on 1 procs for 10 steps with 1680 atoms + +Performance: 0.034 ns/day, 712.539 hours/ns, 1.949 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.1292 | 5.1292 | 5.1292 | 0.0 | 99.98 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00045729 | 0.00045729 | 0.00045729 | 0.0 | 0.01 +Output | 0.00024509 | 0.00024509 | 0.00024509 | 0.0 | 0.00 +Modify | 0.00026488 | 0.00026488 | 0.00026488 | 0.0 | 0.01 +Other | | 0.0001016 | | | 0.00 + +Nlocal: 1680 ave 1680 max 1680 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7518 ave 7518 max 7518 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 638400 ave 638400 max 638400 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 638400 +Ave neighs/atom = 380 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:49 diff --git a/examples/USER/smtbq/log.smtbq.Al2O3 b/examples/USER/smtbq/log.smtbq.Al2O3 new file mode 100644 index 0000000000..b7d2ad5ae3 --- /dev/null +++ b/examples/USER/smtbq/log.smtbq.Al2O3 @@ -0,0 +1,210 @@ +LAMMPS (23 Oct 2015) +# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants + +variable T_depart equal 300 + +variable dt equal 0.0002 + +# ======================================================================= + +units metal +atom_style charge +dimension 3 +boundary p p p + +read_data data.Alpha + triclinic box = (0 0 0) to (23.769 24.7015 25.9564) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1800 atoms +# ^ Orthorombic box of corundum strcture + +mass 1 16.00 +group Oxy type 1 +1080 atoms in group Oxy +compute chargeOxy Oxy property/atom q +compute q_Oxy Oxy reduce ave c_chargeOxy + +mass 2 26.98 +group Al type 2 +720 atoms in group Al +compute chargeAl Al property/atom q +compute q_Al Al reduce ave c_chargeAl + +velocity all create ${T_depart} 277387 +velocity all create 300 277387 + +pair_style smtbq +pair_coeff * * ffield.smtbq.Al2O3 O Al + +neighbor 0.5 bin +neigh_modify every 20 delay 0 check yes + +timestep ${dt} +timestep 0.0002 + +thermo_style custom step temp press pe ke etotal c_q_Al c_q_Oxy lx ly lz vol +thermo_modify flush yes +thermo 1 + + +#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z + +fix 3 all nve +run 10 +Neighbor list info ... + 1 neighbor list requests + update every 20 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.6714 + ghost atom cutoff = 11.6714 + binsize = 5.8357 -> bins = 5 5 5 +Memory usage per processor = 4.12573 Mbytes +Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume + 0 300 91921.482 -11494.543 69.7617 -11424.781 2.6095997 -1.7397331 23.769 24.7015 25.9564 15239.78 + 1 299.96467 91922.303 -11494.535 69.753485 -11424.781 2.6095996 -1.739733 23.769 24.7015 25.9564 15239.78 + 2 299.75126 91933.246 -11494.485 69.703859 -11424.781 2.6095978 -1.7397318 23.769 24.7015 25.9564 15239.78 + 3 299.36045 91954.835 -11494.394 69.61298 -11424.781 2.6095941 -1.7397294 23.769 24.7015 25.9564 15239.78 + 4 298.79335 91986.343 -11494.262 69.481107 -11424.781 2.6095886 -1.7397257 23.769 24.7015 25.9564 15239.78 + 5 298.05151 92027.62 -11494.09 69.3086 -11424.781 2.6095812 -1.7397208 23.769 24.7015 25.9564 15239.78 + 6 297.13689 92078.615 -11493.877 69.095915 -11424.781 2.6095721 -1.7397147 23.769 24.7015 25.9564 15239.78 + 7 296.05187 92139.141 -11493.625 68.843606 -11424.781 2.6095613 -1.7397075 23.769 24.7015 25.9564 15239.78 + 8 294.79923 92209.15 -11493.334 68.552319 -11424.781 2.6095488 -1.7396992 23.769 24.7015 25.9564 15239.78 + 9 293.38215 92288.12 -11493.004 68.222793 -11424.781 2.6095347 -1.7396898 23.769 24.7015 25.9564 15239.78 + 10 291.80421 92376.81 -11492.637 67.855859 -11424.781 2.6095191 -1.7396794 23.769 24.7015 25.9564 15239.78 +Loop time of 169.694 on 1 procs for 10 steps with 1800 atoms + +Performance: 0.001 ns/day, 23568.600 hours/ns, 0.059 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 169.69 | 169.69 | 169.69 | 0.0 |100.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00075507 | 0.00075507 | 0.00075507 | 0.0 | 0.00 +Output | 0.00078607 | 0.00078607 | 0.00078607 | 0.0 | 0.00 +Modify | 0.00034666 | 0.00034666 | 0.00034666 | 0.0 | 0.00 +Other | | 0.0001752 | | | 0.00 + +Nlocal: 1800 ave 1800 max 1800 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11490 ave 11490 max 11490 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 1.4472e+06 ave 1.4472e+06 max 1.4472e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1447200 +Ave neighs/atom = 804 +Neighbor list builds = 0 +Dangerous builds = 0 + +unfix 3 +thermo 1 +fix 1 all box/relax tri 0.0 vmax 0.001 +minimize 1.0e-3 1.0e-5 1000 10000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.6714 + ghost atom cutoff = 11.6714 + binsize = 5.8357 -> bins = 5 5 5 +Memory usage per processor = 5.50073 Mbytes +Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume + 10 291.80421 92376.81 -11492.637 67.855859 -11424.781 2.6095191 -1.7396794 23.769 24.7015 25.9564 15239.78 + 11 291.80421 84416.246 -11494.722 67.855859 -11426.866 2.6087748 -1.7391832 23.787835 24.721015 25.982356 15279.17 +Loop time of 25.4145 on 1 procs for 1 steps with 1800 atoms + +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -11492.6369832 -11492.6369832 -11494.7221261 + Force two-norm initial, final = 1453.27 1325.26 + Force max component initial, final = 968.201 892.249 + Final line search alpha, max atom move = 1.03284e-06 0.000921553 + Iterations, force evaluations = 1 1 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 25.414 | 25.414 | 25.414 | -nan |100.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00013995 | 0.00013995 | 0.00013995 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.0005064 | | | 0.00 + +Nlocal: 1800 ave 1800 max 1800 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11408 ave 11408 max 11408 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 1.44456e+06 ave 1.44456e+06 max 1.44456e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1444562 +Ave neighs/atom = 802.534 +Neighbor list builds = 0 +Dangerous builds = 0 + +unfix 1 +thermo 1 +fix 3 all nve +run 10 +Neighbor list info ... + 1 neighbor list requests + update every 20 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.6714 + ghost atom cutoff = 11.6714 + binsize = 5.8357 -> bins = 5 5 5 +Memory usage per processor = 4.37573 Mbytes +Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume + 11 291.80421 84416.246 -11494.722 67.855859 -11426.866 2.6087748 -1.7391832 23.787835 24.721015 25.982356 15279.17 + 12 290.08293 84514.767 -11494.322 67.455594 -11426.866 2.6087578 -1.7391718 23.787835 24.721015 25.982356 15279.17 + 13 288.21041 84622.406 -11493.886 67.020161 -11426.866 2.6087394 -1.7391596 23.787835 24.721015 25.982356 15279.17 + 14 286.19128 84738.689 -11493.417 66.550634 -11426.866 2.6087199 -1.7391466 23.787835 24.721015 25.982356 15279.17 + 15 284.03049 84864.242 -11492.914 66.048166 -11426.866 2.6086993 -1.7391329 23.787835 24.721015 25.982356 15279.17 + 16 281.73331 84998.125 -11492.38 65.513983 -11426.866 2.6086776 -1.7391184 23.787835 24.721015 25.982356 15279.17 + 17 279.30534 85140.233 -11491.815 64.949384 -11426.866 2.6086551 -1.7391034 23.787835 24.721015 25.982356 15279.17 + 18 276.75244 85290.405 -11491.221 64.355737 -11426.866 2.6086319 -1.7390879 23.787835 24.721015 25.982356 15279.17 + 19 274.08079 85448.449 -11490.6 63.734472 -11426.866 2.608608 -1.739072 23.787835 24.721015 25.982356 15279.17 + 20 271.29678 85614.064 -11489.953 63.087082 -11426.866 2.6085837 -1.7390558 23.787835 24.721015 25.982356 15279.17 + 21 268.40708 85786.72 -11489.281 62.415114 -11426.865 2.608559 -1.7390393 23.787835 24.721015 25.982356 15279.17 +Loop time of 170.699 on 1 procs for 10 steps with 1800 atoms + +Performance: 0.001 ns/day, 23708.143 hours/ns, 0.059 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 170.7 | 170.7 | 170.7 | 0.0 |100.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00068879 | 0.00068879 | 0.00068879 | 0.0 | 0.00 +Output | 0.0008359 | 0.0008359 | 0.0008359 | 0.0 | 0.00 +Modify | 0.00031424 | 0.00031424 | 0.00031424 | 0.0 | 0.00 +Other | | 0.0001593 | | | 0.00 + +Nlocal: 1800 ave 1800 max 1800 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11222 ave 11222 max 11222 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 1.44126e+06 ave 1.44126e+06 max 1.44126e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1441262 +Ave neighs/atom = 800.701 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:06:42 diff --git a/examples/USER/smtbq/log.smtbq.TiO2 b/examples/USER/smtbq/log.smtbq.TiO2 new file mode 100644 index 0000000000..433a7ceabb --- /dev/null +++ b/examples/USER/smtbq/log.smtbq.TiO2 @@ -0,0 +1,255 @@ +LAMMPS (23 Oct 2015) +# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants + +variable T_depart equal 300 + +variable dt equal 0.0002 + +variable a equal 4.5937 +variable c equal 2.9587 +variable ca equal ${c}/${a} +variable ca equal 2.9587/${a} +variable ca equal 2.9587/4.5937 + +variable nx equal 6 +variable ny equal 6 +variable nz equal 11 + +variable bx equal ${a}*${nx} +variable bx equal 4.5937*${nx} +variable bx equal 4.5937*6 +variable by equal ${a}*${ny} +variable by equal 4.5937*${ny} +variable by equal 4.5937*6 +variable bz equal ${c}*${nz} +variable bz equal 2.9587*${nz} +variable bz equal 2.9587*11 +# ======================================================================= + +units metal +atom_style charge +dimension 3 +boundary p p p + + +lattice sc 1.0 +Lattice spacing in x,y,z = 1 1 1 +region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0 +region box_vide prism 0 27.5622 0 ${by} 0 ${bz} 0.0 0.0 0.0 +region box_vide prism 0 27.5622 0 27.5622 0 ${bz} 0.0 0.0 0.0 +region box_vide prism 0 27.5622 0 27.5622 0 32.5457 0.0 0.0 0.0 +create_box 2 box_vide +Created triclinic box = (0 0 0) to (27.5622 27.5622 32.5457) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid + +#lattice sc 1.0 +#region box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz} + +# titanium atoms +lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 +lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 +lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 +Lattice spacing in x,y,z = 4.5937 4.5937 2.9587 + +create_atoms 2 region box_vide +Created 792 atoms + +# Oxygen atoms +lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5 +lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5 +lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5 +Lattice spacing in x,y,z = 4.5937 4.5937 2.9587 + +create_atoms 1 region box_vide +Created 1584 atoms + + +mass 1 16.00 +group Oxy type 1 +1584 atoms in group Oxy +compute chargeOxy Oxy property/atom q +compute q_Oxy Oxy reduce ave c_chargeOxy + +mass 2 47.867 +group Ti type 2 +792 atoms in group Ti +compute chargeTi Ti property/atom q +compute q_Ti Ti reduce ave c_chargeTi + +velocity all create ${T_depart} 277387 +velocity all create 300 277387 + +pair_style smtbq +pair_coeff * * ffield.smtbq.TiO2 O Ti + +neighbor 0.5 bin +neigh_modify every 20 delay 0 check yes + +timestep ${dt} +timestep 0.0002 + +thermo_style custom step temp press pe ke etotal c_q_Ti c_q_Oxy lx ly lz vol +thermo_modify flush yes +thermo 1 + + +#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z + +fix 3 all nve +run 10 +Neighbor list info ... + 1 neighbor list requests + update every 20 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.6744 + ghost atom cutoff = 12.6744 + binsize = 6.3372 -> bins = 5 5 6 +Memory usage per processor = 4.77264 Mbytes +Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume + 0 300 44365.066 -15815.239 92.097853 -15723.142 2.5521775 -1.2760888 27.5622 27.5622 32.5457 24724.15 + 1 299.90455 44375.373 -15815.21 92.06855 -15723.142 2.552178 -1.276089 27.5622 27.5622 32.5457 24724.15 + 2 299.63739 44392.241 -15815.128 91.986534 -15723.142 2.5521725 -1.2760863 27.5622 27.5622 32.5457 24724.15 + 3 299.19899 44415.606 -15814.994 91.85195 -15723.142 2.5521616 -1.2760808 27.5622 27.5622 32.5457 24724.15 + 4 298.59012 44445.345 -15814.808 91.665031 -15723.143 2.5521454 -1.2760727 27.5622 27.5622 32.5457 24724.15 + 5 297.81185 44481.382 -15814.57 91.426105 -15723.144 2.5521238 -1.2760619 27.5622 27.5622 32.5457 24724.15 + 6 296.86552 44523.683 -15814.28 91.135592 -15723.144 2.5520969 -1.2760484 27.5622 27.5622 32.5457 24724.15 + 7 295.75281 44572.175 -15813.939 90.793996 -15723.145 2.5520648 -1.2760324 27.5622 27.5622 32.5457 24724.15 + 8 294.47564 44626.778 -15813.548 90.401913 -15723.147 2.5520274 -1.2760137 27.5622 27.5622 32.5457 24724.15 + 9 293.03623 44687.401 -15813.108 89.960027 -15723.148 2.5519849 -1.2759925 27.5622 27.5622 32.5457 24724.15 + 10 291.43711 44753.932 -15812.618 89.469107 -15723.149 2.5519374 -1.2759687 27.5622 27.5622 32.5457 24724.15 +Loop time of 570.52 on 1 procs for 10 steps with 2376 atoms + +Performance: 0.000 ns/day, 79238.948 hours/ns, 0.018 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 570.52 | 570.52 | 570.52 | 0.0 |100.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00087428 | 0.00087428 | 0.00087428 | 0.0 | 0.00 +Output | 0.00091386 | 0.00091386 | 0.00091386 | 0.0 | 0.00 +Modify | 0.00045085 | 0.00045085 | 0.00045085 | 0.0 | 0.00 +Other | | 0.0001979 | | | 0.00 + +Nlocal: 2376 ave 2376 max 2376 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 13138 ave 13138 max 13138 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 1.9705e+06 ave 1.9705e+06 max 1.9705e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1970496 +Ave neighs/atom = 829.333 +Neighbor list builds = 0 +Dangerous builds = 0 + +unfix 3 +#thermo 15 +fix 1 all box/relax tri 0.0 vmax 0.001 +minimize 1.0e-3 1.0e-5 1000 10000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.6744 + ghost atom cutoff = 12.6744 + binsize = 6.3372 -> bins = 5 5 6 +Memory usage per processor = 6.14764 Mbytes +Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume + 10 291.43711 44753.932 -15812.618 89.469107 -15723.149 2.5519374 -1.2759687 27.5622 27.5622 32.5457 24724.15 + 11 291.43711 39000.467 -15814.109 89.469107 -15724.639 2.5514249 -1.2757124 27.582771 27.582775 32.578246 24785.834 +Loop time of 80.5411 on 1 procs for 1 steps with 2376 atoms + +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -15812.6183471 -15812.6183471 -15814.1085593 + Force two-norm initial, final = 1104.2 951.386 + Force max component initial, final = 759.352 657.815 + Final line search alpha, max atom move = 1.31691e-06 0.000866285 + Iterations, force evaluations = 1 1 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 80.54 | 80.54 | 80.54 | 0.0 |100.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00016761 | 0.00016761 | 0.00016761 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.0006053 | | | 0.00 + +Nlocal: 2376 ave 2376 max 2376 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 13138 ave 13138 max 13138 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 1.96864e+06 ave 1.96864e+06 max 1.96864e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1968636 +Ave neighs/atom = 828.551 +Neighbor list builds = 0 +Dangerous builds = 0 + +unfix 1 +thermo 1 +fix 3 all nve +run 10 +Neighbor list info ... + 1 neighbor list requests + update every 20 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.6744 + ghost atom cutoff = 12.6744 + binsize = 6.3372 -> bins = 5 5 6 +Memory usage per processor = 5.02264 Mbytes +Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume + 11 291.43711 39000.467 -15814.109 89.469107 -15724.639 2.5514249 -1.2757124 27.582771 27.582775 32.578246 24785.834 + 12 289.69465 39072.309 -15813.575 88.934185 -15724.641 2.551372 -1.275686 27.582771 27.582775 32.578246 24785.834 + 13 287.79928 39149.855 -15812.994 88.352321 -15724.642 2.5513146 -1.2756573 27.582771 27.582775 32.578246 24785.834 + 14 285.75427 39232.968 -15812.368 87.724515 -15724.644 2.5512525 -1.2756262 27.582771 27.582775 32.578246 24785.834 + 15 283.56312 39321.472 -15811.697 87.05185 -15724.645 2.5511856 -1.2755928 27.582771 27.582775 32.578246 24785.834 + 16 281.22962 39415.185 -15810.983 86.335481 -15724.647 2.5511143 -1.2755571 27.582771 27.582775 32.578246 24785.834 + 17 278.75777 39513.921 -15810.226 85.57664 -15724.649 2.5510384 -1.2755192 27.582771 27.582775 32.578246 24785.834 + 18 276.15182 39617.471 -15809.428 84.776632 -15724.651 2.5509583 -1.2754791 27.582771 27.582775 32.578246 24785.834 + 19 273.41625 39725.622 -15808.591 83.936831 -15724.654 2.5508739 -1.275437 27.582771 27.582775 32.578246 24785.834 + 20 270.55575 39838.144 -15807.715 83.058679 -15724.656 2.5507855 -1.2753928 27.582771 27.582775 32.578246 24785.834 + 21 267.57523 39954.804 -15806.802 82.14368 -15724.659 2.5506932 -1.2753466 27.582771 27.582775 32.578246 24785.834 +Loop time of 606.774 on 1 procs for 10 steps with 2376 atoms + +Performance: 0.000 ns/day, 84274.222 hours/ns, 0.016 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 606.77 | 606.77 | 606.77 | 0.0 |100.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00085855 | 0.00085855 | 0.00085855 | 0.0 | 0.00 +Output | 0.00087833 | 0.00087833 | 0.00087833 | 0.0 | 0.00 +Modify | 0.00041723 | 0.00041723 | 0.00041723 | 0.0 | 0.00 +Other | | 0.0001888 | | | 0.00 + +Nlocal: 2376 ave 2376 max 2376 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 13138 ave 13138 max 13138 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 1.96049e+06 ave 1.96049e+06 max 1.96049e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1960492 +Ave neighs/atom = 825.123 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:23:48 From 9e92038756b77c93be354a9da8c72d938094ba5d Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 23 Oct 2015 00:20:52 +0000 Subject: [PATCH 20/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14182 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Eqs/pair_smtbq1.jpg | Bin 0 -> 27807 bytes doc/Eqs/pair_smtbq1.tex | 13 +++++++++++++ doc/Eqs/pair_smtbq2.jpg | Bin 0 -> 15544 bytes doc/Eqs/pair_smtbq2.tex | 12 ++++++++++++ doc/Eqs/pair_smtbq3.jpg | Bin 0 -> 6832 bytes doc/Eqs/pair_smtbq3.tex | 10 ++++++++++ 6 files changed, 35 insertions(+) create mode 100644 doc/Eqs/pair_smtbq1.jpg create mode 100755 doc/Eqs/pair_smtbq1.tex create mode 100644 doc/Eqs/pair_smtbq2.jpg create mode 100755 doc/Eqs/pair_smtbq2.tex create mode 100644 doc/Eqs/pair_smtbq3.jpg create mode 100755 doc/Eqs/pair_smtbq3.tex diff --git a/doc/Eqs/pair_smtbq1.jpg b/doc/Eqs/pair_smtbq1.jpg new file mode 100644 index 0000000000000000000000000000000000000000..6bfb07b778e85652a1579691f0b2b2065ba598ca GIT 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+\documentclass[12pt]{article} + +\begin{document} + +\begin{eqnarray*} +\xi^0 & = & \frac{\xi_O}{m} = \frac{\xi_C}{n} \\ +\frac{\beta_O}{\sqrt{m}} & = & \frac{\beta_C}{\sqrt{n}} = \xi^0 \frac{\sqrt{m}+\sqrt{n}}{2}\\ +\end{eqnarray*} + +\end{document} \ No newline at end of file From d3096fc949b0a0d03d48e1f5cfe488180608f38b Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 23 Oct 2015 00:23:02 +0000 Subject: [PATCH 21/31] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14183 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/doc2/Section_commands.html | 10 +- doc/doc2/genindex.html | 8 +- doc/doc2/pair_mgpt.html | 16 +- doc/doc2/pair_smtbq.html | 272 +++++++++++++++++++++++++++++++++ 4 files changed, 295 insertions(+), 11 deletions(-) create mode 100644 doc/doc2/pair_smtbq.html diff --git a/doc/doc2/Section_commands.html b/doc/doc2/Section_commands.html index 411376f9da..4e3e097fb2 100644 --- a/doc/doc2/Section_commands.html +++ b/doc/doc2/Section_commands.html @@ -536,11 +536,11 @@ package. listlj/charmm/coul/long/soft (o)lj/cut/coul/cut/soft (o)lj/cut/coul/long/soft (o) lj/cut/dipole/sf (go)lj/cut/soft (o)lj/cut/tip4p/long/soft (o)lj/sdk (gko) lj/sdk/coul/long (go)lj/sdk/coul/msm (o)lj/sf (o)meam/spline -meam/sw/splinequipreax/csmd/hertz -smd/tlsphsmd/triangulated/surfacesmd/ulsphsph/heatconduction -sph/idealgassph/ljsph/rhosumsph/taitwater -sph/taitwater/morrissrptersoff/table (o)thole -tip4p/long/soft (o) +meam/sw/splinemgptquipreax/c +smd/hertzsmd/tlsphsmd/triangulated/surfacesmd/ulsph +smtbqsph/heatconductionsph/idealgassph/lj +sph/rhosumsph/taitwatersph/taitwater/morrissrp +tersoff/table (o)tholetip4p/long/soft (o)
    diff --git a/doc/doc2/genindex.html b/doc/doc2/genindex.html index 36d13dad48..455592789c 100644 --- a/doc/doc2/genindex.html +++ b/doc/doc2/genindex.html @@ -1795,12 +1795,12 @@
    pair_style lj/smooth
    - -
    pair_style lj/smooth/linear
    +
    +
    pair_style lj96/cut
    @@ -1818,6 +1818,10 @@ +
    pair_style mgpt +
    + +
    pair_style mie/cut
    diff --git a/doc/doc2/pair_mgpt.html b/doc/doc2/pair_mgpt.html index 11ec3c2fff..9d6e62defe 100644 --- a/doc/doc2/pair_mgpt.html +++ b/doc/doc2/pair_mgpt.html @@ -134,12 +134,19 @@ constant-volume calculations and simulations. It is strongly recommended that the user work through and understand these examples before proceeding to more complex simulations.

    +

    IMPORTANT NOTE: For good performance, LAMMPS should be built with the +compiler flags "-O3 -msse3 -funroll-loops" when including this pair +style. The src/MAKE/OPTIONS/Makefile.mpi_fastmgpt is an example +machine Makefile with these options included as part of a standard MPI +build. Note that as-is it will build with whatever low-level compiler +(g++, icc, etc) is the default for your MPI installation. +

    Mixing, shift, table tail correction, restart:

    -

    The (mgpt) pair style does not support the -pair_modify mix, shift, table, and tail options. +

    This pair style does not support the pair_modify +mix, shift, table, and tail options.

    This pair style does not write its information to binary restart files, since it is stored in potential files. Thus, you @@ -154,8 +161,9 @@ script that reads a restart file.

    Restrictions:

    -

    The mgpt pair style is part of the USER-MGPT package and is only -enabled if LAMMPS is built with that package. +

    This pair style is part of the USER-MGPT package and is only enabled +if LAMMPS is built with that package. See the Making +LAMMPS section for more info.

    The MGPT potentials require the newtion setting to be "on" for pair style interactions. diff --git a/doc/doc2/pair_smtbq.html b/doc/doc2/pair_smtbq.html new file mode 100644 index 0000000000..3efce316c9 --- /dev/null +++ b/doc/doc2/pair_smtbq.html @@ -0,0 +1,272 @@ + +

    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
    + + + + + + +
    + +

    pair_style smtbq command +

    +

    Syntax: +

    +
    pair_style smtbq 
+
    +

    Examples: +

    +
    pair_style smtbq
+pair_coeff * * ffield.smtbq.Al2O3 O Al 
+
    +

    Description: +

    +

    This pair stylecomputes a variable charge SMTB-Q (Second-Moment +tight-Binding QEq) potential as described in SMTB-Q_1 and +SMTB-Q_2. Briefly, the energy of metallic-oxygen systems +is given by three contributions: +

    +
    +
    +

    where Etot is the total potential energy of the system, +EES is the electrostatic part of the total energy, +EOO is the interaction between oxygens and +EMO is a short-range interaction between metal and oxygen +atoms. This interactions depend on interatomic distance +rij and/or the charge Qi of atoms +i. Cut-off function enables smooth convergence to zero interaction. +

    +

    The parameters appearing in the upper expressions are set in the +ffield.SMTBQ.Syst file where Syst corresponds to the selected system +(e.g. field.SMTBQ.Al2O3). Exemples for TiO2, +Al2O3 are provided. A single pair_coeff command +is used with the SMTBQ styles which provides the path to the potential +file with parameters for needed elements. These are mapped to LAMMPS +atom types by specifying additional arguments after the potential +filename in the pair_coeff command. Note that atom type 1 must always +correspond to oxygen atoms. As an example, to simulate a TiO2 system, +atom type 1 has to be oxygen and atom type 2 Ti. The following +pair_coeff command should then be used: +

    +
    pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti 
+
    +The electrostatic part of the energy consists of two components + +

    self-energy of atom i in the form of a second order charge dependent +polynomial and a long-range Coulombic electrostatic interaction. The +latter uses the wolf summation method described in Wolf, +spherically truncated at a longer cutoff, Rcoul. The +charge of each ion is modeled by an orbital Slater which depends on +the principal quantum number (n) of the outer orbital shared by the +ion. +

    +

    Interaction between oxygen, EOO, consists of two parts, +an attractive and a repulsive part. The attractive part is effective +only at short range (< r2OO). The attractive +contribution was optimized to study surfaces reconstruction +(e.g. SMTB-Q_2 in TiO2) and is not necessary +for oxide bulk modeling. The repulsive part is the Pauli interaction +between the electron clouds of oxygen. The Pauli repulsion and the +coulombic electrostatic interaction have same cut off value. In the +ffield.SMTBQ.Syst, the keyword 'buck' allows to consider only the +repulsive O-O interactions. The keyword 'buckPlusAttr' allows to +consider the repulsive and the attractive O-O interactions. +

    +

    The short-range interaction between metal-oxygen, EMO is +based on the second moment approximation of the density of states with +a N-body potential for the band energy term, +Eicov, and a Born-Mayer type repulsive terms +as indicated by the keyword 'second_moment' in the +ffield.SMTBQ.Syst. The energy band term is given by: +

    +
    +
    +

    where ηi is the stoichiometry of atom i, +δQi is the charge delocalization of atom i, +compared to its formal charge +QFi. n0, the number of hybridized +orbitals, is calculated with to the atomic orbitals shared +di and the stoichiometry +ηi. rc1 and rc2 are the two +cutoff radius around the fourth neighbors in the cutoff function. +

    +

    In the formalism used here, ξ0 is the energy +parameter. ξ0 is in tight-binding approximation the +hopping integral between the hybridized orbitals of the cation and the +anion. In the literature we find many ways to write the hopping +integral depending on whether one takes the point of view of the anion +or cation. These are equivalent vision. The correspondence between the +two visions is explained in appendix A of the article in the +SrTiO3 SMTB-Q_3 (parameter β shown in +this article is in fact the βO). To summarize the +relationship between the hopping integral ξ0 and the +others, we have in an oxide CnOm the following +relationship: +

    +
    +
    +

    Thus parameter μ, indicated above, is given by : μ = (√n ++ √m) ⁄ 2 +

    +

    The potential offers the possibility to consider the polarizability of +the electron clouds of oxygen by changing the slater radius of the +charge density around the oxygens through the parameters rBB, rB and +rS in the ffield.SMTBQ.Syst. This change in radius is performed +according to the method developed by E. Maras +SMTB-Q_2. This method needs to determine the number of +nearest neighbors around the oxygen. This calculation is based on +first (r1n) and second (r2n) distances +neighbors. +

    +

    The SMTB-Q potential is a variable charge potential. The equilibrium +charge on each atom is calculated by the electronegativity +equalization (QEq) method. See Rick for further detail. One +can adjust the frequency, the maximum number of iterative loop and the +convergence of the equilibrium charge calculation. To obtain the +energy conservation in NVE thermodynamic ensemble, we recommend to use +a convergence parameter in the interval 10-5 - +10-6 eV. +

    +

    The ffield.SMTBQ.Syst files are provided for few systems. They consist +of nine parts and the lines beginning with '#' are comments (note that +the number of comment lines matter). The first sections are on the +potential parameters and others are on the simulation options and +might be modified. Keywords are character type and must be enclosed in +quotation marks (''). +

    +

    1) Number of different element in the oxide: +

    +
    • Nelem= 2 or 3 +
    • Divided line +
    +

    2) Atomic parameters +

    +For the anion (oxygen) + +
    • Name of element (char) and stoichiometry in oxide +
    • Formal charge and mass of element +
    • Principal quantic number of outer orbital (n), electronegativity (χ0i) and hardness (J0i) +
    • Ionic radius parameters : max coordination number (coordBB = 6 by default), bulk coordination number (coordB), surface coordination number (coordS) and rBB, rB and rS the slater radius for each coordination number. (note : If you don't want to change the slater radius, use three identical radius values) +
    • Number of orbital shared by the element in the oxide (di) +
    • Divided line +
    +

    For each cations (metal): +

    +
    • Name of element (char) and stoichiometry in oxide +
    • Formal charge and mass of element +
    • Number of electron in outer orbital (ne), electronegativity (χ0i), hardness (J0i) and rSalter the slater radius for the cation. +
    • Number of orbitals shared by the elements in the oxide (di) +
    • Divided line +
    +

    3) Potential parameters: +

    +
    • Keyword for element1, element2 and interaction potential ('second_moment' or 'buck' or 'buckPlusAttr') between element 1 and 2. If the potential is 'second_moment', specify 'oxide' or 'metal' for metal-oxygen or metal-metal interactions respectively. +
    • Potential parameter: 

      	If type of potential is 'second_moment' : A (eV), p, ξ0 (eV) and q 
      						  rc1 (Å), rc2 (Å) and r0 (Å) 
       	If type of potential is 'buck' : C (eV) and ρ (Å) 
      	If type of potential is 'buckPlusAttr' : C (eV) and ρ (Å) 
      						 D (eV), B (Å-1), r1OO (Å) and r2OO (Å)
      +
    • Divided line +
    +

    4) Tables parameters: +

    +
    • Cutoff radius for the Coulomb interaction (Rcoul) +
    • Starting radius (rmin = 1,18845 Å) and increments (dr = 0,001 Å) for creating the potential table. +
    • Divided line +
    +

    5) Rick model parameter: +

    +
    • Nevery : parameter to set the frequency (1/Nevery) of the charge resolution. The charges are evaluated each Nevery time steps. +
    • Max number of iterative loop (loopmax) and precision criterion (prec) in eV of the charge resolution +
    • Divided line +
    +

    6) Coordination parameter: +

    +
    • First (r1n) and second (r2n) neighbor distances in Å +
    • Divided line +
    +

    7) Charge initialization mode: +

    +
    • Keyword (QInitMode) and initial oxygen charge (Qinit). If keyword = 'true', all oxygen charges are initially set equal to Qinit. The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create_atom"#create_atom command or the charge specified in the file structure using read_data command. +
    • Divided line +
    +8) Mode for the electronegativity equalization (Qeq) + +
    • Keyword mode: 
       
      		QEqAll  (one QEq group)			|   no parameters 
      		QEqAllParallel (several QEq groups)	|   no parameters 
      		Surface			|   zlim   (QEq only for z>zlim)
      +
    • Parameter if necessary +
    • Divided line +
    +9) Verbose + +
    • If you want the code to work in verbose mode or not : 'true' or 'false' +
    • If you want to print or not in file 'Energy_component.txt' the three main contributions to the energy of the system according to the description presented above : 'true' or 'false' and NEnergy. This option writes in file every NEnergy time step. If the value is 'false' then NEnergy = 0. The file take into account the possibility to have several QEq group g then it writes: time step, number of atoms in group g, electrostatic part of energy, EES, the interaction between oxygen, EOO, and short range metal-oxygen interaction, EMO. +
    • If you want to print in file 'Electroneg_component.txt' the electronegativity component (∂Etot ⁄∂Qi) or not: 'true' or 'false' and NElectroneg.This option writes in file every NElectroneg time step. If the value is 'false' then NElectroneg = 0. The file consist in atom number i, atom type (1 for oxygen and # higher than 1 for metal), atom position: x, y and z, atomic charge of atom i, electrostatic part of atom i electronegativity, covalent part of atom i electronegativity, the hopping integral of atom i (Zβ2)i and box electronegativity. +
    +

    IMPORTANT NOTE: This last option slows down the calculation +dramatically. Use only with a single processor simulation. +

    +
    + +

    Mixing, shift, table, tail correction, restart, rRESPA info: +

    +

    This pair style does not support the pair_modify +mix, shift, table, and tail options. +

    +

    This pair style does not write its information to binary restart +files, since it is stored in potential files. Thus, you +needs to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. +

    +

    This pair style can only be used via the pair keyword of the +run_style respa command. It does not support the +inner, middle, outer keywords. +

    +
    + +

    Restriction: +

    +

    This pair style is part of the USER-SMTBQ package and is only enabled +if LAMMPS is built with that package. See the Making +LAMMPS section for more info. +

    +

    This potential requires using atom type 1 for oxygen and atom type +higher than 1 for metal atoms. +

    +

    This pair style requires the newton setting to be "on" +for pair interactions. +

    +

    The SMTB-Q potential files provided with LAMMPS (see the potentials +directory) are parameterized for metal units. +

    +
    + +

    Citing this work: +

    +

    Please cite related publication: N. Salles, O. Politano, E. Amzallag +and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189 +

    +
    + + + +

    (SMTB-Q_1) N. Salles, O. Politano, E. Amzallag, R. Tetot, +Comput. Mater. Sci. 111 (2016) 181-189 +

    + + +

    (SMTB-Q_2) E. Maras, N. Salles, R. Tetot, T. Ala-Nissila, +H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399 +

    + + +

    (SMTB-Q_3) R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface +Science 616, 19-8722 28 (2013) +

    + + +

    (Wolf) D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem +Phys, 110, 8254 (1999). +

    + + +

    (Rick) S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141 +(1994). +

    + From 0a19b07d8e44dcc0af4ff3acd9024354ed4a16da Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 23 Oct 2015 00:23:13 +0000 Subject: [PATCH 22/31] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14184 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 30 +-- doc/Section_commands.txt | 2 + doc/genindex.html | 4 + doc/pair_mgpt.html | 17 +- doc/pair_mgpt.txt | 16 +- doc/pair_smtbq.html | 428 ++++++++++++++++++++++++++++++++++++++ doc/pair_smtbq.txt | 261 +++++++++++++++++++++++ doc/searchindex.js | 2 +- 8 files changed, 736 insertions(+), 24 deletions(-) create mode 100644 doc/pair_smtbq.html create mode 100755 doc/pair_smtbq.txt diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 39b34705b6..8922902e94 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -1150,10 +1150,10 @@ KOKKOS, o = USER-OMP, t = OPT.

    if LAMMPS is built with the appropriate package.

    +---++ @@ -1182,28 +1182,28 @@ if LAMMPS + - - + + + + - - + - + + - - + - - - - - + + + diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index e8a388d2de..6bbf013242 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -918,12 +918,14 @@ package"_Section_start.html#start_3. "lj/sf (o)"_pair_lj_sf.html, "meam/spline"_pair_meam_spline.html, "meam/sw/spline"_pair_meam_sw_spline.html, +"mgpt"_pair_mgpt.html, "quip"_pair_quip.html, "reax/c"_pair_reax_c.html, "smd/hertz"_pair_smd_hertz.html, "smd/tlsph"_pair_smd_tlsph.html, "smd/triangulated/surface"_pair_smd_triangulated_surface.html, "smd/ulsph"_pair_smd_ulsph.html, +"smtbq"_pair_smtbq.html, "sph/heatconduction"_pair_sph_heatconduction.html, "sph/idealgas"_pair_sph_idealgas.html, "sph/lj"_pair_sph_lj.html, diff --git a/doc/genindex.html b/doc/genindex.html index 455592789c..cc20eff0fb 100644 --- a/doc/genindex.html +++ b/doc/genindex.html @@ -1882,6 +1882,10 @@ +
    pair_style smtbq +
    + +
    pair_style snap
    diff --git a/doc/pair_mgpt.html b/doc/pair_mgpt.html index 950cea54d1..17e0253710 100644 --- a/doc/pair_mgpt.html +++ b/doc/pair_mgpt.html @@ -244,10 +244,19 @@ directory. These scripts show the necessary steps to perform constant-volume calculations and simulations. It is strongly recommended that the user work through and understand these examples before proceeding to more complex simulations.

    +
    +

    Warning

    +

    For good performance, LAMMPS should be built with the +compiler flags “-O3 -msse3 -funroll-loops” when including this pair +style. The src/MAKE/OPTIONS/Makefile.mpi_fastmgpt is an example +machine Makefile with these options included as part of a standard MPI +build. Note that as-is it will build with whatever low-level compiler +(g++, icc, etc) is the default for your MPI installation.

    +

    Mixing, shift, table tail correction, restart:

    -

    The (mgpt) pair style does not support the -pair_modify mix, shift, table, and tail options.

    +

    This pair style does not support the pair_modify +mix, shift, table, and tail options.

    This pair style does not write its information to binary restart files, since it is stored in potential files. Thus, you needs to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file.

    @@ -258,8 +267,8 @@ script that reads a restart file.

    Restrictions¶

    -

    The mgpt pair style is part of the USER-MGPT package and is only -enabled if LAMMPS is built with that package.

    +

    This pair style is part of the USER-MGPT package and is only enabled +if LAMMPS is built with that package. See the Making LAMMPS section for more info.

    The MGPT potentials require the newtion setting to be “on” for pair style interactions.

    The stored parmin and potin potential files provided with LAMMPS in diff --git a/doc/pair_mgpt.txt b/doc/pair_mgpt.txt index 69b9cbd097..fc21a488c7 100644 --- a/doc/pair_mgpt.txt +++ b/doc/pair_mgpt.txt @@ -131,12 +131,19 @@ constant-volume calculations and simulations. It is strongly recommended that the user work through and understand these examples before proceeding to more complex simulations. +IMPORTANT NOTE: For good performance, LAMMPS should be built with the +compiler flags "-O3 -msse3 -funroll-loops" when including this pair +style. The src/MAKE/OPTIONS/Makefile.mpi_fastmgpt is an example +machine Makefile with these options included as part of a standard MPI +build. Note that as-is it will build with whatever low-level compiler +(g++, icc, etc) is the default for your MPI installation. + :line [Mixing, shift, table tail correction, restart]: -The (mgpt) pair style does not support the -"pair_modify"_pair_modify.html mix, shift, table, and tail options. +This pair style does not support the "pair_modify"_pair_modify.html +mix, shift, table, and tail options. This pair style does not write its information to "binary restart files"_restart.html, since it is stored in potential files. Thus, you @@ -151,8 +158,9 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] -The {mgpt} pair style is part of the USER-MGPT package and is only -enabled if LAMMPS is built with that package. +This pair style is part of the USER-MGPT package and is only enabled +if LAMMPS is built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. The MGPT potentials require the "newtion"_newton.html setting to be "on" for pair style interactions. diff --git a/doc/pair_smtbq.html b/doc/pair_smtbq.html new file mode 100644 index 0000000000..d8770929a5 --- /dev/null +++ b/doc/pair_smtbq.html @@ -0,0 +1,428 @@ + + + + + + + + + + + pair_style smtbq command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    pair_style smtbq command¶

    +
    +

    Syntax¶

    +
    pair_style smtbq
+
    +
    +
    +
    +

    Examples¶

    +
    pair_style smtbq
+pair_coeff * * ffield.smtbq.Al2O3 O Al
+
    +
    +
    +
    +

    Description¶

    +

    This pair stylecomputes a variable charge SMTB-Q (Second-Moment +tight-Binding QEq) potential as described in SMTB-Q_1 and +SMTB-Q_2. Briefly, the energy of metallic-oxygen systems +is given by three contributions:

    +_images/pair_smtbq1.jpg +

    where E<sub>tot</sub> is the total potential energy of the system, +E<sub>ES</sub> is the electrostatic part of the total energy, +E<sub>OO</sub> is the interaction between oxygens and +E<sub>MO</sub> is a short-range interaction between metal and oxygen +atoms. This interactions depend on interatomic distance +r<sub>ij</sub> and/or the charge Q<sub>i</sub> of atoms +i. Cut-off function enables smooth convergence to zero interaction.

    +

    The parameters appearing in the upper expressions are set in the +ffield.SMTBQ.Syst file where Syst corresponds to the selected system +(e.g. field.SMTBQ.Al2O3). Exemples for TiO<sub>2</sub>, +Al<sub>2</sub>O<sub>3</sub> are provided. A single pair_coeff command +is used with the SMTBQ styles which provides the path to the potential +file with parameters for needed elements. These are mapped to LAMMPS +atom types by specifying additional arguments after the potential +filename in the pair_coeff command. Note that atom type 1 must always +correspond to oxygen atoms. As an example, to simulate a TiO2 system, +atom type 1 has to be oxygen and atom type 2 Ti. The following +pair_coeff command should then be used:

    +
    pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti
+
    +
    +

    The electrostatic part of the energy consists of two components

    +

    self-energy of atom i in the form of a second order charge dependent +polynomial and a long-range Coulombic electrostatic interaction. The +latter uses the wolf summation method described in Wolf, +spherically truncated at a longer cutoff, R<sub>coul</sub>. The +charge of each ion is modeled by an orbital Slater which depends on +the principal quantum number (n) of the outer orbital shared by the +ion.

    +

    Interaction between oxygen, E<sub>OO</sub>, consists of two parts, +an attractive and a repulsive part. The attractive part is effective +only at short range (< r<sub>2</sub><sup>OO</sup>). The attractive +contribution was optimized to study surfaces reconstruction +(e.g. SMTB-Q_2 in TiO<sub>2</sub>) and is not necessary +for oxide bulk modeling. The repulsive part is the Pauli interaction +between the electron clouds of oxygen. The Pauli repulsion and the +coulombic electrostatic interaction have same cut off value. In the +ffield.SMTBQ.Syst, the keyword ‘buck’ allows to consider only the +repulsive O-O interactions. The keyword ‘buckPlusAttr’ allows to +consider the repulsive and the attractive O-O interactions.

    +

    The short-range interaction between metal-oxygen, E<sub>MO</sub> is +based on the second moment approximation of the density of states with +a N-body potential for the band energy term, +E<sup>i</sup><sub>cov</sub>, and a Born-Mayer type repulsive terms +as indicated by the keyword ‘second_moment’ in the +ffield.SMTBQ.Syst. The energy band term is given by:

    +_images/pair_smtbq2.jpg +

    where &#951<sub>i</sub> is the stoichiometry of atom i, +&#948Q<sub>i</sub> is the charge delocalization of atom i, +compared to its formal charge +Q<sup>F</sup><sub>i</sub>. n<sub>0</sub>, the number of hybridized +orbitals, is calculated with to the atomic orbitals shared +d<sub>i</sub> and the stoichiometry +&#951<sub>i</sub>. r<sub>c1</sub> and r<sub>c2</sub> are the two +cutoff radius around the fourth neighbors in the cutoff function.

    +

    In the formalism used here, &#958<sup>0</sup> is the energy +parameter. &#958<sup>0</sup> is in tight-binding approximation the +hopping integral between the hybridized orbitals of the cation and the +anion. In the literature we find many ways to write the hopping +integral depending on whether one takes the point of view of the anion +or cation. These are equivalent vision. The correspondence between the +two visions is explained in appendix A of the article in the +SrTiO<sub>3</sub> SMTB-Q_3 (parameter &#946 shown in +this article is in fact the &#946<sub>O</sub>). To summarize the +relationship between the hopping integral &#958<sup>0</sup> and the +others, we have in an oxide C<sub>n</sub>O<sub>m</sub> the following +relationship:

    +_images/pair_smtbq3.jpg +

    Thus parameter &#956, indicated above, is given by : &#956 = (&#8730n ++ &#8730m) &#8260 2

    +

    The potential offers the possibility to consider the polarizability of +the electron clouds of oxygen by changing the slater radius of the +charge density around the oxygens through the parameters rBB, rB and +rS in the ffield.SMTBQ.Syst. This change in radius is performed +according to the method developed by E. Maras +SMTB-Q_2. This method needs to determine the number of +nearest neighbors around the oxygen. This calculation is based on +first (r<sub>1n</sub>) and second (r<sub>2n</sub>) distances +neighbors.

    +

    The SMTB-Q potential is a variable charge potential. The equilibrium +charge on each atom is calculated by the electronegativity +equalization (QEq) method. See Rick for further detail. One +can adjust the frequency, the maximum number of iterative loop and the +convergence of the equilibrium charge calculation. To obtain the +energy conservation in NVE thermodynamic ensemble, we recommend to use +a convergence parameter in the interval 10<sup>-5</sup> - +10<sup>-6</sup> eV.

    +

    The ffield.SMTBQ.Syst files are provided for few systems. They consist +of nine parts and the lines beginning with ‘#’ are comments (note that +the number of comment lines matter). The first sections are on the +potential parameters and others are on the simulation options and +might be modified. Keywords are character type and must be enclosed in +quotation marks (‘’).

    +
      +
    1. Number of different element in the oxide:
      2. +
    +
      +
    • N<sub>elem</sub>= 2 or 3
      • +
    • Divided line
      • +
    +
      +
    1. Atomic parameters
      2. +
    +

    For the anion (oxygen)

    +
      +
    • Name of element (char) and stoichiometry in oxide
      • +
    • Formal charge and mass of element
      • +
    • Principal quantic number of outer orbital (n), electronegativity (&#967<sup>0</sup><sub>i</simulationub>) and hardness (J<sup>0</sup><sub>i</sub>)
      • +
    • Ionic radius parameters : max coordination number (coordBB = 6 by default), bulk coordination number (coordB), surface coordination number (coordS) and rBB, rB and rS the slater radius for each coordination number. (<b>note : If you don’t want to change the slater radius, use three identical radius values</b>)
      • +
    • Number of orbital shared by the element in the oxide (d<sub>i</sub>)
      • +
    • Divided line
      • +
    +

    For each cations (metal):

    +
      +
    • Name of element (char) and stoichiometry in oxide
      • +
    • Formal charge and mass of element
      • +
    • Number of electron in outer orbital (ne), electronegativity (&#967<sup>0</sup><sub>i</simulationub>), hardness (J<sup>0</sup><sub>i</sub>) and r<sub>Salter</sub> the slater radius for the cation.
      • +
    • Number of orbitals shared by the elements in the oxide (d<sub>i</sub>)
      • +
    • Divided line
      • +
    +
      +
    1. Potential parameters:
      2. +
    +
      +
    • Keyword for element1, element2 and interaction potential (‘second_moment’ or ‘buck’ or ‘buckPlusAttr’) between element 1 and 2. If the potential is ‘second_moment’, specify ‘oxide’ or ‘metal’ for metal-oxygen or metal-metal interactions respectively.
      • +
    • Potential parameter: <pre><br/> If type of potential is ‘second_moment’ : A (eV), p, &#958<sup>0</sup> (eV) and q <br/> r<sub>c1</sub> (&#197), r<sub>c2</sub> (&#197) and r<sub>0</sub> (&#197) <br/> If type of potential is ‘buck’ : C (eV) and &#961 (&#197) <br/> If type of potential is ‘buckPlusAttr’ : C (eV) and &#961 (&#197) <br/> D (eV), B (&#197<sup>-1</sup>), r<sub>1</sub><sup>OO</sup> (&#197) and r<sub>2</sub><sup>OO</sup> (&#197) </pre>
      • +
    • Divided line
      • +
    +
      +
    1. Tables parameters:
      2. +
    +
      +
    • Cutoff radius for the Coulomb interaction (R<sub>coul</sub>)
      • +
    • Starting radius (r<sub>min</sub> = 1,18845 &#197) and increments (dr = 0,001 &#197) for creating the potential table.
      • +
    • Divided line
      • +
    +
      +
    1. Rick model parameter:
      2. +
    +
      +
    • Nevery : parameter to set the frequency (1/Nevery) of the charge resolution. The charges are evaluated each Nevery time steps.
      • +
    • Max number of iterative loop (loopmax) and precision criterion (prec) in eV of the charge resolution
      • +
    • Divided line
      • +
    +
      +
    1. Coordination parameter:
      2. +
    +
      +
    • First (r<sub>1n</sub>) and second (r<sub>2n</sub>) neighbor distances in &#197
      • +
    • Divided line
      • +
    +
      +
    1. Charge initialization mode:
      2. +
    +
      +
    • Keyword (QInitMode) and initial oxygen charge (Q<sub>init</sub>). If keyword = ‘true’, all oxygen charges are initially set equal to Q<sub>init</sub>. The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = ‘false’, all atom charges are initially set equal to 0 if you use “create_atom”#create_atom command or the charge specified in the file structure using read_data command.
      • +
    • Divided line
      • +
    +
      +
    1. Mode for the electronegativity equalization (Qeq)
      2. +
    +
      +
    • Keyword mode: <pre> <br/> QEqAll (one QEq group) | no parameters <br/> QEqAllParallel (several QEq groups) | no parameters <br/> Surface | zlim (QEq only for z>zlim) </pre>
      • +
    • Parameter if necessary
      • +
    • Divided line
      • +
    +
      +
    1. Verbose
      2. +
    +
      +
    • If you want the code to work in verbose mode or not : ‘true’ or ‘false’
      • +
    • If you want to print or not in file ‘Energy_component.txt’ the three main contributions to the energy of the system according to the description presented above : ‘true’ or ‘false’ and N<sub>Energy</sub>. This option writes in file every N<sub>Energy</sub> time step. If the value is ‘false’ then N<sub>Energy</sub> = 0. The file take into account the possibility to have several QEq group g then it writes: time step, number of atoms in group g, electrostatic part of energy, E<sub>ES</sub>, the interaction between oxygen, E<sub>OO</sub>, and short range metal-oxygen interaction, E<sub>MO</sub>.
      • +
    • If you want to print in file ‘Electroneg_component.txt’ the electronegativity component (&#8706E<sub>tot</sub> &#8260&#8706Q<sub>i</sub>) or not: ‘true’ or ‘false’ and N<sub>Electroneg</sub>.This option writes in file every N<sub>Electroneg</sub> time step. If the value is ‘false’ then N<sub>Electroneg</sub> = 0. The file consist in atom number i, atom type (1 for oxygen and # higher than 1 for metal), atom position: x, y and z, atomic charge of atom i, electrostatic part of atom i electronegativity, covalent part of atom i electronegativity, the hopping integral of atom i (Z&#946<sup>2</sup>)<sub>i<sub> and box electronegativity.
      • +
    +
    +

    Warning

    +

    This last option slows down the calculation +dramatically. Use only with a single processor simulation.

    +
    +
    +

    Mixing, shift, table, tail correction, restart, rRESPA info:

    +

    This pair style does not support the pair_modify +mix, shift, table, and tail options.

    +

    This pair style does not write its information to binary restart files, since it is stored in potential files. Thus, you +needs to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file.

    +

    This pair style can only be used via the pair keyword of the +run_style respa command. It does not support the +inner, middle, outer keywords.

    +
    +

    Restriction:

    +

    This pair style is part of the USER-SMTBQ package and is only enabled +if LAMMPS is built with that package. See the Making LAMMPS section for more info.

    +

    This potential requires using atom type 1 for oxygen and atom type +higher than 1 for metal atoms.

    +

    This pair style requires the newton setting to be “on” +for pair interactions.

    +

    The SMTB-Q potential files provided with LAMMPS (see the potentials +directory) are parameterized for metal units.

    +
    +

    Citing this work:

    +

    Please cite related publication: N. Salles, O. Politano, E. Amzallag +and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189

    +
    +

    (SMTB-Q_1) N. Salles, O. Politano, E. Amzallag, R. Tetot, +Comput. Mater. Sci. 111 (2016) 181-189

    +

    (SMTB-Q_2) E. Maras, N. Salles, R. Tetot, T. Ala-Nissila, +H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399

    +

    (SMTB-Q_3) R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface +Science 616, 19-8722 28 (2013)

    +

    (Wolf) D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem +Phys, 110, 8254 (1999).

    +

    (Rick) S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141 +(1994).

    +
    +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/pair_smtbq.txt b/doc/pair_smtbq.txt new file mode 100755 index 0000000000..8dc612ed92 --- /dev/null +++ b/doc/pair_smtbq.txt @@ -0,0 +1,261 @@ +"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 + +pair_style smtbq command :h3 + +[Syntax:] + +pair_style smtbq :pre + +[Examples:] + +pair_style smtbq +pair_coeff * * ffield.smtbq.Al2O3 O Al :pre + +[Description:] + +This pair stylecomputes a variable charge SMTB-Q (Second-Moment +tight-Binding QEq) potential as described in "SMTB-Q_1"_#SMTB-Q_1 and +"SMTB-Q_2"_#SMTB-Q_2. Briefly, the energy of metallic-oxygen systems +is given by three contributions: + +:c,image(Eqs/pair_smtbq1.jpg) + +where {Etot} is the total potential energy of the system, +{EES} is the electrostatic part of the total energy, +{EOO} is the interaction between oxygens and +{EMO} is a short-range interaction between metal and oxygen +atoms. This interactions depend on interatomic distance +{rij} and/or the charge {Qi} of atoms +{i}. Cut-off function enables smooth convergence to zero interaction. + +The parameters appearing in the upper expressions are set in the +ffield.SMTBQ.Syst file where Syst corresponds to the selected system +(e.g. field.SMTBQ.Al2O3). Exemples for TiO2, +Al2O3 are provided. A single pair_coeff command +is used with the SMTBQ styles which provides the path to the potential +file with parameters for needed elements. These are mapped to LAMMPS +atom types by specifying additional arguments after the potential +filename in the pair_coeff command. Note that atom type 1 must always +correspond to oxygen atoms. As an example, to simulate a TiO2 system, +atom type 1 has to be oxygen and atom type 2 Ti. The following +pair_coeff command should then be used: + +pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti :pre + +The electrostatic part of the energy consists of two components : +self-energy of atom {i} in the form of a second order charge dependent +polynomial and a long-range Coulombic electrostatic interaction. The +latter uses the wolf summation method described in "Wolf"_#Wolf, +spherically truncated at a longer cutoff, {Rcoul}. The +charge of each ion is modeled by an orbital Slater which depends on +the principal quantum number ({n}) of the outer orbital shared by the +ion. + +Interaction between oxygen, {EOO}, consists of two parts, +an attractive and a repulsive part. The attractive part is effective +only at short range (< r2OO). The attractive +contribution was optimized to study surfaces reconstruction +(e.g. "SMTB-Q_2"_#SMTB-Q_2 in TiO2) and is not necessary +for oxide bulk modeling. The repulsive part is the Pauli interaction +between the electron clouds of oxygen. The Pauli repulsion and the +coulombic electrostatic interaction have same cut off value. In the +ffield.SMTBQ.Syst, the keyword {'buck'} allows to consider only the +repulsive O-O interactions. The keyword {'buckPlusAttr'} allows to +consider the repulsive and the attractive O-O interactions. + +The short-range interaction between metal-oxygen, {EMO} is +based on the second moment approximation of the density of states with +a N-body potential for the band energy term, +{Eicov}, and a Born-Mayer type repulsive terms +as indicated by the keyword {'second_moment'} in the +ffield.SMTBQ.Syst. The energy band term is given by: + +:c,image(Eqs/pair_smtbq2.jpg) + +where {ηi} is the stoichiometry of atom {i}, +{δQi} is the charge delocalization of atom {i}, +compared to its formal charge +{QFi}. n0, the number of hybridized +orbitals, is calculated with to the atomic orbitals shared +{di} and the stoichiometry +{ηi}. {rc1} and {rc2} are the two +cutoff radius around the fourth neighbors in the cutoff function. + +In the formalism used here, {ξ0} is the energy +parameter. {ξ0} is in tight-binding approximation the +hopping integral between the hybridized orbitals of the cation and the +anion. In the literature we find many ways to write the hopping +integral depending on whether one takes the point of view of the anion +or cation. These are equivalent vision. The correspondence between the +two visions is explained in appendix A of the article in the +SrTiO3 "SMTB-Q_3"_#SMTB-Q_3 (parameter {β} shown in +this article is in fact the {βO}). To summarize the +relationship between the hopping integral {ξ0} and the +others, we have in an oxide CnOm the following +relationship: + +:c,image(Eqs/pair_smtbq3.jpg) + +Thus parameter μ, indicated above, is given by : μ = (√n ++ √m) ⁄ 2 + +The potential offers the possibility to consider the polarizability of +the electron clouds of oxygen by changing the slater radius of the +charge density around the oxygens through the parameters {rBB, rB and +rS} in the ffield.SMTBQ.Syst. This change in radius is performed +according to the method developed by E. Maras +"SMTB-Q_2"_#SMTB-Q_2. This method needs to determine the number of +nearest neighbors around the oxygen. This calculation is based on +first ({r1n}) and second ({r2n}) distances +neighbors. + +The SMTB-Q potential is a variable charge potential. The equilibrium +charge on each atom is calculated by the electronegativity +equalization (QEq) method. See "Rick"_#Rick for further detail. One +can adjust the frequency, the maximum number of iterative loop and the +convergence of the equilibrium charge calculation. To obtain the +energy conservation in NVE thermodynamic ensemble, we recommend to use +a convergence parameter in the interval 10-5 - +10-6 eV. + +The ffield.SMTBQ.Syst files are provided for few systems. They consist +of nine parts and the lines beginning with '#' are comments (note that +the number of comment lines matter). The first sections are on the +potential parameters and others are on the simulation options and +might be modified. Keywords are character type and must be enclosed in +quotation marks (''). + +1) Number of different element in the oxide: + +Nelem= 2 or 3 +Divided line :ul + +2) Atomic parameters + +For the anion (oxygen) : + +Name of element (char) and stoichiometry in oxide +Formal charge and mass of element +Principal quantic number of outer orbital ({n}), electronegativity ({χ0i}) and hardness ({J0i}) + Ionic radius parameters : max coordination number ({coordBB} = 6 by default), bulk coordination number {(coordB)}, surface coordination number {(coordS)} and {rBB, rB and rS} the slater radius for each coordination number. (note : If you don't want to change the slater radius, use three identical radius values) +Number of orbital shared by the element in the oxide ({di}) +Divided line :ul + +For each cations (metal): + +Name of element (char) and stoichiometry in oxide +Formal charge and mass of element +Number of electron in outer orbital {(ne)}, electronegativity ({χ0i}), hardness ({J0i}) and {rSalter} the slater radius for the cation. +Number of orbitals shared by the elements in the oxide ({di}) +Divided line :ul + +3) Potential parameters: + +Keyword for element1, element2 and interaction potential ('second_moment' or 'buck' or 'buckPlusAttr') between element 1 and 2. If the potential is 'second_moment', specify 'oxide' or 'metal' for metal-oxygen or metal-metal interactions respectively. +Potential parameter: 

    	If type of potential is 'second_moment' : {A (eV)}, {p}, {ξ0} (eV) and {q} 
    						  {rc1} (Å), {rc2} (Å) and {r0} (Å) 
     	If type of potential is 'buck' : {C} (eV) and {ρ} (Å) 
    	If type of potential is 'buckPlusAttr' : {C} (eV) and {ρ} (Å) 
    						 {D} (eV), {B} (Å-1), {r1OO} (Å) and {r2OO} (Å)
    +Divided line :ul + +4) Tables parameters: + +Cutoff radius for the Coulomb interaction ({Rcoul}) +Starting radius ({rmin} = 1,18845 Å) and increments ({dr} = 0,001 Å) for creating the potential table. +Divided line :ul + +5) Rick model parameter: + +{Nevery} : parameter to set the frequency ({1/Nevery}) of the charge resolution. The charges are evaluated each {Nevery} time steps. +Max number of iterative loop ({loopmax}) and precision criterion ({prec}) in eV of the charge resolution +Divided line :ul + +6) Coordination parameter: + +First ({r1n}) and second ({r2n}) neighbor distances in Å +Divided line :ul + +7) Charge initialization mode: + +Keyword ({QInitMode}) and initial oxygen charge ({Qinit}). If keyword = 'true', all oxygen charges are initially set equal to {Qinit}. The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create_atom"#create_atom command or the charge specified in the file structure using "read_data"_#read_data.html command. +Divided line :ul + +8) Mode for the electronegativity equalization (Qeq) : + +Keyword mode: 
     
    		QEqAll  (one QEq group)			|   no parameters 
    		QEqAllParallel (several QEq groups)	|   no parameters 
    		Surface			|   zlim   (QEq only for z>zlim)
    +Parameter if necessary +Divided line :ul + +9) Verbose : + +If you want the code to work in verbose mode or not : 'true' or 'false' +If you want to print or not in file 'Energy_component.txt' the three main contributions to the energy of the system according to the description presented above : 'true' or 'false' and {NEnergy}. This option writes in file every {NEnergy} time step. If the value is 'false' then {NEnergy} = 0. The file take into account the possibility to have several QEq group {g} then it writes: time step, number of atoms in group {g}, electrostatic part of energy, {EES}, the interaction between oxygen, {EOO}, and short range metal-oxygen interaction, {EMO}. +If you want to print in file 'Electroneg_component.txt' the electronegativity component ({∂Etot ⁄∂Qi}) or not: 'true' or 'false' and {NElectroneg}.This option writes in file every {NElectroneg} time step. If the value is 'false' then {NElectroneg} = 0. The file consist in atom number {i}, atom type (1 for oxygen and # higher than 1 for metal), atom position: {x}, {y} and {z}, atomic charge of atom {i}, electrostatic part of atom {i} electronegativity, covalent part of atom {i} electronegativity, the hopping integral of atom {i} {(Zβ2)i} and box electronegativity. :ul + +IMPORTANT NOTE: This last option slows down the calculation +dramatically. Use only with a single processor simulation. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info:] + +This pair style does not support the "pair_modify"_pair_modify.html +mix, shift, table, and tail options. + +This pair style does not write its information to "binary restart +files"_restart.html, since it is stored in potential files. Thus, you +needs to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +:line + +[Restriction:] + +This pair style is part of the USER-SMTBQ package and is only enabled +if LAMMPS is built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +This potential requires using atom type 1 for oxygen and atom type +higher than 1 for metal atoms. + +This pair style requires the "newton"_newton.html setting to be "on" +for pair interactions. + +The SMTB-Q potential files provided with LAMMPS (see the potentials +directory) are parameterized for metal "units"_unit.html. + +:line + +[Citing this work:] + +Please cite related publication: N. Salles, O. Politano, E. Amzallag +and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189 + +:line + +:link(SMTB-Q_1) +[(SMTB-Q_1)] N. Salles, O. Politano, E. Amzallag, R. Tetot, +Comput. Mater. Sci. 111 (2016) 181-189 + +:link(SMTB-Q_2) +[(SMTB-Q_2)] E. Maras, N. Salles, R. Tetot, T. Ala-Nissila, +H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399 + +:link(SMTB-Q_3) +[(SMTB-Q_3)] R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface +Science 616, 19-8722 28 (2013) + +:link(Wolf) +[(Wolf)] D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem +Phys, 110, 8254 (1999). + +:link(Rick) +[(Rick)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141 +(1994). diff --git a/doc/searchindex.js b/doc/searchindex.js index 073e615520..64b464ec73 100644 --- a/doc/searchindex.js +++ b/doc/searchindex.js @@ -1 +1 @@ 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248,249,250,252,257,258,264,269,270,272,275,279,283,291,293,296,304,309,311,312,313,315,316,317,318,319,323,325,327,331,334,335,340,347,353,354,356,357,359,361,362,363,364,365,369,376,378,385,386,387,388,394,395,396,407,408,409,410,411,412,413,417,421,423,424,431,441,443,444,445,448,454,456,458,459,460,461,462,464,465,467,469,471,473,476,477,480,484,485,486,487,488,489],afterrun:467,afterward:3,afterword:41,ag1:164,ag2:164,again:[6,11,12,16,17,62,140,145,151,159,188,191,217,232,279,334,347,358,408,409,454,456,457,459,461,466,473,475,485,487],against:[11,12,13,64,218,358,423,424],aggreg:[6,12,65,68,69,79,92,108,115,232,248,291,293,306,454,486],aggress:[232,473],agilio:[9,13],agre:[3,8,185,356,365,396,424],agreement:[5,7],ahd:393,ahead:327,aidan:[0,5,7,9,13,351],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:190,akohlmei:[7,9,13,192,233],aktulga:[7,9,286,424],al2o3_001:[118,294],al3:164,ala:239,alain:9,alat:[274,410],alb:[421,443,445],albeit:292,albert:9,alchem:[87,159],alcohol:323,alcu:[364,369],alcu_eam:421,alderton:382,alejandr:[252,253],alessandro:13,algebra:413,algorithm:[0,1,6,7,8,9,41,61,191,200,211,214,217,239,241,242,264,276,293,296,315,316,320,323,328,354,355,356,360,363,387,409,413,428,430,454,456,473],alia:[12,16],alias:[1,349],aliceblu:191,align:[6,12,29,41,71,167,185,207,211,234,351,459,462,480],alkali:387,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,153,158,159,160,161,162,163,164,165,166,167,168,169,171,173,178,184,185,188,189,190,191,192,194,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,245,247,248,250,252,253,254,255,256,257,258,259,260,261,262,263,264,265,267,268,269,270,271,272,273,274,275,276,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,304,305,307,308,309,310,311,312,315,316,317,318,319,320,321,322,323,325,326,327,328,329,330,331,332,333,334,335,338,343,346,347,348,349,350,351,353,356,357,358,359,360,362,363,364,365,366,368,369,370,372,373,374,375,376,378,379,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,403,407,408,409,410,411,412,413,414,415,416,417,418,420,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,452,453,454,456,457,458,459,460,461,462,463,464,466,467,468,469,470,471,472,473,474,476,477,478,480,484,485,486,487,488,489],allen:[29,87,382,390],allentildeslei:87,allign:3,allindex:332,alloc:[3,5,6,8,9,11,12,60,226,322,357,359,363,419,424,459,467],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,142,144,145,158,163,164,165,167,173,184,185,188,190,191,192,194,195,197,199,200,201,203,204,205,206,207,208,209,211,213,214,215,216,217,218,222,223,226,228,229,230,231,233,236,239,242,243,247,249,252,253,274,278,280,281,282,283,287,293,294,296,297,299,300,304,308,315,316,317,318,320,321,322,323,324,325,331,333,335,343,348,349,351,356,357,358,359,362,363,366,369,370,371,372,373,374,379,385,387,391,392,393,394,399,403,408,409,413,415,421,424,425,428,430,439,449,451,454,457,459,461,462,463,464,465,466,469,471,472,473,476,477,485,486],almost:[2,3,12,60,234,283,320,349,360,363,439],alo:379,alon:[6,7,214,289,423,424,457],alond:13,along:[6,8,9,12,29,40,87,118,164,165,187,188,190,214,234,239,240,244,249,251,283,293,296,297,301,305,306,315,319,320,326,329,331,351,354,355,356,358,379,382,391,394,397,399,403,410,423,424,442,459,462,469,470,485],alonso:[411,412],alpha:[6,12,51,195,239,275,283,288,356,364,367,370,379,383,385,386,388,393,398,399,410,416,420,444,446,477,480],alpha_:446,alpha_c:407,alpha_i:[431,446],alpha_ialpha_j:446,alpha_lj:407,alphabet:[2,3,22,37,44,55,63,173,184,194,335,343,357,376,440,459],alphanumer:[3,63,194,282,290,333,357,485],alreadi:[3,7,8,9,12,16,17,18,42,165,166,168,189,199,203,207,208,211,213,217,243,281,283,308,331,357,358,383,392,394,401,409,439,449,452,455,459,460,464,469,485],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,149,151,152,153,154,155,157,158,159,160,161,162,163,165,166,167,168,169,171,173,184,185,186,188,189,190,191,192,194,195,196,197,199,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,223,226,227,228,229,230,232,233,236,237,238,239,249,250,252,253,254,255,256,257,258,263,266,267,269,270,271,272,274,275,276,278,279,280,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,301,302,305,306,308,311,312,313,3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335,343,358,376,440],client:[233,235],climb:[251,358,473],clinic:[7,13],clo:[154,187,486],clock:[12,454,473],clockwis:326,close:[3,6,11,12,13,39,41,67,141,168,188,213,214,215,230,237,239,252,270,293,296,326,329,347,349,352,354,355,358,363,365,369,379,380,410,415,427,429,445,463,469,480,482],closer:[3,41,116,163,187,188,211,215,219,317,358],closest:[213,274,293,323,390,425,439,449],cloud:480,clovertown:18,clsuter:72,clump1:[278,293],clump2:[278,293],clump3:[278,293],clump:293,cluster:[],clutter:[3,9],cmap:459,cmatrix:230,cmax:410,cmd:[11,12,276,470],cmin:410,cmm:[],cn1:204,cn2:204,cna:[],cnn:204,cnr:[9,13],cnt:[394,463],co2:[40,164,296,357],coars:[7,9,29,36,40,54,177,278,293,308,392,426,471],coarser:[349,485],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,171,172,173,178,334,335,340,376,394,398,415,428,430,432,459,461],coeffcient:459,coeffici:[],coefficienct:383,coefficient0:385,coefficient1:385,coeffieci:[6,367],coeffincientn:385,coexist:[9,228,387],cohes:[6,388,410],coincid:[122,329,374,408,409,454],colberg:189,cold:[6,150,228,232,359,480],coldest:316,coleman8:9,coleman:[9,118,164,294],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,145,153,160,162,165,188,191,203,216,242,248,278,288,291,293,331,348,357,359,377,397,459,466,472,478,489],collid:[222,308,330],colliex:164,collinear:[3,278],collis:[3,239,308,326,330,384,391,452],colllis:308,colloid:[],colombo:39,colon:[192,331,460],color1:191,color2:191,color:[3,9,41,188,190,191,211,229,283,288],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,145,153,160,162,163,164,185,188,191,194,202,203,204,206,207,208,209,242,249,250,283,293,309,310,320,330,389,393,423,424,460,474,476,485],colvar:[],colvarmodul:12,com:[],comamnd:217,comand:[214,461],comannd:363,comb3:[],comb:[],comb_1:285,comb_2:285,combiant:380,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,144,158,188,190,200,206,233,242,252,276,282,312,321,329,332,334,348,349,351,355,363,377,379,380,387,388,394,406,407,431,441,443,445,448,451,462,467,472,480,485],come:[],comfort:[12,13],comm:[0,3,12,61,73,189,233,235,236,349,358,363,383,415,420,442],comm_modifi:[],comm_modift:61,comm_styl:[],command:[],comment:[2,7,11,12,38,56,171,185,188,237,293,320,357,358,364,385,386,388,398,410,417,424,431,441,442,443,444,445,448,456,457,459,480,485],commerci:7,commmand:[3,6,12,59,107,271,453,454,456,473,488],common:[],commonli:[3,6,12,17,25,57,59,105,167,188,190,192,344,392,401,431,443,445,459,462,471],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,169,190,191,211,212,213,215,216,217,233,235,239,241,242,243,252,275,282,284,285,286,293,308,320,331,346,348,359,360,361,363,384,419,456,457,461,468,469,485,487,489],communc:348,comp:[7,189,235,236,296,349,358,387,415,420,425,438,442,444],compact:[63,194,376,440],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,148,163,164,173,184,191,221,284,331,333,348,349,356,358,410,454,473,474,480,484],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,172,173,184,334,335,343,375,440],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,176,188,192,196,202,203,204,206,207,208,209,211,275,287,312,315,322,325,328,348,363,395,413,415,442,456,457,485],compens:[6,212,213,291,359,387],compet:319,competit:349,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,163,188,189,190,192,233,319,349,363,413,459,460,464,485],compl:17,complain:[12,17],complement:410,complementari:[7,379,399],complet:[3,6,9,12,15,41,59,71,191,207,211,216,242,276,279,282,308,319,321,333,347,358,363,388,428,430,447,454,459,464,467,471,473,476,480,485],complex:[6,8,11,12,13,25,40,42,62,140,142,153,165,166,239,304,329,346,358,387,413,442,457,459,462,485],compli:[315,319],complic:[6,7,9,12,13,201,228,457],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,160,161,162,188,190,191,197,198,202,203,204,205,206,207,208,209,210,214,215,217,218,223,226,231,235,236,239,242,244,248,249,251,252,253,256,257,258,269,270,272,273,275,276,277,280,291,293,295,296,297,301,302,305,308,311,312,313,315,322,323,328,329,330,348,351,355,356,357,358,363,383,387,391,408,409,428,430,431,459,460,469,477,485,486],componenet:6,composit:[6,201,239,385],compound:[378,387,388,448],compres:[71,114,203],compress:[3,59,71,114,168,188,190,191,203,217,250,256,280,283],compris:[40,329,397,425,447],compton:[118,164],comptu:3,compuat:349,comput:[],computation:[3,6,212,213,320,369],computational:480,compute_arrai:8,compute_fep:[196,407],compute_group_group:228,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,294],compute_scalar:8,compute_temp:8,compute_ti:196,compute_vector:8,compute_xrd:164,concaten:[2,3,488],concav:329,concentr:385,concept:[6,145,155,203,468],conceptu:[3,6,71,153,215,217,358,379,394,410,464],concern:[6,73,87,189,229],concis:[11,319],conclud:12,concret:8,concurr:[9,16,349,485],conden:[320,443,445],condens:[6,147,320,365,381,385,399,448],condit:[],conducit:6,conduct:[],cone:462,confer:413,confid:[3,473],config:[12,188,456],configfil:216,configur:[1,2,6,12,15,17,38,59,122,167,185,187,188,190,194,215,216,217,218,222,228,235,236,264,276,284,319,346,356,358,365,369,386,410,413,441,443,445,448,454,459,461,462,473],confin:[459,473],conflict:[3,12,40,415,457],conform:[3,6,13,59,214,215,251,292,297,319,342,358,387,471],confus:[3,448],conjuct:383,conjug:[7,8,236,355,387,423,424],conjunct:[6,7,71,86,87,114,148,153,159,165,169,191,195,196,236,239,243,264,279,280,284,285,286,288,293,308,316,323,328,348,349,358,370,372,376,379,383,387,393,399,415,418,426,446,459,462,466,480,489],connect:[3,6,87,150,168,214,233,278,293,296,305,358,380,391,439,445,456,457,463,480],conput:3,consecut:[3,11,12,39,71,165,191,195,196,218,233,234,379,399,403,454,460,462],consequ:[1,6,201,320,398,473],conserv:[3,194,201,214,221,222,229,232,236,238,239,243,248,250,252,264,293,296,311,312,316,323,324,328,358,382,383,391,405,468,473],consid:[6,9,70,71,78,87,115,147,150,151,168,188,191,195,196,202,204,207,211,213,214,218,240,253,275,293,315,316,319,320,323,349,376,387,394,424,425,439,454,455,457,460,461,462,464,467,469,477,480,485],consider:[6,8,236,237,311,312,313,363,468],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,145,148,150,165,177,187,192,197,198,203,217,218,221,223,226,229,236,237,238,249,252,254,255,256,257,258,259,260,262,263,264,265,267,268,269,270,271,272,280,283,288,290,292,293,311,312,313,314,324,348,349,351,357,358,363,365,369,371,377,379,387,390,394,408,409,410,413,415,425,428,430,442,449,457,459,460,462,463,464,471,480,485],consistent_fe_initi:200,consit:293,constant:[],constitu:[3,6,242,293,325,329,377,425],constitut:[428,430],constrain:[3,6,8,143,144,145,146,148,151,152,153,154,155,157,158,194,203,218,228,229,234,242,246,278,279,291,293,296,306,316,323,356,357,387,464,471,480],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,118,140,164,215,252,275,292,329,359,363,382,413,415,439,441,442,462,463,478,485],constructor:8,consult:424,consum:[1,288,419,485],consumpt:346,contact:[],contact_stiff:[427,429],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,145,153,163,164,165,167,171,173,184,185,188,190,191,192,194,195,196,200,202,203,204,206,207,208,209,211,216,218,223,230,234,235,236,237,239,250,264,274,275,278,279,281,283,286,290,293,294,298,308,315,319,320,329,330,333,347,349,357,358,361,362,364,365,366,369,378,379,382,385,386,387,394,395,410,413,417,421,422,423,424,431,441,442,443,444,445,446,448,454,455,456,457,459,460,461,462,464,466,468,471,473,476,477,480,485,487,489],content:[12,18,424,475,477],context:[3,6,8,12,17,117,191,212,213,218,278,290,324,355,451,459,466,475,484,485,486],contibut:70,contigu:456,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,161,191,194,195,196,201,203,204,205,206,207,208,209,211,214,215,216,217,218,228,229,230,232,233,234,236,237,238,244,249,250,252,254,255,256,257,258,269,270,271,272,277,279,282,283,293,294,297,307,308,310,317,318,320,326,329,333,347,362,363,369,383,384,401,404,423,424,425,428,430,444,454,457,459,461,462,467,473,476,477,485,487],continuum:[6,7,9,200,320,428,430],contour_integr:200,contract:[59,215,217,252,280,293],contradictori:3,contrain:296,contraint:264,contrari:[230,237],contrast:[1,6,42,55,64,147,150,217,331,428,430,451,488],contrib:320,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,196,201,202,203,204,206,207,208,209,215,228,236,239,242,243,247,253,270,271,278,279,287,290,293,294,296,322,348,356,358,366,383,384,385,387,394,408,409,413,415,423,424,471,477,480],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,174,188,190,194,200,201,211,215,216,217,232,233,236,237,252,254,255,256,257,258,280,285,293,299,300,311,312,313,320,324,346,348,360,387,390,413,423,424,427,429,441,445,454,456,468,474,475],control_typ:200,controlfil:424,convect:91,conveni:[6,12,29,188,192,209,294,351,431,485],convent:[3,8,9,29,176,183,184,191,292,305,332,385,387,485],converg:[3,6,41,88,188,190,192,197,211,214,215,223,226,256,283,285,288,292,296,354,355,356,358,378,379,399,454,466,473],convers:[3,8,140,190,191,201,204,280,348,379,380,381,387,399,403,407,418,457,473,484],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,165,172,188,190,191,209,250,331,334,336,339,342,351,358,364,385,413,443,445,452,457,459,460,461,466,476,480,484,485,487,489],convex:329,convinc:[7,12],cook:9,cooki:7,cool:[7,155,232,291],cooordin:188,cooper:[5,7],coord123:114,coord1:[3,114,203,207,208],coord2:[3,114,203,207,208],coord3:[3,114,203,207,208],coord:[],coordiat:356,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,148,154,160,162,163,165,169,187,188,189,190,191,192,194,197,202,203,206,207,208,211,212,213,214,215,216,217,218,221,223,224,226,228,231,232,233,234,235,236,237,249,251,252,254,255,257,258,270,273,274,275,278,279,280,290,291,293,295,296,297,302,305,306,307,308,310,318,319,320,327,328,330,331,351,356,357,358,363,364,365,368,386,454,459,460,462,464,467,469,473,480,485,486],coordn:[114,203],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,190,320,358,376,423,457],copper:452,coproccesor:16,coprocessor:[1,4,7,9,16,17,363,472],coproprocessor:17,copy_arrai:8,copyright:[7,8,278],coral:191,core:[],core_shel:147,coreshel:[6,9,372,379,381],cornel:[6,171,471],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,190,329,330,351,447,459],cornflowerblu:191,cornsilk:191,corpor:16,corr:378,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,147,152,159,190,217,228,230,236,252,253,270,278,280,283,319,325,329,348,358,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,448,450,451,452,459,474,477,480],correction_max_iter:200,correctli:[3,8,9,11,17,71,81,102,103,143,144,146,148,150,151,152,153,154,157,158,161,188,191,197,218,223,226,237,246,252,253,286,293,296,305,307,326,329,358,359,363,381,409,413,456,457,459,469,484,486],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,143,144,152,159,164,171,172,173,174,175,176,177,179,180,182,183,185,188,190,191,195,196,197,203,205,206,207,208,210,213,215,217,224,226,227,231,236,239,240,248,249,250,252,254,255,256,257,258,259,264,267,269,270,272,275,276,280,285,293,295,296,311,313,315,324,325,326,328,329,330,332,334,335,336,337,338,339,342,344,349,353,355,357,358,364,365,367,370,371,372,373,374,375,376,377,378,379,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,413,415,416,417,418,420,421,423,424,425,426,431,432,441,442,443,444,445,447,448,450,451,452,454,456,457,459,460,462,472,473,474,476,477,480,485],correspondingli:[408,409,468],cosin:[],cosineshift:27,cosmo:[230,235],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,164,190,191,203,207,208,211,212,213,225,252,285,320,348,349,361,379,399,403,413,415,441,456,468],costheta0:[441,443,445,448],costheta:421,costli:[11,88,230,359],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,145,155,160,162,178,188,190,191,195,196,203,204,207,211,217,226,235,282,283,284,288,291,293,295,308,309,315,319,320,321,325,329,331,333,340,345,347,354,356,359,363,366,389,393,394,423,424,455,456,457,459,461,463,466,467,475,480,485,486],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,116,141,166,170,284,286,321,348,349,356,363,370,372,373,374,375,378,379,380,381,382,387,391,392,394,399,403,407,415,418,423,424,426,440,445,446,448,451,464,471,477,480,484],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,114,116,117,153,163,169,197,198,201,203,206,207,208,210,211,218,223,225,228,234,252,264,279,296,311,312,329,349,356,357,358,360,363,389,393,415,477,485],counter:[326,454,465,467,473],counteract:228,counterbal:232,counterpart:[188,293,454],counterproduct:18,coupl:[],courant:298,cours:[3,8,126,128,159,188,195,196,229,292,305,319,325,327,328,330,331,349,408,432,456,459,472,480,485,487],courtesi:351,coval:[6,29,387,410,480],covari:230,cover:[6,71,185,191,200,239,387,397,447],coverag:[71,207],cpc:235,cpp:[1,3,6,8,9,11,12,13,87,188,195,196,226,296],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,191,194,205,221,237,321,346,349,363,376,440,454,472,473,476,477,478,485],cpuremain:477,cr2:164,cr3:164,crack:[4,359],crada:[5,7],crai:[5,7,13,18,188],crash:[3,12,359,480],craympi:363,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:200,create_faceset:200,create_group:189,create_nodeset:200,createatom:[],creation:[],crimson:191,critchlei:278,criteria:[3,116,166,190,191,212,213,214,247,356,420,447,461,464,485],criterion:[12,41,121,163,165,168,201,211,214,228,264,285,298,326,331,356,358,378,387,391,464,473,474],criterioni:473,critic:[6,48,49,250,315,320,356],cross:[3,12,22,71,89,144,173,188,190,202,207,213,217,249,251,270,293,301,305,307,316,323,335,351,358,374,383,384,385,392,393,394,399,401,403,421,426,428,430,443,445,452,459,463,469,487],crossov:1,crossterm:459,crozier:[0,7,13],crucial:283,crystal:[4,6,13,73,274,275,318,351,359,463,477,480],crystallin:[6,275,351,444,480],crystallis:315,crystallogr:[118,164],crystallograph:[351,477],crystallographi:[118,164,351],cs1:164,cs_chunk:6,cs_im:[40,459],cs_re:[40,459],csanyi:[140,422,431],cscl:410,csequ:6,csh:[11,12,376],cshrc:[11,12],csic:[386,441,443,445,448],csinfo:6,csisi:[386,441,443,445,448],csld:[],cst:385,cstherm:6,cstyle:456,csvr:[],ctcm:[364,385],ctemp_cor:221,cterm:297,ctr:9,ctype:11,cu1:164,cu2:164,cu3au:410,cube:[6,41,163,168,211,221,329,351,480],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:369,cummul:[3,6,209,212,213,214,216,225,230,236,238,308,311,312,313,314,316,323,393,477],cumul:[6,201,203,206,207,208,222,228,236,250,252,256,264,293,294,358],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,145,153,155,161,163,166,169,188,189,190,191,192,195,196,200,203,207,208,209,211,212,213,214,215,216,217,218,222,223,226,228,230,233,234,236,242,249,252,253,257,258,264,269,270,272,278,284,285,287,290,291,292,293,296,297,298,299,300,301,302,304,306,307,308,311,312,313,319,320,323,324,325,326,327,328,330,331,333,346,347,348,349,352,353,355,356,357,358,363,369,376,378,382,385,387,388,391,394,395,398,408,409,410,411,412,415,421,423,424,427,428,429,430,432,443,445,446,449,454,455,456,457,459,460,461,462,463,465,466,467,469,471,473,474,476,477,485,486,487,488,489],curv:[6,165,228,275],curvatur:[390,425,452],custom:[],cut0:457,cut1:468,cut2:468,cut:[],cuthi:[274,286],cutinn:[371,408,409],cutlo:[274,286],cutmax:421,cutoff1:[375,382,399,403,407,418,426],cutoff2:[370,372,373,375,381,382,399,403,407,418,426],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,163,166,168,213,214,219,274,283,284,286,288,290,293,308,321,325,329,331,346,348,349,356,359,360,361,363,364,365,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,383,384,385,386,387,388,389,390,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,431,432,433,434,435,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,457,461,464,468,480,485],cutoffa:386,cutoffc:386,cuu3:385,cval:164,cvd:315,cvel:297,cvff:[],cwiggl:[3,249,325,328,330,485],cyan:[2,190,191],cycl:[3,228,250,252,253,256],cyclic:[3,185],cygwin:12,cylind:[3,4,190,234,279,326,329,462],cylindr:[6,234,305,326],cypress:363,cyrot:369,cyrstal:275,d3q15:239,d3q19:239,d_double_doubl:15,d_e:320,d_flag2:282,d_flag:282,d_name:[113,188,282,310,469],d_single_doubl:15,d_single_singl:15,d_sx:282,d_sy:282,d_sz:282,daan:318,dai:12,daili:12,daivi:270,damag:[],dammak:288,damp:[3,6,194,199,236,237,238,243,252,253,256,280,283,288,293,311,312,324,326,327,355,356,358,370,372,374,379,382,387,391,399,407,418,426,440,446,473,480],damp_com:237,damp_drud:237,dampen:[293,480],dampflag:[326,391],dan:17,danger:[3,12,228,331,383,477],dangl:168,daniel:9,darden:[349,382],darkblu:191,darkcyan:191,darken:190,darkgoldenrod:191,darkgrai:191,darkgreen:191,darkkhaki:191,darkmagenta:191,darkolivegreen:191,darkorang:191,darkorchid:191,darkr:191,darksalmon:191,darkseagreen:191,darkslateblu:191,darkslategrai:191,darkturquois:191,darkviolet:191,dasgupta:284,dash:[391,476],dat:[6,91,185,200,455],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,294],dataset:294,datatyp:3,date:[0,6,12,13,423,424,485],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,188,204],davi:325,david:[9,19,348,349,443,445],daw:[385,421],dbg:14,dcd:[3,6,7,188,189,190,191,192,276,460,464],ddim:187,deactiv:407,dealt:235,debug:[6,7,11,12,13,14,17,118,122,164,165,276,281,346,348,363,395,415,449,457,458,461,466,469,476,485],deby:[],decai:[379,452],decid:[3,6,12,16,71,249,282,293,321,474],decipher:351,declar:189,declin:308,decod:190,decompos:[87,431],decomposit:[3,5,7,18,62,200,276],decoupl:[6,480],decreas:[3,188,197,198,205,214,217,223,226,228,236,319,348],decrement:297,deepli:345,deeppink:191,deepskyblu:191,def:[12,13,457],defaul:61,defect:[6,70,163,413],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,171,172,173,174,175,176,177,179,180,182,183,184,185,186,187,188,189,190,191,194,195,196,197,198,199,200,201,202,203,204,206,207,208,209,210,211,212,213,214,215,217,218,221,222,223,226,227,228,231,234,235,236,237,238,239,247,249,251,252,253,254,255,256,257,258,260,261,262,265,267,268,269,270,271,272,274,275,276,278,279,280,282,284,286,291,293,294,295,296,298,302,306,308,310,311,312,313,314,316,317,318,320,322,323,325,326,327,328,329,330,331,333,334,335,336,337,338,339,342,343,344,346,348,349,351,353,355,356,357,358,359,360,361,362,363,365,366,367,368,370,371,372,373,374,375,376,377,379,380,382,383,384,386,387,389,390,391,392,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,413,414,415,416,417,418,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,456,457,459,460,462,463,464,465,468,469,470,471,473,474,476,477,480,481,482,483,484,485,486],definit:[2,3,6,8,12,13,78,80,116,140,191,203,204,205,206,207,208,209,217,234,256,294,310,322,325,328,330,332,343,346,357,366,369,377,387,397,421,428,430,431,447,457,459,461,468,470,484,485],defint:477,deform:[],deg2theta:164,deg:480,degener:[3,278],degrad:[8,18,275,349,468],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,164,165,171,172,175,176,183,185,187,190,203,214,221,228,230,231,236,237,242,252,253,256,257,258,269,270,272,276,278,292,293,296,311,312,313,318,334,336,339,342,344,356,382,385,393,469,477,480,486],degress:[145,203],del:473,delai:[3,6,12,359,384,477],deleg:394,delet:[2,3,7,8,12,54,57,60,63,163,168,169,194,203,204,206,207,208,209,212,214,225,228,252,294,311,312,331,333,347,357,359,362,415,459,460,462,470,471,476,481,483,485,486],delete_atom:[],delete_bond:[],delete_el:200,deli:187,delimit:[457,485],deloc:[253,387],delr:410,delt_lo:473,delta:[],delta_1:369,delta_3:369,delta_7:369,delta_conf:3,delta_ij:[410,421],delta_mu:3,delta_pi:369,delta_r:421,delta_sigma:369,delx:187,delz:187,demand:288,demo:11,demon:273,demonstr:[283,410],den:279,dendrim:393,denniston:[9,239,241,242,243,275],denomin:[7,170],denot:[118,221,237,275,286,288,379,392,394,424,428,430],dens:[71,214,387],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,151,163,165,195,196,200,203,207,208,211,217,226,239,242,245,246,275,279,280,284,320,325,351,353,357,364,369,385,410,411,412,421,425,434,436,437,438,459,468,469,477,484],density_continu:430,density_summ:430,depart:[0,7],departur:[250,283],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,143,148,152,153,159,165,166,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,190,191,194,195,196,197,198,201,203,205,206,207,209,210,211,213,215,217,223,224,227,230,231,232,234,236,237,239,241,242,249,252,254,255,256,257,258,259,267,269,270,272,274,285,288,290,293,295,296,302,308,311,312,313,315,317,319,320,322,324,325,328,329,330,331,333,334,335,336,337,338,339,342,344,349,351,356,357,359,360,361,363,364,365,367,368,369,370,371,372,373,374,375,376,377,378,379,380,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,413,414,416,417,418,420,421,423,424,425,426,431,432,440,441,442,443,444,445,446,447,448,450,451,452,454,456,459,461,462,465,469,471,473,476,477,479,485,486],dependend:6,depflag:12,dephas:[454,473],depos:218,deposit:[],deprec:[284,423],depth:[51,144,190,320,390,425],dequidt:9,der:[87,107,377,378,407,423,424,451,480],deriv:[6,7,8,9,38,56,63,87,140,159,185,204,215,217,228,236,249,252,254,255,256,257,258,274,280,284,288,317,318,320,325,326,329,355,357,365,369,377,382,387,388,392,401,405,406,410,413,423,424,440,442,451,480],derjagin:451,derlet:274,descend:191,descent:[7,355],descib:[40,284],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,144,145,149,150,153,156,158,159,163,164,165,167,168,177,182,185,188,189,194,195,196,203,204,205,206,207,208,209,211,214,215,216,217,218,220,221,229,230,233,234,235,236,237,238,239,241,242,243,247,251,252,253,256,263,271,274,276,281,282,283,284,285,286,293,297,305,308,309,310,311,312,313,314,315,316,317,318,323,325,326,328,333,348,349,351,354,355,356,357,358,362,365,366,368,370,371,372,374,375,376,377,378,379,382,385,387,388,390,391,392,394,399,400,401,402,403,404,405,406,407,408,409,410,413,414,420,421,422,423,424,425,426,431,432,439,440,441,442,443,444,445,446,448,450,451,452,454,456,457,459,460,462,463,469,472,473,476,485,486,487],descript:[],descriptor:[140,188,395],deserno:349,design:[0,3,6,7,8,9,11,13,14,15,17,118,147,150,164,200,214,220,221,252,253,274,275,294,315,320,366,367,368,371,374,379,381,387,407,408,409,411,412,421,424,442,468],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,112,117,141,147,165,178,187,203,209,215,217,226,228,229,236,237,238,242,252,270,278,279,280,281,284,288,293,296,308,311,312,313,314,319,326,340,345,348,349,351,354,356,357,358,383,385,393,408,409,441,443,445,455,456,457,459,463,468,473,474,476,477,485,486,487],desk:7,desktop:[4,6,7,10,12,190],despit:480,destabil:369,destre:342,destroi:[11,39,212,213],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,143,144,145,148,158,159,160,162,165,166,169,170,173,184,188,190,191,194,195,196,200,203,204,205,206,207,209,211,213,214,215,216,217,218,226,228,229,230,231,233,234,236,238,239,243,249,250,251,252,253,254,255,256,257,258,262,264,269,270,271,272,275,278,279,280,282,283,285,286,287,293,296,308,311,312,313,314,315,316,318,319,320,321,322,323,324,331,333,335,343,348,349,352,356,357,359,360,363,364,365,366,368,369,371,373,374,375,376,377,378,379,382,383,387,388,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,410,414,415,420,423,424,425,431,432,440,447,450,451,457,459,460,461,462,464,465,468,469,471,474,477,478,485,486,489],detect:[2,3,12,61,63,86,227,279,319,358,378,393,398,454,456,459,470,473,485],determ:363,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,153,154,163,164,165,187,188,190,191,192,193,197,198,199,202,203,204,205,206,207,208,209,210,211,215,217,218,221,223,228,231,232,234,236,237,242,247,249,250,252,257,258,269,270,272,274,276,280,283,290,291,292,293,294,295,298,300,302,308,311,312,313,315,321,322,325,326,327,328,329,330,331,343,348,349,351,357,359,360,363,365,366,373,378,382,384,385,389,391,394,395,403,410,413,415,424,425,439,442,446,451,456,459,460,462,464,466,469,473,475,476,478,484,485,486],detil:108,devan:[9,426],devanathan:445,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,233,256,278,283,284,287,365,369,387,412,413,448,461],devemi:9,deviat:[250,256,274,389],deviator:9,devic:[1,3,12,15,17,233,363],device_typ:363,devin:[285,378],devis:412,dfactor:190,dff:480,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,349],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,287,413],dhi:[59,187,217,279],dhug:[250,283],dhugoniot:[250,283],dia:410,diagnost:[],diagon:[3,6,83,140,141,142,215,252,280,293,323,428,430],diagonalstyl:431,diagram:[41,118,164,184,211,276],diallo:393,diam:[190,191,279,357],diamet:[3,6,40,113,165,188,190,191,195,196,236,279,293,308,324,326,357,377,390,391,397,401,425,447,451,459,460,469],diamond:[351,387,410],diamter:[40,279],dick:6,dicsuss:249,dictat:[201,250],did:[3,12,356,383,384,385,391,415,443,445,467],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,161,322,348],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,143,144,145,146,148,151,152,153,154,155,157,158,159,165,166,168,173,184,185,187,188,190,191,194,196,199,201,203,206,211,212,213,214,215,216,217,221,227,228,229,230,231,232,233,236,237,239,249,252,253,254,255,257,258,260,262,265,267,268,269,272,274,276,278,280,283,284,285,288,291,293,296,297,305,306,308,311,312,313,316,317,318,320,323,324,325,326,329,333,334,343,345,347,348,349,351,352,354,355,357,358,360,361,362,363,364,365,369,373,374,376,377,378,383,385,387,390,391,392,394,397,399,400,402,403,410,411,412,414,415,417,421,423,424,425,426,427,428,430,431,432,440,441,442,443,445,447,448,451,453,454,456,457,459,461,462,463,464,467,468,469,471,473,474,476,477,478,480,484,485,486,487],differenti:[1,3,6,29,185,348,379,421,444],difficult:[215,276,363,393,468],difficulti:[296,423],diffract:[],diffus:[],digit:[2,3,191,333,413],dih_table1:185,dih_table2:185,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:213,dihydrid:387,dij:296,dilat:[],dim1:3,dim2:3,dim:[3,59,71,143,146,147,148,151,152,153,154,155,157,165,187,207,217,234,326,351,410,462,484,485,486],dimdim:485,dimems:275,dimens:[],dimension:[3,39,112,118,140,143,145,146,147,148,151,152,153,154,155,157,164,186,203,207,251,275,320,351,354,358,421,459,469],dimensionless:[105,121,122,124,127,129,131,136,140,320,349,431,451],dimentionless:135,dimer:[6,293,410],dimgrai:191,dimstr:[41,211],dinola:[280,311],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,188,310,480],dir1:470,dir2:470,dir:[1,3,4,8,9,11,12,250,274,283,307,421,423,424,457,470,485],dirac:140,direc:421,direct:[],directli:[3,6,8,9,11,12,87,113,140,142,188,189,190,197,223,230,234,239,275,294,312,324,326,327,328,329,351,355,363,364,365,370,372,373,379,382,385,387,399,403,415,418,426,439,457,469,470,471,477,485],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,192,216,235,278,284,287,304,308,317,318,358,362,364,365,369,376,378,379,385,386,388,395,396,407,410,411,412,413,417,421,422,423,424,431,441,443,444,445,448,457,459,460,461,470,485],disabl:[3,12,16,320,398,457,472,485],disadvantag:[6,211],disallow:[188,217,252],disappear:461,discard:[2,3,41,71,205,207,211,321,329,456,461,462],discontinu:[9,185,356,405],discourag:410,discov:[13,321],discret:[6,8,40,42,190,191,236,239],discuss:[],disk:[6,84,85,158,186,218,228,279,457],disloc:[70,413],disord:[39,70,413],disp:[],dispar:425,disperion:[382,403],dispers:[3,6,7,9,163,275,348,349,373,382,403,408,415,424,442,448],displac:[],displace_atom:[],displace_box:59,displacemet:462,displai:[11,13,22,37,44,55,173,184,188,190,335,343,376,440],dispters:3,disregard:413,dissip:[6,229,236,275,317,318,371,383,391,408,409,440],dissolut:212,dist:[6,69,91,108,117,188,276,292,384,439,454,486],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,154,160,163,165,166,167,168,172,187,188,190,191,199,203,207,208,212,213,214,215,217,218,219,222,228,234,239,249,250,251,252,256,264,274,275,279,283,284,291,292,293,296,297,301,305,306,307,308,315,316,318,319,320,323,325,326,327,328,329,330,334,348,349,351,354,356,358,359,360,363,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,383,384,385,386,387,389,390,391,392,393,397,398,399,400,401,402,403,404,405,406,407,408,409,410,413,414,415,416,417,418,419,420,421,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,454,457,459,462,468,469,473,477,480,484,486],distinct:[6,221,290,348,425],distinguish:[6,86,140,242,387,458],distort:364,distrbut:364,distribut:[],distro:[111,376,420,421],ditto:[8,11,12,14,15,16,17,18,115,213,452,457],div:8,divd:117,diverg:[3,12,39,293,318,461,480,487],divid:[3,6,16,41,91,112,117,126,128,141,162,163,173,184,191,203,204,206,211,217,274,316,323,328,348,356,358,388,424,448,468,476,485],divis:[6,239,369,397,407,456,459,477,485],dl_poli:[6,7],dlambda:159,dlammps_async_imd:233,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,190],dlammps_gzip:[3,12,188,190,319,459,460,464],dlammps_jpeg:[3,12,190],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,190],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,188],dlen:469,dlmp_intel_offload:[12,16],dlo:[59,187,217,279],dlopen:6,dlvo:[7,377,451],dm_lb:239,dmax:[308,354],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,141,144,145,158,160,162,165,166,167,173,184,188,189,190,191,192,194,195,196,201,202,203,204,205,206,207,208,209,218,228,236,237,247,252,253,257,258,262,269,270,271,272,279,282,293,305,308,311,312,313,322,326,329,331,333,335,343,347,356,357,358,363,364,365,368,376,378,379,385,386,388,393,394,396,397,410,411,412,415,417,420,421,422,431,440,441,443,445,447,448,457,459,460,461,462,464,467,468,469,476,477,485,486,487,488],docuement:425,dodgerblu:191,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,116,117,118,142,144,145,147,148,153,155,159,164,165,166,167,169,171,173,178,184,185,187,188,189,190,191,194,200,201,203,207,210,211,213,214,215,217,221,223,225,228,229,232,234,236,237,239,242,248,252,253,254,255,257,258,269,270,271,272,280,281,282,286,288,291,293,308,311,313,315,316,320,323,324,325,328,329,330,331,336,337,339,340,342,347,348,349,350,351,357,358,359,364,365,366,367,368,369,371,373,374,375,377,378,379,380,382,383,384,385,386,387,389,390,391,392,394,395,396,397,398,401,402,404,405,406,408,409,410,411,412,413,415,421,422,423,424,425,427,428,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,450,451,452,454,455,456,457,459,460,461,462,463,466,467,469,470,471,472,473,476,477,480,485,489],doegenomestolif:7,doesn:[3,7,8,12,165,188,201,207,208,305,357,359,363,365,378,386,396,423,424,441,443,444,445,448,459,461],dof:[3,8,112,144,145,158,203,293,486],dof_per_atom:[145,203],dof_per_chunk:[145,203],doff:[357,459],doi:[6,216],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,154,164,167,187,189,190,191,194,201,211,215,217,218,232,235,239,252,253,276,288,293,320,325,326,348,349,358,363,384,415,454,456,459,463,476],domin:[1,387,473],don:[0,8,11,12,13,116,168,197,223,237,282,329,410,457,459],donadio:312,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,159,162,165,168,185,188,190,191,200,201,203,205,206,207,208,209,211,212,213,214,215,217,218,226,228,233,234,236,237,244,252,257,258,269,270,272,273,275,276,277,282,290,293,294,296,308,311,312,313,315,317,318,331,333,347,348,349,356,358,359,362,363,365,373,385,394,395,396,403,409,410,415,423,439,442,447,454,455,456,457,460,463,464,467,477,478,480,485,486],donor:393,dot:[141,161,197,223,231,251],doti:[369,421],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,217,226,281,329,333,347,349,362,363,369,388,392,413,423,424,455,459,463,467,472,485,486],dover:200,down:[3,6,7,8,11,39,71,215,228,236,308,324,363,387,415,458,478],downhil:[354,355],download:[5,7,8,9,11,12,13,17,233,395,422],downsid:6,downward:290,dozen:[8,12,107,194,423,424],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:245,dproduct:366,dr_ewald:[118,294],drag:[],dragforc:239,drai:[250,283],drain:[232,324,356],dramat:[59,187,212,213,214,215,217,252,308,311,312,349,363,415,456],drautz:369,draw:190,drawback:282,drawn:[188,190,191,229,454],drayleigh:[250,283],dreid:[],drfourth:105,drho:[113,364,385],drift:[6,103,105,229,230,236,237,248,291,308,468,476,480],drive:[11,12,198,215,217,231,252,274,280,293,327,358],driven:[6,177],driver:[6,12,14,15,194,226,233],drop:[3,191,383],droplet:394,drsquar:105,drude:[],dry:225,dsecriptor:395,dsf:[],dsmc:[],dstyle:279,dt_collis:239,dt_lb:239,dt_md:239,dt_srd:308,dtilt:[59,217],dtneb:473,dtqm:283,dtype:[115,213],dual:[16,17,308,363],dudarev:164,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,93,102,103,104,1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,21,23,24,25,26,27,28,29,30,31,32,35,36,38,40,43,45,46,47,48,49,51,53,54,56,63,65,69,82,83,84,85,86,87,88,91,94,95,96,97,98,99,101,102,107,108,109,110,112,123,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,188,191,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,334,336,337,338,339,342,344,348,349,354,355,356,358,359,363,364,365,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,423,424,425,426,431,432,433,434,439,440,441,442,443,444,445,447,448,449,450,451,452,454,457,459,464,468,469,471,473,475,476,477,480,484,485,488],energy_update_freq:424,enforc:[6,57,58,104,187,188,189,190,192,194,201,214,217,252,273,275,285,293,296,333,348,399,456,485,486],enforce2d:[],eng:[11,65,69,108,188,226,331,333,378,412],eng_previ:333,engin:[200,217,278,297,317,385,411],engr:[423,424],enhanc:[196,200,454],enlarg:[59,190],enough:[3,40,61,86,165,166,168,211,237,279,283,288,293,321,325,326,329,359,363,379,419,459,463,464],enpub:385,enrti:[],ensembl:[],ensight:6,ensur:[3,6,140,188,201,205,215,228,229,252,298,319,349,369,384,407,441,448],enter:[57,155,388,413,448,473],enthalpi:[123,254,255,385,476,477,485],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,141,145,164,165,191,194,195,196,203,207,208,211,214,216,225,228,229,232,236,237,248,252,254,255,256,257,258,274,276,278,291,293,306,320,322,333,363,382,403,415,442,459,467,468],entireti:[397,447],entiti:[6,8,40,42,188,293],entri:[3,8,12,38,42,56,65,69,79,92,108,115,118,127,130,131,132,133,134,136,137,138,163,185,191,206,207,208,216,283,331,357,369,386,410,417,424,431,441,442,443,444,445,448,485],entropi:473,entry1:[38,56,191,376,442],entry2:191,entryn:191,enumer:[166,188],enumuer:6,env:363,environ:[1,3,6,11,12,16,17,18,190,230,235,274,363,364,369,376,378,386,387,421,443,456,470,485],epair:[107,191,389,393,423,424,477],epen:[423,424],epfl:[230,235],epp:382,epq:382,eps0:451,eps14:407,epsilon0:445,epsilon:[3,6,36,45,46,50,53,54,87,171,195,196,228,293,308,325,329,354,356,368,374,375,377,379,380,381,382,390,392,393,394,397,398,399,400,401,402,403,404,405,406,407,414,418,425,426,435,441,447,450,451,468,480,484],epsilon_0:452,epsilon_14:374,epsilon_:425,epsilon_d:380,epsilon_i:[390,415,425],epsilon_i_:425,epsilon_i_a:[390,425],epsilon_i_b:[390,425],epsilon_i_c:[390,425],epsilon_ij:415,epsilon_j:[390,415,425],epsilon_j_:425,epsilon_j_a:[390,425],epsilon_j_b:[390,425],epsilon_j_c:[390,425],epsilon_lj:425,epton:420,eqch:160,eqeq:[423,424],eqp:382,eqq:382,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,144,159,161,165,190,191,194,195,196,197,198,201,204,205,206,209,210,211,215,217,218,223,228,229,231,232,234,236,237,239,242,243,249,250,256,266,274,276,279,281,283,284,285,288,290,292,293,295,297,302,304,311,312,313,316,317,318,320,322,323,325,328,330,331,333,347,351,356,358,359,360,362,363,378,383,389,390,393,408,413,414,421,423,424,425,427,428,429,431,432,442,447,448,452,455,456,457,459,461,462,466,467,470,473,475,477,485,486],equat:[3,6,7,8,9,91,112,118,164,173,184,194,215,221,222,230,236,237,239,242,250,251,252,253,256,270,274,276,283,284,288,296,308,316,320,323,325,326,328,330,342,348,349,377,382,383,387,388,391,396,408,409,410,415,425,428,430,434,435,437,438,446,452,480],equi:253,equidist:251,equil:[3,284,352,466,489],equilater:469,equilibr:[3,4,5,6,7,9,59,91,165,194,201,204,214,215,228,250,252,253,270,271,283,284,285,286,316,317,318,323,378,379,423,424,455,469],equilibria:323,equilibribum:[212,213],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,148,149,172,174,215,217,228,229,230,237,239,252,256,270,283,288,292,296,297,305,308,315,316,318,323,334,336,339,342,378,410,417,480],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:200,equival:[6,12,13,59,61,124,125,133,138,163,167,191,206,209,215,217,228,236,252,270,280,292,293,328,383,387,443,445,459,462,467,468,477,480],equlibrium:6,equliibr:[284,286],er3:164,eradiu:[40,113,387,459],eras:[295,317],erat:[217,409],erc:379,erfc:[379,399,415],erforc:113,erg:484,erhart:[201,385,443,445],ermscal:366,ernst:9,eror:3,eros:410,erose_form:410,erot:[],errata:[443,445],erratum:325,erron:3,error:[],erta:391,ervel:[113,459],escap:[218,480],especi:[8,11,16,153,165,194,201,211,228,283,288,291,292,363,456],espresso:[9,287],essenti:[8,11,12,27,88,128,146,147,148,151,152,153,154,155,157,174,204,256,275,324,349,365,379,399,445,464,477],essex:29,establish:[87,232],estim:[1,3,6,10,12,38,41,56,91,141,200,211,222,250,308,315,348,349,354,415,424,442,473,477],esu:484,esub:410,eta:[6,239,252,283,284,286,324,386,388,390,421,444,448,484],eta_dot:252,eta_ij:421,eta_ji:388,etag:[40,459],etail:477,etap:252,etap_dot:252,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,143,145,146,147,148,149,151,152,153,154,155,157,159,165,167,168,169,178,188,190,191,194,195,200,201,202,203,206,207,208,209,212,213,217,218,226,228,229,236,252,279,290,294,320,321,329,333,347,348,356,357,358,359,361,385,386,394,407,409,419,423,424,441,443,445,448,454,457,459,460,461,466,468,469,473,475,476,477,478,480,484,485,487,489],ethernet:18,etol:[356,358,454,473],etot0:283,etot:[6,94,96,97,110,141,151,191,221,237,250,283,476,477],eu2:164,eu3:164,euler:[356,358],eulerian:200,euqat:433,europhi:239,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,87,88,91,107,117,140,142,145,155,163,165,188,190,191,195,196,197,198,200,202,203,204,205,206,207,208,209,210,217,223,229,231,232,234,235,236,237,275,281,284,295,298,302,311,312,313,322,325,328,330,331,333,348,349,354,356,363,413,415,421,427,429,442,454,455,457,461,462,464,466,467,468,469,473,475,477,485,486],evalut:[333,457],evan:[153,270],evanseck:[6,20,171,374,471],evapor:[],evaul:[8,356],evdwl:[107,423,424,477],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,119,166,167,181,185,188,191,194,195,196,201,202,203,206,207,208,209,211,212,213,215,217,218,221,234,237,250,252,253,275,288,290,293,294,304,308,316,320,323,325,329,331,341,348,354,356,358,363,368,387,388,391,394,415,425,448,449,459,460,462,464,465,466,468,469,471,474,476,477,478,480,489],evenli:[3,41,141,185,211,239,397,449,459],event:[],eventu:[3,6,12,15,167,284,473],ever:[54,56,235,308],evera:[377,390,425,440],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,113,119,128,153,168,188,189,190,191,192,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,222,225,226,228,230,232,233,234,239,240,248,252,253,256,273,274,275,279,280,281,282,283,284,285,286,288,290,291,293,294,296,297,308,310,311,312,313,314,315,316,319,320,321,322,323,331,333,347,349,358,359,360,363,383,384,394,407,423,424,436,453,454,455,459,461,463,464,466,467,468,473,474,475,477,485,489],everyth:[8,107],everywher:[116,401],eviri:387,evolut:[230,239,276,454],evolv:[239,276,321],ewald:[2,3,5,6,7,8,12,88,110,118,141,321,348,349,356,370,372,373,379,382,387,399,403,418,426,440,442,461],ewald_disp:382,ewalddisp:3,exact:[22,41,44,71,122,159,168,173,211,214,229,230,236,237,238,279,288,289,308,320,335,348,376,461,466,473,485,487,489],exactli:[3,6,12,14,17,38,41,56,59,71,91,116,144,149,156,165,185,195,196,206,211,217,222,229,236,237,238,253,263,264,271,275,283,308,313,314,327,363,376,383,385,391,394,397,408,415,442,461,462,469,473,485],exager:480,examin:[6,8,9,17,214,275],examp:[457,485],exampl:[],exce:[3,6,16,17,18,41,58,71,167,203,207,208,211,215,217,222,225,252,275,299,300,308,356,363,459,485],exceed:[3,41,59,211,217,252,308,467],excel:387,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,191,194,197,203,204,206,210,211,215,217,224,227,228,231,234,236,238,252,253,254,255,256,257,258,259,263,264,267,269,270,271,272,276,285,286,293,295,296,305,308,311,313,314,320,324,328,331,333,334,335,336,337,338,339,342,343,344,348,349,351,353,357,358,359,361,362,363,364,365,367,370,371,372,373,374,375,376,377,378,379,381,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,411,416,417,418,420,423,424,425,426,432,440,441,442,443,444,445,447,448,450,451,452,454,456,457,459,461,462,464,467,468,469,470,471,473,477,480,484,485,486,488],excess:[205,387],exchang:[2,3,6,8,9,61,62,194,200,201,228,236,285,293,316,320,323,348,363,387,474],exchange:348,excit:[9,387],exclud:[3,6,9,12,16,17,63,71,112,140,145,152,153,169,188,203,207,212,213,240,248,278,291,293,315,326,331,356,357,359,371,391,394,408,409,415,439,471],exclus:[1,3,9,12,16,87,363,378,413,415,468,478],excurs:454,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,166,190,233,287,333,347,350,362,455,457,467,470,473,485],exemplari:229,exemplifi:387,exert:[6,234,237,288,327,328,329,349],exhaust:[200,362,485],exhibit:[252,355,387,468],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,122,165,166,184,189,190,191,194,199,210,213,215,218,228,278,279,281,331,334,336,337,339,343,352,357,363,394,423,449,455,457,459,460,461,470,471,472,485,486,487],exit:[2,3,11,12,41,57,188,211,347,362,457,458,467,476,485],exlanatori:3,exp:[],expand:[],expans:[12,140,188,470,485],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,146,157,163,185,211,223,228,230,249,274,280,282,283,288,293,331,349,359,376,410,413,415,454,457,459,461,464,468,473,485],expens:[6,10,71,191,274,278,293,320,331,348,349,359,363,457],experi:[6,13,15,17,210,218,233,242,251,280,292,293,354,358,383,415,468,473],experienc:[6,12,241,242],experiment:[228,348,363,473],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,145,153,185,188,190,191,194,203,204,209,211,213,215,217,252,274,282,293,305,331,333,347,348,351,357,358,362,368,385,397,432,447,457,460,461,464,466,469,480,485,489],explan:[3,6,59,113,140,188,203,251,274,394,453,456,457,459,468],explanatori:[3,8,117,188,202,203,206,207,208,293,357,456,485],explantori:[3,289],explic:414,explicit:[6,9,11,22,44,77,87,113,116,159,173,195,196,217,299,300,335,353,365,366,369,374,376,385,387,398,408,446,453,456,460,463],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,143,152,155,163,165,171,172,174,175,176,177,179,180,182,183,185,188,191,197,207,210,217,224,227,229,231,236,252,254,255,256,257,258,259,267,269,270,272,282,283,285,293,295,296,311,313,314,320,324,328,334,336,337,338,339,342,344,357,363,364,365,367,370,371,372,373,374,375,376,377,378,379,380,382,383,384,385,386,388,389,390,391,392,393,394,397,398,399,400,401,402,403,404,405,406,407,408,411,413,415,416,417,418,420,425,426,432,433,434,435,436,437,438,440,441,442,443,444,445,446,447,448,450,451,452,459,461,468,469,471,472,478,480],explictli:[16,472],exploit:[9,15,17,276],explor:[118,164],expon:[3,284,286,385,390,393,407,414,426],exponenti:[87,421,441,448,452,473,485],expos:11,exposit:[200,383,384],express:[6,140,151,165,195,196,215,249,274,284,320,326,333,369,385,387,401,410,431,440,485],expressiont:369,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,194,197,198,201,209,210,216,219,223,226,227,228,230,231,232,234,236,238,250,252,256,264,274,275,291,292,293,295,297,302,305,307,311,312,313,314,315,317,318,320,322,325,329,330,390,410,413,424,425,431,476,477],extent:[1,3,41,45,57,71,163,167,188,199,207,211,234,327,330,348,351,365,427,429,442,456,459,462],exterior:[3,6,329],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,143,144,146,148,151,152,153,154,155,157,158,164,165,166,167,171,191,206,211,213,252,281,282,283,293,308,356,357,360,361,382,391,394,397,410,415,456,457,459,462,471,480,485],extract:[3,6,11,13,36,63,87,107,115,117,119,195,196,286,358,379,388,410,431,457,464,476],extract_atom:11,extract_comput:[11,457],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,190,205,215,217,252,318,387,444,480],extrema:407,extrins:200,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[161,322],f_a:[443,444,445],f_ave:117,f_c:444,f_f:445,f_fix_id:283,f_harm:318,f_i:421,f_id:[6,71,117,119,188,194,202,203,204,205,206,207,208,209,247,310,322,477,485],f_ij:421,f_indent:209,f_int:317,f_jj:91,f_k:421,f_langevin:320,f_max:[283,288],f_msst:250,f_r:[237,443,444,445],f_sigma:369,f_solid:318,f_ss:6,f_temp:237,face:[3,6,57,59,71,153,163,167,199,207,208,325,327,328,329,330,351,390,410,425,459,462],face_threshold:163,facet:163,facil:[0,12],facilit:[6,13],fact:[6,8,16,230,308,318,391,471],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,116,118,140,159,164,167,171,182,188,190,191,195,196,204,211,215,217,218,228,233,236,238,239,250,252,253,256,276,280,292,296,298,300,308,312,316,323,324,325,329,339,349,351,357,363,365,366,369,370,372,374,379,380,381,383,387,391,394,398,399,410,413,415,417,418,424,426,432,441,446,456,459,462,463,468,471,473,474,477,480,484,485],factori:[3,457],factoriz:348,fail:[3,11,12,59,169,215,218,348,356,358,381,424,457],failur:[121,428,458,485],fairli:[11,415,468,473],faken:73,falcon:233,fall:[3,6,191,206,279,457,485],fals:[86,331,333,485],fame:8,famili:[448,456],familiar:[0,11],fan:421,far:[3,6,12,17,57,59,61,86,188,191,192,211,212,213,215,218,252,274,292,293,308,325,336,339,354,358,359,447,457,459,464,477],farago:236,farrel:[443,445],farther:188,fashion:[6,8,41,71,165,191,194,195,196,201,207,211,213,218,228,230,234,249,250,252,254,255,256,257,258,266,269,270,271,272,282,283,285,293,297,301,307,310,318,320,324,325,326,328,330,358,394,408,462,471,485,488],fasolino:396,fast:[6,7,9,12,13,17,39,188,261,283,321,348,349,371,408,409,413,440,442,461,466,468,477,486,489],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,143,152,171,172,174,175,176,177,179,180,182,183,185,188,191,194,197,210,211,217,224,227,231,235,236,252,254,255,256,257,258,259,267,269,270,272,280,284,285,293,295,296,308,311,313,315,317,320,324,328,334,336,337,338,339,342,344,348,349,360,361,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,382,383,385,386,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,411,416,417,418,420,425,426,432,440,441,442,443,444,445,447,448,450,451,452,454,468,472,480],fastest:[1,6,14,17,153,207,320,321,363,456],fatal:[3,476],fault:[70,424],faulti:12,fava:390,favor:214,favorit:7,fbmc:315,fcc:[],fcm:[266,485],fdirect:221,fdotr:395,fdti:87,fe2:164,fe3:164,fe_md_boundari:200,featu:8,featur:[],fecr:385,feedback:[7,233],feel:[7,233,234,242,274,329,331,358,415],felling:412,felt:329,femtosecond:484,fene:[],fennel:[379,399],fep:[],ferguson:[6,171,471],fermi:[1,12,15,151,363,445],fermion:[9,387],ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,192,202,203,204,206,207,208,209,237,252,279,282,284,296,322,348,356,357,358,365,456,459,464,468,470,478,485,487],fewer:[1,3,11,15,16,61,242,468],fewest:3,fextern:226,feynman:276,fff:457,ffield:[378,388,423,424],ffmpeg:[3,12,190],ffplai:190,fft:[1,3,7,12,14,15,88,109,110,141,275,348,349,468],fft_inc:[12,349],fft_lib:12,fft_path:12,fftbench:[348,478],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:439,fictiti:[6,197,198,223,226,230,276,292,379,399,403,439],field1:[460,464],field2:460,field:[],fifth:[305,417],figur:[1,3,8,11,12,283,456,457],fij:382,file0:274,file1:[11,13,274,319,333,357,464,466,470],file2:[11,13,319,333,357,464,466,470],file:[],file_from:189,filen:357,filenam:[3,12,13,38,41,56,185,188,190,191,192,200,203,204,205,206,207,208,209,211,216,274,278,281,284,285,286,289,290,293,294,319,320,345,346,347,357,358,364,365,369,379,385,386,388,396,410,411,412,417,421,422,423,424,431,441,442,443,444,445,448,455,456,457,460,461,466,470,477,485,487,488,489],filennam:466,filep:[3,188,191,461,466,489],filepo:290,fill:[7,9,165,190,279,320,351,359,369,413,424,462],filter:[191,200],final_integr:8,final_integrate_respa:8,finchham:[6,147,381],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,168,185,192,201,214,215,225,228,251,274,280,288,292,354,356,358,359,379,394,399,403,410,440,442,480,485],find_custom:8,fine:[16,17,169,197,223,318,359,363,485],finer:[140,165,485],finest:348,finger:[165,187,249,462],finish:[6,11,41,211,333,345,347,348,360,362,363,447,464,485,486],finit:[],finni:[7,385,440],finvers:221,fiorin:[9,216],fire:[354,355,356,358,473],firebrick:191,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,150,153,159,161,163,164,166,167,168,172,185,188,189,190,191,192,194,195,203,204,206,207,208,209,211,214,217,228,229,234,239,249,250,251,252,274,276,281,282,283,285,290,293,296,297,305,306,308,309,310,317,318,319,320,322,326,331,333,334,340,351,356,357,358,359,362,363,364,365,368,369,370,372,374,376,378,379,385,387,388,391,392,394,395,396,398,399,403,408,409,410,412,413,415,417,421,423,424,431,439,441,442,443,444,445,448,452,454,455,456,457,459,460,461,464,466,468,471,472,473,476,477,480,485,486,487,489],fischer:[6,9,19,20,171,374,471],fit:[3,6,9,12,38,56,185,292,308,365,369,396,410,415,435,442,444,467,485],five:[73,151,283,357,369,411,459,473],fix:[],fix_adapt:[159,196,407],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,201,279],fix_evapor:201,fix_flux:200,fix_gcmc:[201,357],fix_gl:230,fix_gld:230,fix_grav:279,fix_id:[3,215,250,252,254,255,256,257,258,280,283],fix_modifi:[],fix_mov:[187,326],fix_nh:8,fix_npt:230,fix_nvt:[201,228],fix_poem:[3,6],fix_pour:[3,218],fix_qbmsst:9,fix_qeq:[3,378],fix_rattl:296,fix_reax_bond:423,fix_rigid:[242,368],fix_saed_vtk:294,fix_setforc:8,fix_shak:296,fix_srd:3,fix_styl:256,fix_temp_rescal:314,fixedpoint:[215,252],fixextern:226,fixid:200,fji:382,flag1:[220,361],flag2:[220,361],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,93,103,104,106,118,160,164,168,188,190,191,192,209,214,216,220,233,236,240,242,248,249,275,282,293,305,307,308,315,319,328,331,346,349,357,361,362,363,365,393,398,410,439,454,456,457,459,460,461,463,464,465,469,485],flag_buck:373,flag_coul:[373,382,403],flag_lj:[382,403],flagfld:[371,408,409],flaghi:[3,371,408,409],flaglog:[371,408,409],flagn:220,flagvf:[371,408,409],flat:[6,320,325,326,330],flavor:[2,7,12],fld:[9,325,371,408,409],flen:366,flex_press:366,flexibl:[3,6,8,166,190,203,207,216,230,253,316,323,387,444,477],flip:[3,6,217,252,327,328],floor:485,flop:12,floralwhit:191,flow:[],fluctuat:[6,64,87,215,228,229,236,239,252,256,274,275,318,320,342],fluid:[],fluid_veloc:243,flush:[3,191,476],flux:[],flv:190,fly:[7,9,12,41,190,194,200,205,218,221,293,296,321,369,413,477,480],fmackai:9,fmag:219,fmass:276,fmax:[356,477],fmomentum:221,fmsec:[2,191,236,237,249,252,280,293,311,312,468,479,484,486],fname:347,fno:[12,16],fnorm:[356,477],fnpt:221,fnvt:221,foce:394,fock:366,focu:296,fogarti:[9,286,424],foil:[140,274,431],fold:[306,468],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,144,145,151,153,158,161,163,165,166,171,174,175,176,177,179,180,182,183,185,188,189,190,191,194,200,201,202,203,204,205,206,207,208,209,211,216,217,218,221,222,226,228,229,230,233,235,236,237,239,242,250,252,256,257,258,269,270,272,275,276,278,281,282,283,284,286,288,290,292,293,294,296,310,311,312,313,316,317,318,31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:[275,283,288,378,480],supercomput:[12,18,457],superpos:[394,440],superposit:7,supinski:413,supplement:[230,423,424],supplementari:[216,390,425],suppli:[12,185,228,250,320],support:[1,3,6,7,8,9,11,12,13,14,15,16,17,18,19,40,41,42,61,87,88,102,107,188,189,190,191,192,195,196,197,198,203,211,214,215,216,223,226,230,231,234,236,237,238,239,247,250,252,254,255,256,257,258,269,270,271,272,274,275,280,283,285,287,292,293,298,299,300,301,302,304,305,307,311,312,313,314,318,323,325,329,346,347,348,349,355,356,357,363,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,450,451,452,456,460,461,466,468,469,470,472,473,480,484,485,488,489],suppos:[3,8,388,485],suppress:[6,12,163],sure:[6,8,11,13,14,185,195,196,215,293,296,330,385,442],surf:166,surfac:[2,3,4,6,8,9,40,42,57,70,118,140,163,165,168,190,194,218,225,234,239,242,274,285,292,301,304,305,308,315,320,325,329,330,358,369,394,408,409,413,429,447,451,456,462],surface_mov:320,surfact:[380,389],surpris:387,surrog:9,surround:[38,56,70,165,185,191,215,252,254,255,257,258,274,280,293,442,480],suspect:3,suspens:[408,409],sustain:[188,215,391],suzuki:[252,293],svg:6,svn:[7,11,12],sw_exampl:422,swamp:293,swap:[],swegat:319,swiggl:[3,249,325,328,330,462,485],swiler:[140,431],switch7_section_start:389,switchflag:[140,431],swm4:480,swol:53,swope:6,sxx:191,sy0302:9,symbol:[6,12,118,164,290,369,387,431],symmetr:[6,70,87,93,112,131,132,133,136,137,138,141,195,196,215,252,253,316,323,364,376,382,385,443,445,485],symmetri:[3,5,6,7,8,63,64,70,167,188,250,274,334,349,364,459,480],sync:[3,6,478],synchron:[1,230,358,478],synechococcu:7,syntax:[],sysdim:275,sysmt:17,sysstem:369,system:[],system_:276,systemat:[6,9,205,228,236,413],systemx:3,t10:474,t11:474,t12:474,t13:474,t14:474,t15:474,t3e:12,t_chain:3,t_corr:3,t_correl:454,t_dephas:454,t_e:320,t_e_min:320,t_equil:[317,318],t_event:[3,454,473],t_hi:473,t_infil:320,t_init:[283,320],t_iter:3,t_lb:239,t_lo:473,t_order:3,t_oufil:320,t_out:320,t_outfil:320,t_qm:283,t_switch:[317,318],t_target:371,ta06a:431,ta4:413,ta5:164,ta6:413,tab:[2,459],tabbernor:118,tabinn:415,tabul:[3,7,13,22,37,38,44,55,56,65,71,79,92,185,308,348,364,369,370,372,373,374,375,376,379,385,387,399,403,418,421,424,426,440,442,443,449,461],tabular:421,tabulate_long_rang:424,tad:[],tadmor:9,tag:[200,220,480],tagint:3,tail:[3,87,110,159,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,448,450,451,452,461,477,485],tailor:[71,321],tait:[9,437,438],taitwat:[],take:[1,2,3,6,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,56,59,77,87,89,91,109,112,113,116,117,141,143,152,159,163,169,171,172,173,174,175,176,177,179,180,182,183,185,188,190,191,195,196,197,210,211,215,217,224,227,231,235,236,237,252,254,255,256,257,258,259,267,269,270,272,285,293,295,296,305,306,307,308,310,311,312,313,321,324,328,331,334,335,336,337,338,339,342,344,348,349,353,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,382,383,385,386,388,389,390,391,392,393,397,399,400,401,402,403,404,405,406,407,408,411,413,416,417,418,420,423,424,425,426,432,439,441,442,443,444,445,446,447,448,450,451,452,453,457,460,467,468,469,476,477,478,485],taken:[6,59,147,165,187,214,218,228,229,230,236,237,238,239,279,283,286,320,338,385,387,390,441,448,454,468,469],talk:[6,7],talli:[8,41,107,113,203,206,207,208,211,213,236,238,253,308,316,323,387,389,393,424],tan:[191,485],tandem:[4,16,293],tang:413,tangent:251,tangenti:[6,108,308,326,330,391],tanh:320,tantalum:[4,413,431],taper:[3,286],tar:12,tarbal:[0,8,11,12],target:[3,6,7,8,9,11,12,17,39,41,191,199,211,215,216,218,228,229,230,236,237,238,252,253,254,255,256,257,258,269,270,271,272,276,280,283,288,293,297,306,311,312,313,314,319,320,323,324,327,346,349,371,383,454,465,467,486],target_fil:319,task:[1,6,7,12,13,14,15,16,17,18,54,191,233,276,321,363,457,478],taskset:16,tatb:[4,289],tatom:480,tau:[3,154,205,236,237,239,252,280,293,311,312,317,318,320,479,484],tau_1:229,tau_k:229,tau_n_k:229,tb3:164,tbead:157,tbp:369,tchain:[252,253,256,270,271,293],tcl:288,tcom:237,tcsh:[11,12,376],tdamp:[236,252,253,256,293,311,312],tdephas:454,tdrude:[150,221,237,480],teal:191,tech:[7,9,13],technic:[6,7,9,239,286,308,424],techniqu:[6,7,9,87,194,215,250,283,293,324,327,349,415,442,480],technolgi:9,technolog:[9,14,19,233],tell:[2,6,11,12,37,55,184,194,275,343,359,423,424,440,457,461,480],telsa:17,temeperatur:11,temp:[],temp_drud:480,temp_eff:97,tempcom:[144,158],temper:[],temperar:276,temperatur:[],temperature_definit:200,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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":212,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,145,153,154,158,164,165,168,170,184,186,187,188,190,191,192,193,195,196,197,199,200,201,203,207,208,209,212,213,215,216,217,218,222,225,228,229,234,236,237,238,239,240,242,247,250,252,253,256,270,271,275,276,279,280,281,282,283,285,288,290,291,293,294,308,310,315,316,317,318,321,323,325,327,331,343,346,348,349,351,352,354,355,357,359,360,361,363,366,369,371,387,408,409,413,415,423,424,439,440,454,455,456,459,460,462,464,466,467,468,471,473,475,476,477,478,479,484,486,487,488],"function":485,"long":[205,370,372,373,374,375,379,381,382,399,403,407,418,426],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[195,196],addforc:197,addit:[12,13],addtorqu:198,adiabat:6,adjust_dt:298,adp:364,airebo:365,alloi:385,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:199,arrai:6,aspher:[6,82,144,254,257,260,261,269],atc:[9,200],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,163,199,201,202,282,485],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:210,awpmd:[9,366],balanc:[41,211],barostat:6,basal:67,beck:367,berendsen:[280,311],between:6,binary2txt:13,bodi:[6,8,42,68,262,368],bond:[8,13,69,212,213,214,289],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:369,born:[370,381],boundari:[7,57],box:[6,58,215],brownian:371,buck:[372,373,381],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,171,374,407],chunk:[6,66,71,75,90,93,104,106,114,145,160,162,203],citat:7,class2:[21,43,172,334,375],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[325,377,451],colvar:[9,13,216],com:[74,75,146],comb3:378,comb:[285,378],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,481,482,483,484,485,486,487,488,489],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,485],compute_modifi:102,condit:7,conduct:[6,316],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:[204,205],cosin:[23,24,25,26,27,28,174],cossq:336,coul:[370,372,373,374,375,379,380,381,392,399,403,407,418,426],coupl:6,creat:213,create_atom:165,create_bond:166,create_box:167,createatom:13,creation:7,csld:312,csvr:312,cubic:401,cuda:[9,14,109,112,143,152,197,210,224,227,231,252,259,295,296,311,313,324,370,372,374,375,385,391,392,399,400,402,405,416,441,443],custom:8,cut:[49,366,372,375,379,382,387,389,399,400,407,414,418],cvff:337,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[379,399],deform:[148,149,217],delete_atom:168,delete_bond:169,delta:24,deposit:218,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,481,482,483,484,485,486,487,488,489],diagnost:7,diel:380,dielectr:170,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:173,dihedral_styl:[2,171,172,174,175,176,177,178,179,180,181,182,183,184,185],dilat:80,dimens:186,dipol:[6,29,382],direct:221,discuss:6,disp:6,displac:[81,86],displace_atom:187,distribut:[7,12],document:0,dpd:383,drag:219,dreid:[6,393],drude:[6,9,150,220,221,237],dsf:[379,399],dsmc:384,dump:[6,8,188,189,190,192],dump_modifi:191,dynam:284,eam:[13,385],echo:193,edip:386,eff:[9,13,96,97,149,151,156,238,253,263,271,314,387],efield:223,eim:388,elast:6,emac:13,enforce2d:224,ensembl:7,erot:[82,83,84,85],error:3,evapor:225,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,472,473,474,475,476,477,478,479,481,482,483,484,485,486,487,488,489],exp:[27,174],expand:[46,402],extend:[8,11],extern:226,fcc:274,featur:[7,8,485],fene:[45,46],fep:[9,13,87,196],field:[6,7],file:6,finit:6,fix:[2,6,8,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,485],fix_modifi:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,26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0,441,442,443,444,445,446,447,448,450,451,452],pair_writ:449,pairwis:8,parallel:11,paramet:6,pars:2,partial:152,particl:[6,7,42],partit:453,past:5,per:6,perform:[1,10],peri:420,period:25,phonon:[9,13,275],pimd:276,piston:327,planeforc:277,plastic:111,plastic_strain:124,plastic_strain_r:125,pmb:420,poem:[9,278],point:284,polariz:6,poli:[371,408,409],polym:13,polymorph:421,post:7,potenti:[2,6,8],pour:279,pppm:6,prd:454,pre:7,press:280,pressur:112,previou:12,print:[281,455],problem:[3,4],process:[6,7],processor:456,profil:153,properti:[6,113,114,115,282],pymol_aspher:13,python:[9,11,13,457],qbmsst:283,qeq:[284,285,286],qmmm:[9,287],qtb:[9,288],quadrat:183,quantiti:6,quartic:[35,54],quip:422,quit:458,ramp:154,rattl:296,rdf:116,read_data:459,read_dump:460,read_restart:461,reax:[9,13,286,289,290,423,424],reaxc:9,rebo:365,recent:291,reduc:117,refer:485,reflect:328,region:[8,117,155,156,329,462,485],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,182,183,184,185,186,187,188,189,190,191,192,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,227,228,229,230,231,232,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,288,289,290,291,293,294,295,297,298,299,300,301,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,342,343,344,345,346,347,348,349,351,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,464,465,466,467,468,469,471,472,473,474,475,476,477,478,479,481,482,483,485,486,487,488,489],relax:215,replic:463,replica:[6,7],report:3,requir:12,rerun:464,rescal:[313,314],reset:222,reset_timestep:465,resquar:425,restart2data:13,restart:[6,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,466],restrain:292,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,481,482,483,484,485,486,487,488,489],rho:126,rhosum:436,rigid:[6,83,98,242,293],ring:342,rotat:157,rule:2,run:[6,11,12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,467],run_styl:468,scalabl:10,scalar:6,screen:12,script:[2,6,8,11],sdk:[36,426],self:307,serial:11,set:[6,469],setforc:295,setvel:302,shake:296,share:[11,12],shell:[6,470],shield:284,shift:[26,27,48,49,174],simpl:31,simul:6,size:6,slater:284,slice:119,sllod:[270,271],small:293,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,297,298,299,300,301,302,304,427,428,429,430],smooth:[405,406],sna:140,snad:140,snap:431,snapshot:6,snav:140,soft:[407,432],solver:2,sourc:7,spatial:[207,208],spc:6,speci:290,special:[7,415,485],special_bond:471,sph:[9,433,434,435,436,437,438],sphere:[84,85,158,208,242,255,258,267,272],spheric:6,spline:[411,412],spring:[305,306,307,318],squar:28,srd:[308,330],srp:439,standard:9,start:[12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330],state:310,stationari:246,stop:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330],store:[309,310],strategi:1,streitz:379,stress:[141,142],structur:2,style:[1,2,6,8],submit:8,suffix:472,summari:6,swap:[201,214],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,481,482,483,484,485,486,487,488,489],system:6,tabl:[0,6,38,56,185,442,443],tad:473,taitwat:[437,438],talli:142,temp:[143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,311,312,313,314],temper:474,temperatur:6,tersoff:[443,444,445],test:11,tfmc:315,thermal:[6,316],thermo:[6,475],thermo_modifi:476,thermo_styl:477,thermodynam:[6,8],thermostat:6,thole:446,time:[6,209],timer:478,timestep:479,tip3p:6,tip4p:[6,379,399,403,407],tip:12,tlsph:428,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:319,tool:[12,13],torqu:160,transform:221,tri:[268,447]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\ No newline at end of file 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187,188,189,190,191,192,194,195,196,200,201,203,204,211,212,213,214,215,217,221,228,239,240,241,242,243,248,249,250,252,257,258,264,269,270,272,275,279,283,291,293,296,304,309,311,312,313,315,316,317,318,319,323,325,327,331,334,335,340,347,353,354,356,357,359,361,362,363,364,365,369,376,378,385,386,387,388,394,395,396,407,408,409,410,411,412,413,417,421,423,424,431,432,442,444,445,446,449,455,457,459,460,461,462,463,465,466,468,470,472,474,477,478,481,485,486,487,488,489,490],afterrun:468,afterward:3,afterword:41,ag1:164,ag2:164,again:[6,11,12,16,17,62,140,145,151,159,188,191,217,232,279,334,347,358,408,409,455,457,458,460,462,467,474,476,486,488],against:[11,12,13,64,218,358,423,424],aggreg:[6,12,65,68,69,79,92,108,115,232,248,291,293,306,455,487],aggress:[232,474],agilio:[9,13],agre:[3,8,185,356,365,396,424],agreement:[5,7],ahd:393,ahead:327,aidan:[0,5,7,9,13,351],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:190,akohlmei:[7,9,13,192,233],aktulga:[7,9,286,424],al2o3:431,al2o3_001:[118,294],al3:164,ala:[239,431],alain:9,alat:[274,410],alb:[421,444,446],albeit:292,albert:9,alchem:[87,159],alcohol:323,alcu:[364,369],alcu_eam:421,alderton:382,alejandr:[252,253],alessandro:13,algebra:413,algorithm:[0,1,6,7,8,9,41,61,191,200,211,214,217,239,241,242,264,276,293,296,315,316,320,323,328,354,355,356,360,363,387,409,413,428,430,455,457,474],alia:[12,16],alias:[1,349],aliceblu:191,align:[6,12,29,41,71,167,185,207,211,234,351,460,463,481],alkali:387,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,153,158,159,160,161,162,163,164,165,166,167,168,169,171,173,178,184,185,188,189,190,191,192,194,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,245,247,248,250,252,253,254,255,256,257,258,259,260,261,262,263,264,265,267,268,269,270,271,272,273,274,275,276,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,304,305,307,308,309,310,311,312,315,316,317,318,319,320,321,322,323,325,326,327,328,329,330,331,332,333,334,335,338,343,346,347,348,349,350,351,353,356,357,358,359,360,362,363,364,365,366,368,369,370,372,373,374,375,376,378,379,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,403,407,408,409,410,411,412,413,414,415,416,417,418,420,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,454,455,457,458,459,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,477,478,479,481,485,486,487,488,489,490],allen:[29,87,382,390],allentildeslei:87,allign:3,allindex:332,alloc:[3,5,6,8,9,11,12,60,226,322,357,359,363,419,424,460,468],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,142,144,145,158,163,164,165,167,173,184,185,188,190,191,192,194,195,197,199,200,201,203,204,205,206,207,208,209,211,213,214,215,216,217,218,222,223,226,228,229,230,231,233,236,239,242,243,247,249,252,253,274,278,280,281,282,283,287,293,294,296,297,299,300,304,308,315,316,317,318,320,321,322,323,324,325,331,333,335,343,348,349,351,356,357,358,359,362,363,366,369,370,371,372,373,374,379,385,387,391,392,393,394,399,403,408,409,413,415,421,424,425,428,430,431,440,450,452,455,458,460,462,463,464,465,466,467,470,472,473,474,477,478,486,487],almost:[2,3,12,60,234,283,320,349,360,363,440],alo:379,alon:[6,7,214,289,423,424,458],alond:13,along:[6,8,9,12,29,40,87,118,164,165,187,188,190,214,234,239,240,244,249,251,283,293,296,297,301,305,306,315,319,320,326,329,331,351,354,355,356,358,379,382,391,394,397,399,403,410,423,424,443,460,463,470,471,486],alonso:[411,412],alpha:[6,12,51,195,239,275,283,288,356,364,367,370,379,383,385,386,388,393,398,399,410,416,420,445,447,478,481],alpha_:447,alpha_c:407,alpha_i:[432,447],alpha_ialpha_j:447,alpha_lj:407,alphabet:[2,3,22,37,44,55,63,173,184,194,335,343,357,376,441,460],alphanumer:[3,63,194,282,290,333,357,486],alreadi:[3,7,8,9,12,16,17,18,42,165,166,168,189,199,203,207,208,211,213,217,243,281,283,308,331,357,358,383,392,394,401,409,440,450,453,456,460,461,465,470,486],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,149,151,152,153,154,155,157,158,159,160,161,162,163,165,166,167,168,169,171,173,184,185,186,188,189,190,191,192,194,195,196,197,199,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,223,226,227,228,229,230,232,233,236,237,238,239,249,250,252,253,254,255,256,257,258,263,266,267,2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6],clariti:333,clark:418,class2:[],classic:[0,3,5,6,7,8,9,226,276,283,288,320,344,387],classifi:[9,441,449],claus:458,clean:[6,12,14,15,17,468],cleanli:[459,489],clear:[],clearli:7,clebsch:140,clermont:[9,13],clever:464,click:[2,11,22,37,44,55,165,173,184,190,233,335,343,358,376,441],client:[233,235],climb:[251,358,474],clinic:[7,13],clo:[154,187,487],clock:[12,455,474],clockwis:326,close:[3,6,11,12,13,39,41,67,141,168,188,213,214,215,230,237,239,252,270,293,296,326,329,347,349,352,354,355,358,363,365,369,379,380,410,415,427,429,446,464,470,481,483],closer:[3,41,116,163,187,188,211,215,219,317,358],closest:[213,274,293,323,390,425,440,450],cloud:[431,481],clovertown:18,clsuter:72,clump1:[278,293],clump2:[278,293],clump3:[278,293],clump:293,cluster:[],clutter:[3,9],cmap:460,cmatrix:230,cmax:410,cmd:[11,12,276,471],cmin:410,cmm:[],cn1:204,cn2:204,cna:[],cnn:204,cnr:[9,13],cnt:[394,464],co2:[40,164,296,357],coars:[7,9,29,36,40,54,177,278,293,308,392,426,472],coarser:[349,486],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,171,172,173,178,334,335,340,376,394,398,415,428,430,433,460,462],coeffcient:460,coeffici:[],coefficienct:383,coefficient0:385,coefficient1:385,coeffieci:[6,367],coeffincientn:385,coexist:[9,228,387],cohes:[6,388,410],coincid:[122,329,374,408,409,455],colberg:189,cold:[6,150,228,232,359,481],coldest:316,coleman8:9,coleman:[9,118,164,294],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,145,153,160,162,165,188,191,203,216,242,248,278,288,291,293,331,348,357,359,377,397,460,467,473,479,490],collid:[222,308,330],colliex:164,collinear:[3,278],collis:[3,239,308,326,330,384,391,453],colllis:308,colloid:[],colombo:39,colon:[192,331,461],color1:191,color2:191,color:[3,9,41,188,190,191,211,229,283,288],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,145,153,160,162,163,164,185,188,191,194,202,203,204,206,207,208,209,242,249,250,283,293,309,310,320,330,389,393,423,424,461,475,477,486],colvar:[],colvarmodul:12,com:[],comamnd:217,comand:[214,462],comannd:363,comb3:[],comb:[],comb_1:285,comb_2:285,combiant:380,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,144,158,188,190,200,206,233,242,252,276,282,312,321,329,332,334,348,349,351,355,363,377,379,380,387,388,394,406,407,432,442,444,446,449,452,463,468,473,481,486],come:[],comfort:[12,13],comm:[0,3,12,61,73,189,233,235,236,349,358,363,383,415,420,443],comm_modifi:[],comm_modift:61,comm_styl:[],command:[],comment:[2,7,11,12,38,56,171,185,188,237,293,320,357,358,364,385,386,388,398,410,417,424,431,432,442,443,444,445,446,449,457,458,460,481,486],commerci:7,commmand:[3,6,12,59,107,271,454,455,457,474,489],common:[],commonli:[3,6,12,17,25,57,59,105,167,188,190,192,344,392,401,432,444,446,460,463,472],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,169,190,191,211,212,213,215,216,217,233,235,239,241,242,243,252,275,282,284,285,286,293,308,320,331,346,348,359,360,361,363,384,419,457,458,462,469,470,486,488,490],communc:348,comp:[7,189,235,236,296,349,358,387,415,420,425,439,443,445],compact:[63,194,376,441],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,148,163,164,173,184,191,221,284,331,333,348,349,356,358,410,431,455,474,475,481,485],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,172,173,184,334,335,343,375,441],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,176,188,192,196,202,203,204,206,207,208,209,211,275,287,312,315,322,325,328,348,363,395,413,415,443,457,458,486],compens:[6,212,213,291,359,387],compet:319,competit:349,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,163,188,189,190,192,233,319,349,363,413,460,461,465,486],compl:17,complain:[12,17],complement:410,complementari:[7,379,399],complet:[3,6,9,12,15,41,59,71,191,207,211,216,242,276,279,282,308,319,321,333,347,358,363,388,428,430,448,455,460,465,468,472,474,477,481,486],complex:[6,8,11,12,13,25,40,42,62,140,142,153,165,166,239,304,329,346,358,387,413,443,458,460,463,486],compli:[315,319],complic:[6,7,9,12,13,201,228,458],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,160,161,162,188,190,191,197,198,202,203,204,205,206,207,208,209,210,214,215,217,218,223,226,231,235,236,239,242,244,248,249,251,252,253,256,257,258,269,270,272,273,275,276,277,280,291,293,295,296,297,301,302,305,308,311,312,313,315,322,323,328,329,330,348,351,355,356,357,358,363,383,387,391,408,409,428,430,431,432,460,461,470,478,486,487],componenet:6,composit:[6,201,239,385],compound:[378,387,388,449],compres:[71,114,203],compress:[3,59,71,114,168,188,190,191,203,217,250,256,280,283],compris:[40,329,397,425,448],compton:[118,164],comptu:3,compuat:349,comput:[],computation:[3,6,212,213,320,369],computational:481,compute_arrai:8,compute_fep:[196,407],compute_group_group:228,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,294],compute_scalar:8,compute_temp:8,compute_ti:196,compute_vector:8,compute_xrd:164,concaten:[2,3,489],concav:329,concentr:385,concept:[6,145,155,203,469],conceptu:[3,6,71,153,215,217,358,379,394,410,465],concern:[6,73,87,189,229],concis:[11,319],conclud:12,concret:8,concurr:[9,16,349,486],conden:[320,444,446],condens:[6,147,320,365,381,385,399,449],condit:[],conducit:6,conduct:[],cone:463,confer:413,confid:[3,474],config:[12,188,457],configfil:216,configur:[1,2,6,12,15,17,38,59,122,167,185,187,188,190,194,215,216,217,218,222,228,235,236,264,276,284,319,346,356,358,365,369,386,410,413,442,444,446,449,455,460,462,463,474],confin:[460,474],conflict:[3,12,40,415,458],conform:[3,6,13,59,214,215,251,292,297,319,342,358,387,472],confus:[3,449],conjuct:383,conjug:[7,8,236,355,387,423,424],conjunct:[6,7,71,86,87,114,148,153,159,165,169,191,195,196,236,239,243,264,279,280,284,285,286,288,293,308,316,323,328,348,349,358,370,372,376,379,383,387,393,399,415,418,426,447,460,463,467,481,490],connect:[3,6,87,150,168,214,233,278,293,296,305,358,380,391,440,446,457,458,464,481],conput:3,consecut:[3,11,12,39,71,165,191,195,196,218,233,234,379,399,403,455,461,463],consequ:[1,6,201,320,398,474],conserv:[3,194,201,214,221,222,229,232,236,238,239,243,248,250,252,264,293,296,311,312,316,323,324,328,358,382,383,391,405,431,469,474],consid:[6,9,70,71,78,87,115,147,150,151,168,188,191,195,196,202,204,207,211,213,214,218,240,253,275,293,315,316,319,320,323,349,376,387,394,424,425,431,440,455,456,458,461,462,463,465,468,470,478,481,486],consider:[6,8,236,237,311,312,313,363,469],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,145,148,150,165,177,187,192,197,198,203,217,218,221,223,226,229,236,237,238,249,252,254,255,256,257,258,259,260,262,263,264,265,267,268,269,270,271,272,280,283,288,290,292,293,311,312,313,314,324,348,349,351,357,358,363,365,369,371,377,379,387,390,394,408,409,410,413,415,425,428,430,431,443,450,458,460,461,463,464,465,472,481,486],consistent_fe_initi:200,consit:293,constant:[],constitu:[3,6,242,293,325,329,377,425],constitut:[428,430],constrain:[3,6,8,143,144,145,146,148,151,152,153,154,155,157,158,194,203,218,228,229,234,242,246,278,279,291,293,296,306,316,323,356,357,387,465,472,481],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,118,140,164,215,252,275,292,329,359,363,382,413,415,440,442,443,463,464,479,486],constructor:8,consult:424,consum:[1,288,419,486],consumpt:346,contact:[],contact_stiff:[427,429],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,145,153,163,164,165,167,171,173,184,185,188,190,191,192,194,195,196,200,202,203,204,206,207,208,209,211,216,218,223,230,234,235,236,237,239,250,264,274,275,278,279,281,283,286,290,293,294,298,308,315,319,320,329,330,333,347,349,357,358,361,362,364,365,366,369,378,379,382,385,386,387,394,395,410,413,417,421,422,423,424,432,442,443,444,445,446,447,449,455,456,457,458,460,461,462,463,465,467,469,472,474,477,478,481,486,488,490],content:[12,18,424,476,478],context:[3,6,8,12,17,117,191,212,213,218,278,290,324,355,452,460,467,476,485,486,487],contibut:70,contigu:457,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,161,191,194,195,196,201,203,204,205,206,207,208,209,211,214,215,216,217,218,228,229,230,232,233,234,236,237,238,244,249,250,252,254,255,256,257,258,269,270,271,272,277,279,282,283,293,294,297,307,308,310,317,318,320,326,329,333,347,362,363,369,383,384,401,404,423,424,425,428,430,445,455,458,460,462,463,468,474,477,478,486,488],continuum:[6,7,9,200,320,428,430],contour_integr:200,contract:[59,215,217,252,280,293],contradictori:3,contrain:296,contraint:264,contrari:[230,237],contrast:[1,6,42,55,64,147,150,217,331,428,430,452,489],contrib:320,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,196,201,202,203,204,206,207,208,209,215,228,236,239,242,243,247,253,270,271,278,279,287,290,293,294,296,322,348,356,358,366,383,384,385,387,394,408,409,413,415,423,424,431,472,478,481],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,174,188,190,194,200,201,211,215,216,217,232,233,236,237,252,254,255,256,257,258,280,285,293,299,300,311,312,313,320,324,346,348,360,387,390,413,423,424,427,429,442,446,455,457,469,475,476],control_typ:200,controlfil:424,convect:91,conveni:[6,12,29,188,192,209,294,351,432,486],convent:[3,8,9,29,176,183,184,191,292,305,332,385,387,486],converg:[3,6,41,88,188,190,192,197,211,214,215,223,226,256,283,285,288,292,296,354,355,356,358,378,379,399,431,455,467,474],convers:[3,8,140,190,191,201,204,280,348,379,380,381,387,399,403,407,418,458,474,485],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,165,172,188,190,191,209,250,331,334,336,339,342,351,358,364,385,413,444,446,453,458,460,461,462,467,477,481,485,486,488,490],convex:329,convinc:[7,12],cook:9,cooki:7,cool:[7,155,232,291],cooordin:188,cooper:[5,7],coord123:114,coord1:[3,114,203,207,208],coord2:[3,114,203,207,208],coord3:[3,114,203,207,208],coord:[],coordb:431,coordbb:431,coordiat:356,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,148,154,160,162,163,165,169,187,188,189,190,191,192,194,197,202,203,206,207,208,211,212,213,214,215,216,217,218,221,223,224,226,228,231,232,233,234,235,236,237,249,251,252,254,255,257,258,270,273,274,275,278,279,280,290,291,293,295,296,297,302,305,306,307,308,310,318,319,320,327,328,330,331,351,356,357,358,363,364,365,368,386,431,455,460,461,463,465,468,470,474,481,486,487],coordn:[114,203],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,190,320,358,376,423,458],copper:453,coproccesor:16,coprocessor:[1,4,7,9,16,17,363,473],coproprocessor:17,copy_arrai:8,copyright:[7,8,278],coral:191,core:[],core_shel:147,coreshel:[6,9,372,379,381],cornel:[6,171,472],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,190,329,330,351,448,460],cornflowerblu:191,cornsilk:191,corpor:16,corr:378,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,147,152,159,190,217,228,230,236,252,253,270,278,280,283,319,325,329,348,358,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,451,452,453,460,475,478,481],correction_max_iter:200,correctli:[3,8,9,11,17,71,81,102,103,143,144,146,148,150,151,152,153,154,157,158,161,188,191,197,218,223,226,237,246,252,253,286,293,296,305,307,326,329,358,359,363,381,409,413,457,458,460,470,485,487],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,143,144,152,159,164,171,172,173,174,175,176,177,179,180,182,183,185,188,190,191,195,196,197,203,205,206,207,208,210,213,215,217,224,226,227,231,236,239,240,248,249,250,252,254,255,256,257,258,259,264,267,269,270,272,275,276,280,285,293,295,296,311,313,315,324,325,326,328,329,330,332,334,335,336,337,338,339,342,344,349,353,355,357,358,364,365,367,370,371,372,373,374,375,376,377,378,379,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,413,415,416,417,418,420,421,423,424,425,426,431,432,433,442,443,444,445,446,448,449,451,452,453,455,457,458,460,461,463,473,474,475,477,478,481,486],correspondingli:[408,409,469],cosin:[],cosineshift:27,cosmo:[230,235],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,164,190,191,203,207,208,211,212,213,225,252,285,320,348,349,361,379,399,403,413,415,442,457,469],costheta0:[442,444,446,449],costheta:421,costli:[11,88,230,359],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,145,155,160,162,178,188,190,191,195,196,203,204,207,211,217,226,235,282,283,284,288,291,293,295,308,309,315,319,320,321,325,329,331,333,340,345,347,354,356,359,363,366,389,393,394,423,424,456,457,458,460,462,464,467,468,476,481,486,487],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,116,141,166,170,284,286,321,348,349,356,363,370,372,373,374,375,378,379,380,381,382,387,391,392,394,399,403,407,415,418,423,424,426,431,441,446,447,449,452,465,472,478,481,485],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,114,116,117,153,163,169,197,198,201,203,206,207,208,210,211,218,223,225,228,234,252,264,279,296,311,312,329,349,356,357,358,360,363,389,393,415,478,486],counter:[326,455,466,468,474],counteract:228,counterbal:232,counterpart:[188,293,455],counterproduct:18,coupl:[],courant:298,cours:[3,8,126,128,159,188,195,196,229,292,305,319,325,327,328,330,331,349,408,433,457,460,473,481,486,488],courtesi:351,cov:431,coval:[6,29,387,410,431,481],covari:230,cover:[6,71,185,191,200,239,387,397,448],coverag:[71,207],cpc:235,cpp:[1,3,6,8,9,11,12,13,87,188,195,196,226,296],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,191,194,205,221,237,321,346,349,363,376,441,455,473,474,477,478,479,486],cpuremain:478,cr2:164,cr3:164,crack:[4,359],crada:[5,7],crai:[5,7,13,18,188],crash:[3,12,359,481],craympi:363,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:200,create_faceset:200,create_group:189,create_nodeset:200,createatom:[],creation:[],crimson:191,critchlei:278,criteria:[3,116,166,190,191,212,213,214,247,356,420,448,462,465,486],criterion:[12,41,121,163,165,168,201,211,214,228,264,285,298,326,331,356,358,378,387,391,431,465,474,475],criterioni:474,critic:[6,48,49,250,315,320,356],cross:[3,12,22,71,89,144,173,188,190,202,207,213,217,249,251,270,293,301,305,307,316,323,335,351,358,374,383,384,385,392,393,394,399,401,403,421,426,428,430,444,446,453,460,464,470,488],crossov:1,crossterm:460,crozier:[0,7,13],crucial:283,crystal:[4,6,13,73,274,275,318,351,359,464,478,481],crystallin:[6,275,351,445,481],crystallis:315,crystallogr:[118,164],crystallograph:[351,478],crystallographi:[118,164,351],cs1:164,cs_chunk:6,cs_im:[40,460],cs_re:[40,460],csanyi:[140,422,432],cscl:410,csequ:6,csh:[11,12,376],cshrc:[11,12],csic:[386,442,444,446,449],csinfo:6,csisi:[386,442,444,446,449],csld:[],cst:385,cstherm:6,cstyle:457,csvr:[],ctcm:[364,385],ctemp_cor:221,cterm:297,ctr:9,ctype:11,cu1:164,cu2:164,cu3au:410,cube:[6,41,163,168,211,221,329,351,481],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:369,cummul:[3,6,209,212,213,214,216,225,230,236,238,308,311,312,313,314,316,323,393,478],cumul:[6,201,203,206,207,208,222,228,236,250,252,256,264,293,294,358],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,145,153,155,161,163,166,169,188,189,190,191,192,195,196,200,203,207,208,209,211,212,213,214,215,216,217,218,222,223,226,228,230,233,234,236,242,249,252,253,257,258,264,269,270,272,278,284,285,287,290,291,292,293,296,297,298,299,300,301,302,304,306,307,308,311,312,313,319,320,323,324,325,326,327,328,330,331,333,346,347,348,349,352,353,355,356,357,358,363,369,376,378,382,385,387,388,391,394,395,398,408,409,410,411,412,415,421,423,424,427,428,429,430,433,444,446,447,450,455,456,457,458,460,461,462,463,464,466,467,468,470,472,474,475,477,478,486,487,488,489,490],curv:[6,165,228,275],curvatur:[390,425,453],custom:[],cut0:458,cut1:469,cut2:469,cut:[],cuthi:[274,286],cutinn:[371,408,409],cutlo:[274,286],cutmax:421,cutoff1:[375,382,399,403,407,418,426],cutoff2:[370,372,373,375,381,382,399,403,407,418,426],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,163,166,168,213,214,219,274,283,284,286,288,290,293,308,321,325,329,331,346,348,349,356,359,360,361,363,364,365,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,383,384,385,386,387,388,389,390,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,431,432,433,434,435,436,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,458,462,465,469,481,486],cutoffa:386,cutoffc:386,cuu3:385,cval:164,cvd:315,cvel:297,cvff:[],cwiggl:[3,249,325,328,330,486],cyan:[2,190,191],cycl:[3,228,250,252,253,256],cyclic:[3,185],cygwin:12,cylind:[3,4,190,234,279,326,329,463],cylindr:[6,234,305,326],cypress:363,cyrot:369,cyrstal:275,d3q15:239,d3q19:239,d_double_doubl:15,d_e:320,d_flag2:282,d_flag:282,d_name:[113,188,282,310,470],d_single_doubl:15,d_single_singl:15,d_sx:282,d_sy:282,d_sz:282,daan:318,dai:12,daili:12,daivi:270,damag:[],dammak:288,damp:[3,6,194,199,236,237,238,243,252,253,256,280,283,288,293,311,312,324,326,327,355,356,358,370,372,374,379,382,387,391,399,407,418,426,441,447,474,481],damp_com:237,damp_drud:237,dampen:[293,481],dampflag:[326,391],dan:17,danger:[3,12,228,331,383,478],dangl:168,daniel:9,darden:[349,382],darkblu:191,darkcyan:191,darken:190,darkgoldenrod:191,darkgrai:191,darkgreen:191,darkkhaki:191,darkmagenta:191,darkolivegreen:191,darkorang:191,darkorchid:191,darkr:191,darksalmon:191,darkseagreen:191,darkslateblu:191,darkslategrai:191,darkturquois:191,darkviolet:191,dasgupta:284,dash:[391,477],dat:[6,91,185,200,456],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,294],dataset:294,datatyp:3,date:[0,6,12,13,423,424,486],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,188,204],davi:325,david:[9,19,348,349,444,446],daw:[385,421],dbg:14,dcd:[3,6,7,188,189,190,191,192,276,461,465],ddim:187,deactiv:407,dealt:235,debug:[6,7,11,12,13,14,17,118,122,164,165,276,281,346,348,363,395,415,450,458,459,462,467,470,477,486],deby:[],decai:[379,453],decid:[3,6,12,16,71,249,282,293,321,475],decipher:351,declar:189,declin:308,decod:190,decompos:[87,432],decomposit:[3,5,7,18,62,200,276],decoupl:[6,481],decreas:[3,188,197,198,205,214,217,223,226,228,236,319,348],decrement:297,deepli:345,deeppink:191,deepskyblu:191,def:[12,13,458],defaul:61,defect:[6,70,163,413],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,171,172,173,174,175,176,177,179,180,182,183,184,185,186,187,188,189,190,191,194,195,196,197,198,199,200,201,202,203,204,206,207,208,209,210,211,212,213,214,215,217,218,221,222,223,226,227,228,231,234,235,236,237,238,239,247,249,251,252,253,254,255,256,257,258,260,261,262,265,267,268,269,270,271,272,274,275,276,278,279,280,282,284,286,291,293,294,295,296,298,302,306,308,310,311,312,313,314,316,317,318,320,322,323,325,326,327,328,329,330,331,333,334,335,336,337,338,339,342,343,344,346,348,349,351,353,355,356,357,358,359,360,361,362,363,365,366,367,368,370,371,372,373,374,375,376,377,379,380,382,383,384,386,387,389,390,391,392,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,413,414,415,416,417,418,420,421,423,424,425,426,427,428,429,430,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,457,458,460,461,463,464,465,466,469,470,471,472,474,475,477,478,481,482,483,484,485,486,487],definit:[2,3,6,8,12,13,78,80,116,140,191,203,204,205,206,207,208,209,217,234,256,294,310,322,325,328,330,332,343,346,357,366,369,377,387,397,421,428,430,432,448,458,460,462,469,471,485,486],defint:478,deform:[],deg2theta:164,deg:481,degener:[3,278],degrad:[8,18,275,349,469],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,164,165,171,172,175,176,183,185,187,190,203,214,221,228,230,231,236,237,242,252,253,256,257,258,269,270,272,276,278,292,293,296,311,312,313,318,334,336,339,342,344,356,382,385,393,470,478,481,487],degress:[145,203],del:474,delai:[3,6,12,359,384,478],deleg:394,delet:[2,3,7,8,12,54,57,60,63,163,168,169,194,203,204,206,207,208,209,212,214,225,228,252,294,311,312,331,333,347,357,359,362,415,460,461,463,471,472,477,482,484,486,487],delete_atom:[],delete_bond:[],delete_el:200,deli:187,delimit:[458,486],deloc:[253,387,431],delr:410,delt_lo:474,delta:[],delta_1:369,delta_3:369,delta_7:369,delta_conf:3,delta_ij:[410,421],delta_mu:3,delta_pi:369,delta_r:421,delta_sigma:369,delx:187,delz:187,demand:288,demo:11,demon:273,demonstr:[283,410],den:279,dendrim:393,denniston:[9,239,241,242,243,275],denomin:[7,170],denot:[118,221,237,275,286,288,379,392,394,424,428,430],dens:[71,214,387],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,151,163,165,195,196,200,203,207,208,211,217,226,239,242,245,246,275,279,280,284,320,325,351,353,357,364,369,385,410,411,412,421,425,431,435,437,438,439,460,469,470,478,485],density_continu:430,density_summ:430,depart:[0,7],departur:[250,283],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,143,148,152,153,159,165,166,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,190,191,194,195,196,197,198,201,203,205,206,207,209,210,211,213,215,217,223,224,227,230,231,232,234,236,237,239,241,242,249,252,254,255,256,257,258,259,267,269,270,272,274,285,288,290,293,295,296,302,308,311,312,313,315,317,319,320,322,324,325,328,329,330,331,333,334,335,336,337,338,339,342,344,349,351,356,357,359,360,361,363,364,365,367,368,369,370,371,372,373,374,375,376,377,378,379,380,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,413,414,416,417,418,420,421,423,424,425,426,431,432,433,441,442,443,444,445,446,447,448,449,451,452,453,455,457,460,462,463,466,470,472,474,477,478,480,486,487],dependend:6,depflag:12,dephas:[455,474],depos:218,deposit:[],deprec:[284,423],depth:[51,144,190,320,390,425],dequidt:9,der:[87,107,377,378,407,423,424,452,481],deriv:[6,7,8,9,38,56,63,87,140,159,185,204,215,217,228,236,249,252,254,255,256,257,258,274,280,284,288,317,318,320,325,326,329,355,357,365,369,377,382,387,388,392,401,405,406,410,413,423,424,441,443,452,481],derjagin:452,derlet:274,descend:191,descent:[7,355],descib:[40,284],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,144,145,149,150,153,156,158,159,163,164,165,167,168,177,182,185,188,189,194,195,196,203,204,205,206,207,208,209,211,214,215,216,217,218,220,221,229,230,233,234,235,236,237,238,239,241,242,243,247,251,252,253,256,263,271,274,276,281,282,283,284,285,286,293,297,305,308,309,310,311,312,313,314,315,316,317,318,323,325,326,328,333,348,349,351,354,355,356,357,358,362,365,366,368,370,371,372,374,375,376,377,378,379,382,385,387,388,390,391,392,394,399,400,401,402,403,404,405,406,407,408,409,410,413,414,420,421,422,423,424,425,426,431,432,433,440,441,442,443,444,445,446,447,449,451,452,453,455,457,458,460,461,463,464,470,473,474,477,486,487,488],descript:[],descriptor:[140,188,395],deserno:349,design:[0,3,6,7,8,9,11,13,14,15,17,118,147,150,164,200,214,220,221,252,253,274,275,294,315,320,366,367,368,371,374,379,381,387,407,408,409,411,412,421,424,443,469],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,112,117,141,147,165,178,187,203,209,215,217,226,228,229,236,237,238,242,252,270,278,279,280,281,284,288,293,296,308,311,312,313,314,319,326,340,345,348,349,351,354,356,357,358,383,385,393,408,409,442,444,446,456,457,458,460,464,469,474,475,477,478,486,487,488],desk:7,desktop:[4,6,7,10,12,190],despit:481,destabil:369,destre:342,destroi:[11,39,212,213],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,143,144,145,148,158,159,160,162,165,166,169,170,173,184,188,190,191,194,195,196,200,203,204,205,206,207,209,211,213,214,215,216,217,218,226,228,229,230,231,233,234,236,238,239,243,249,250,251,252,253,254,255,256,257,258,262,264,269,270,271,272,275,278,279,280,282,283,285,286,287,293,296,308,311,312,313,314,315,316,318,319,320,321,322,323,324,331,333,335,343,348,349,352,356,357,359,360,363,364,365,366,368,369,371,373,374,375,376,377,378,379,382,383,387,388,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,410,414,415,420,423,424,425,431,432,433,441,448,451,452,458,460,461,462,463,465,466,469,470,472,475,478,479,486,487,490],detect:[2,3,12,61,63,86,227,279,319,358,378,393,398,455,457,460,471,474,486],determ:363,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,153,154,163,164,165,187,188,190,191,192,193,197,198,199,202,203,204,205,206,207,208,209,210,211,215,217,218,221,223,228,231,232,234,236,237,242,247,249,250,252,257,258,269,270,272,274,276,280,283,290,291,292,293,294,295,298,300,302,308,311,312,313,315,321,322,325,326,327,328,329,330,331,343,348,349,351,357,359,360,363,365,366,373,378,382,384,385,389,391,394,395,403,410,413,415,424,425,431,440,443,447,452,457,460,461,463,465,467,470,474,476,477,479,485,486,487],detil:108,devan:[9,426],devanathan:446,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,233,256,278,283,284,287,365,369,387,412,413,431,449,462],devemi:9,deviat:[250,256,274,389],deviator:9,devic:[1,3,12,15,17,233,363],device_typ:363,devin:[285,378],devis:412,dfactor:190,dff:481,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,349],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,287,413],dhi:[59,187,217,279],dhug:[250,283],dhugoniot:[250,283],dia:410,diagnost:[],diagon:[3,6,83,140,141,142,215,252,280,293,323,428,430],diagonalstyl:432,diagram:[41,118,164,184,211,276],diallo:393,diam:[190,191,279,357],diamet:[3,6,40,113,165,188,190,191,195,196,236,279,293,308,324,326,357,377,390,391,397,401,425,448,452,460,461,470],diamond:[351,387,410],diamter:[40,279],dick:6,dicsuss:249,dictat:[201,250],did:[3,12,356,383,384,385,391,415,444,446,468],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,161,322,348],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,143,144,145,146,148,151,152,153,154,155,157,158,159,165,166,168,173,184,185,187,188,190,191,194,196,199,201,203,206,211,212,213,214,215,216,217,221,227,228,229,230,231,232,233,236,237,239,249,252,253,254,255,257,258,260,262,265,267,268,269,272,274,276,278,280,283,284,285,288,291,293,296,297,305,306,308,311,312,313,316,317,318,320,323,324,325,326,329,333,334,343,345,347,348,349,351,352,354,355,357,358,360,361,362,363,364,365,369,373,374,376,377,378,383,385,387,390,391,392,394,397,399,400,402,403,410,411,412,414,415,417,421,423,424,425,426,427,428,430,431,432,433,441,442,443,444,446,448,449,452,454,455,457,458,460,462,463,464,465,468,469,470,472,474,475,477,478,479,481,485,486,487,488],differenti:[1,3,6,29,185,348,379,421,445],difficult:[215,276,363,393,469],difficulti:[296,423],diffract:[],diffus:[],digit:[2,3,191,333,413],dih_table1:185,dih_table2:185,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:213,dihydrid:387,dij:296,dilat:[],dim1:3,dim2:3,dim:[3,59,71,143,146,147,148,151,152,153,154,155,157,165,187,207,217,234,326,351,410,463,485,486,487],dimdim:486,dimems:275,dimens:[],dimension:[3,39,112,118,140,143,145,146,147,148,151,152,153,154,155,157,164,186,203,207,251,275,320,351,354,358,421,460,470],dimensionless:[105,121,122,124,127,129,131,136,140,320,349,432,452],dimentionless:135,dimer:[6,293,410],dimgrai:191,dimstr:[41,211],dinola:[280,311],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,188,310,481],dir1:471,dir2:471,dir:[1,3,4,8,9,11,12,250,274,283,307,421,423,424,458,471,486],dirac:140,direc:421,direct:[],directli:[3,6,8,9,11,12,87,113,140,142,188,189,190,197,223,230,234,239,275,294,312,324,326,327,328,329,351,355,363,364,365,370,372,373,379,382,385,387,399,403,415,418,426,440,458,470,471,472,478,486],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,192,216,235,278,284,287,304,308,317,318,358,362,364,365,369,376,378,379,385,386,388,395,396,407,410,411,412,413,417,421,422,423,424,431,432,442,444,445,446,449,458,460,461,462,471,486],disabl:[3,12,16,320,398,458,473,486],disadvantag:[6,211],disallow:[188,217,252],disappear:462,discard:[2,3,41,71,205,207,211,321,329,457,462,463],discontinu:[9,185,356,405],discourag:410,discov:[13,321],discret:[6,8,40,42,190,191,236,239],discuss:[],disk:[6,84,85,158,186,218,228,279,458],disloc:[70,413],disord:[39,70,413],disp:[],dispar:425,disperion:[382,403],dispers:[3,6,7,9,163,275,348,349,373,382,403,408,415,424,443,449],displac:[],displace_atom:[],displace_box:59,displacemet:463,displai:[11,13,22,37,44,55,173,184,188,190,335,343,376,441],dispters:3,disregard:413,dissip:[6,229,236,275,317,318,371,383,391,408,409,441],dissolut:212,dist:[6,69,91,108,117,188,276,292,384,440,455,487],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,154,160,163,165,166,167,168,172,187,188,190,191,199,203,207,208,212,213,214,215,217,218,219,222,228,234,239,249,250,251,252,256,264,274,275,279,283,284,291,292,293,296,297,301,305,306,307,308,315,316,318,319,320,323,325,326,327,328,329,330,334,348,349,351,354,356,358,359,360,363,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,383,384,385,386,387,389,390,391,392,393,397,398,399,400,401,402,403,404,405,406,407,408,409,410,413,414,415,416,417,418,419,420,421,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,455,458,460,463,469,470,474,478,481,485,487],distinct:[6,221,290,348,425],distinguish:[6,86,140,242,387,459],distort:364,distrbut:364,distribut:[],distro:[111,376,420,421],ditto:[8,11,12,14,15,16,17,18,115,213,453,458],div:8,divd:117,diverg:[3,12,39,293,318,462,481,488],divid:[3,6,16,41,91,112,117,126,128,141,162,163,173,184,191,203,204,206,211,217,274,316,323,328,348,356,358,388,424,431,449,469,477,486],divis:[6,239,369,397,407,457,460,478,486],dl_poli:[6,7],dlambda:159,dlammps_async_imd:233,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,190],dlammps_gzip:[3,12,188,190,319,460,461,465],dlammps_jpeg:[3,12,190],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,190],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,188],dlen:470,dlmp_intel_offload:[12,16],dlo:[59,187,217,279],dlopen:6,dlvo:[7,377,452],dm_lb:239,dmax:[308,354],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,141,144,145,158,160,162,165,166,167,173,184,188,189,190,191,192,194,195,196,201,202,203,204,205,206,207,208,209,218,228,236,237,247,252,253,257,258,262,269,270,271,272,279,282,293,305,308,311,312,313,322,326,329,331,333,335,343,347,356,357,358,363,364,365,368,376,378,379,385,386,388,393,394,396,397,410,411,412,415,417,420,421,422,432,441,442,444,446,448,449,458,460,461,462,463,465,468,469,470,477,478,486,487,488,489],docuement:425,dodgerblu:191,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,116,117,118,142,144,145,147,148,153,155,159,164,165,166,167,169,171,173,178,184,185,187,188,189,190,191,194,200,201,203,207,210,211,213,214,215,217,221,223,225,228,229,232,234,236,237,239,242,248,252,253,254,255,257,258,269,270,271,272,280,281,282,286,288,291,293,308,311,313,315,316,320,323,324,325,328,329,330,331,336,337,339,340,342,347,348,349,350,351,357,358,359,364,365,366,367,368,369,371,373,374,375,377,378,379,380,382,383,384,385,386,387,389,390,391,392,394,395,396,397,398,401,402,404,405,406,408,409,410,411,412,413,415,421,422,423,424,425,427,428,429,430,431,432,433,434,435,436,437,438,439,440,442,443,444,445,446,447,448,449,451,452,453,455,456,457,458,460,461,462,463,464,467,468,470,471,472,473,474,477,478,481,486,490],doegenomestolif:7,doesn:[3,7,8,12,165,188,201,207,208,305,357,359,363,365,378,386,396,423,424,442,444,445,446,449,460,462],dof:[3,8,112,144,145,158,203,293,487],dof_per_atom:[145,203],dof_per_chunk:[145,203],doff:[357,460],doi:[6,216],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,154,164,167,187,189,190,191,194,201,211,215,217,218,232,235,239,252,253,276,288,293,320,325,326,348,349,358,363,384,415,455,457,460,464,477],domin:[1,387,474],don:[0,8,11,12,13,116,168,197,223,237,282,329,410,431,458,460],donadio:312,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,159,162,165,168,185,188,190,191,200,201,203,205,206,207,208,209,211,212,213,214,215,217,218,226,228,233,234,236,237,244,252,257,258,269,270,272,273,275,276,277,282,290,293,294,296,308,311,312,313,315,317,318,331,333,347,348,349,356,358,359,362,363,365,373,385,394,395,396,403,409,410,415,423,440,443,448,455,456,457,458,461,464,465,468,478,479,481,486,487],donor:393,dot:[141,161,197,223,231,251],doti:[369,421],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,217,226,281,329,333,347,349,362,363,369,388,392,413,423,424,456,460,464,468,473,486,487],dover:200,down:[3,6,7,8,11,39,71,215,228,236,308,324,363,387,415,431,459,479],downhil:[354,355],download:[5,7,8,9,11,12,13,17,233,395,422],downsid:6,downward:290,dozen:[8,12,107,194,423,424],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:245,dproduct:366,dr_ewald:[118,294],drag:[],dragforc:239,drai:[250,283],drain:[232,324,356],dramat:[59,187,212,213,214,215,217,252,308,311,312,349,363,415,431,457],drautz:369,draw:190,drawback:282,drawn:[188,190,191,229,455],drayleigh:[250,283],dreid:[],drfourth:105,drho:[113,364,385],drift:[6,103,105,229,230,236,237,248,291,308,469,477,4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228,236,252,270,280,292,293,328,383,387,431,444,446,460,463,468,469,478,481],equlibrium:6,equliibr:[284,286],er3:164,eradiu:[40,113,387,460],eras:[295,317],erat:[217,409],erc:379,erfc:[379,399,415],erforc:113,erg:485,erhart:[201,385,444,446],ermscal:366,ernst:9,eror:3,eros:410,erose_form:410,erot:[],errata:[444,446],erratum:325,erron:3,error:[],erta:391,ervel:[113,460],escap:[218,481],especi:[8,11,16,153,165,194,201,211,228,283,288,291,292,363,457],espresso:[9,287],essenti:[8,11,12,27,88,128,146,147,148,151,152,153,154,155,157,174,204,256,275,324,349,365,379,399,446,465,478],essex:29,establish:[87,232],estim:[1,3,6,10,12,38,41,56,91,141,200,211,222,250,308,315,348,349,354,415,424,443,474,478],esu:485,esub:410,eta:[6,239,252,283,284,286,324,386,388,390,421,445,449,485],eta_dot:252,eta_ij:421,eta_ji:388,etag:[40,460],etail:478,etap:252,etap_dot:252,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,143,145,146,147,148,149,151,152,153,154,155,157,159,165,167,168,169,178,188,190,191,194,195,200,201,202,203,206,207,208,209,212,213,217,218,226,228,229,236,252,279,290,294,320,321,329,333,347,348,356,357,358,359,361,385,386,394,407,409,413,419,423,424,442,444,446,449,455,458,460,461,462,467,469,470,474,476,477,478,479,481,485,486,488,490],ethernet:18,etol:[356,358,455,474],etot0:283,etot:[6,94,96,97,110,141,151,191,221,237,250,283,477,478],eu2:164,eu3:164,euler:[356,358],eulerian:200,euqat:434,europhi:239,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,87,88,91,107,117,140,142,145,155,163,165,188,190,191,195,196,197,198,200,202,203,204,205,206,207,208,209,210,217,223,229,231,232,234,235,236,237,275,281,284,295,298,302,311,312,313,322,325,328,330,331,333,348,349,354,356,363,413,415,421,427,429,431,443,455,456,458,462,463,465,467,468,469,470,474,476,478,486,487],evalut:[333,458],evan:[153,270],evanseck:[6,20,171,374,472],evapor:[],evaul:[8,356],evdwl:[107,423,424,478],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,119,166,167,181,185,188,191,194,195,196,201,202,203,206,207,208,209,211,212,213,215,217,218,221,234,237,250,252,253,275,288,290,293,294,304,308,316,320,323,325,329,331,341,348,354,356,358,363,368,387,388,391,394,415,425,449,450,460,461,463,465,466,467,469,470,472,475,477,478,479,481,490],evenli:[3,41,141,185,211,239,397,450,460],event:[],eventu:[3,6,12,15,167,284,474],ever:[54,56,235,308],evera:[377,390,425,441],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,113,119,128,153,168,188,189,190,191,192,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,222,225,226,228,230,232,233,234,239,240,248,252,253,256,273,274,275,279,280,281,282,283,284,285,286,288,290,291,293,294,296,297,308,310,311,312,313,314,315,316,319,320,321,322,323,331,333,347,349,358,359,360,363,383,384,394,407,423,424,431,437,454,455,456,460,462,464,465,467,468,469,474,475,476,478,486,490],everyth:[8,107],everywher:[116,401],eviri:387,evolut:[230,239,276,455],evolv:[239,276,321],ewald:[2,3,5,6,7,8,12,88,110,118,141,321,348,349,356,370,372,373,379,382,387,399,403,418,426,441,443,462],ewald_disp:382,ewalddisp:3,exact:[22,41,44,71,122,159,168,173,211,214,229,230,236,237,238,279,288,289,308,320,335,348,376,462,467,474,486,488,490],exactli:[3,6,12,14,17,38,41,56,59,71,91,116,144,149,156,165,185,195,196,206,211,217,222,229,236,237,238,253,263,264,271,275,283,308,313,314,327,363,376,383,385,391,394,397,408,415,443,462,463,470,474,486],exager:481,examin:[6,8,9,17,214,275],examp:[458,486],exampl:[],exce:[3,6,16,17,18,41,58,71,167,203,207,208,211,215,217,222,225,252,275,299,300,308,356,363,460,486],exceed:[3,41,59,211,217,252,308,468],excel:387,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,191,194,197,203,204,206,210,211,215,217,224,227,228,231,234,236,238,252,253,254,255,256,257,258,259,263,264,267,269,270,271,272,276,285,286,293,295,296,305,308,311,313,314,320,324,328,331,333,334,335,336,337,338,339,342,343,344,348,349,351,353,357,358,359,361,362,363,364,365,367,370,371,372,373,374,375,376,377,378,379,381,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,411,416,417,418,420,423,424,425,426,433,441,442,443,444,445,446,448,449,451,452,453,455,457,458,460,462,463,465,468,469,470,471,472,474,478,481,485,486,487,489],excess:[205,387],exchang:[2,3,6,8,9,61,62,194,200,201,228,236,285,293,316,320,323,348,363,387,475],exchange:348,excit:[9,387],exclud:[3,6,9,12,16,17,63,71,112,140,145,152,153,169,188,203,207,212,213,240,248,278,291,293,315,326,331,356,357,359,371,391,394,408,409,415,440,472],exclus:[1,3,9,12,16,87,363,378,413,415,469,479],excurs:455,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,166,190,233,287,333,347,350,362,456,458,468,471,474,486],exempl:431,exemplari:229,exemplifi:387,exert:[6,234,237,288,327,328,329,349],exhaust:[200,362,486],exhibit:[252,355,387,469],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,122,165,166,184,189,190,191,194,199,210,213,215,218,228,278,279,281,331,334,336,337,339,343,352,357,363,394,423,450,456,458,460,461,462,471,472,473,486,487,488],exit:[2,3,11,12,41,57,188,211,347,362,458,459,468,477,486],exlanatori:3,exp:[],expand:[],expans:[12,140,188,471,486],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,146,157,163,185,211,223,228,230,249,274,280,282,283,288,293,331,349,359,376,410,413,415,455,458,460,462,465,469,474,486],expens:[6,10,71,191,274,278,293,320,331,348,349,359,363,458],experi:[6,13,15,17,210,218,233,242,251,280,292,293,354,358,383,415,469,474],experienc:[6,12,241,242],experiment:[228,348,363,474],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,145,153,185,188,190,191,194,203,204,209,211,213,215,217,252,274,282,293,305,331,333,347,348,351,357,358,362,368,385,397,431,433,448,458,461,462,465,467,470,481,486,490],explan:[3,6,59,113,140,188,203,251,274,394,454,457,458,460,469],explanatori:[3,8,117,188,202,203,206,207,208,293,357,457,486],explantori:[3,289],explic:414,explicit:[6,9,11,22,44,77,87,113,116,159,173,195,196,217,299,300,335,353,365,366,369,374,376,385,387,398,408,447,454,457,461,464],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,143,152,155,163,165,171,172,174,175,176,177,179,180,182,183,185,188,191,197,207,210,217,224,227,229,231,236,252,254,255,256,257,258,259,267,269,270,272,282,283,285,293,295,296,311,313,314,320,324,328,334,336,337,338,339,342,344,357,363,364,365,367,370,371,372,373,374,375,376,377,378,379,380,382,383,384,385,386,388,389,390,391,392,393,394,397,398,399,400,401,402,403,404,405,406,407,408,411,413,415,416,417,418,420,425,426,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,451,452,453,460,462,469,470,472,473,479,481],explictli:[16,473],exploit:[9,15,17,276],explor:[118,164],expon:[3,284,286,385,390,393,407,414,426],exponenti:[87,421,442,449,453,474,486],expos:11,exposit:[200,383,384],express:[6,140,151,165,195,196,215,249,274,284,320,326,333,369,385,387,401,410,431,432,441,486],expressiont:369,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,194,197,198,201,209,210,216,219,223,226,227,228,230,231,232,234,236,238,250,252,256,264,274,275,291,292,293,295,297,302,305,307,311,312,313,314,315,317,318,320,322,325,329,330,390,410,413,424,425,432,477,478],extent:[1,3,41,45,57,71,163,167,188,199,207,211,234,327,330,348,351,365,427,429,443,457,460,463],exterior:[3,6,329],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,143,144,146,148,151,152,153,154,155,157,158,164,165,166,167,171,191,206,211,213,252,281,282,283,293,308,356,357,360,361,382,391,394,397,410,415,457,458,460,463,472,481,486],extract:[3,6,11,13,36,63,87,107,115,117,119,195,196,286,358,379,388,410,432,458,465,477],extract_atom:11,extract_comput:[11,458],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,190,205,215,217,252,318,387,445,481],extrema:407,extrins:200,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[161,322],f_a:[444,445,446],f_ave:117,f_c:445,f_f:446,f_fix_id:283,f_harm:318,f_i:421,f_id:[6,71,117,119,188,194,202,203,204,205,206,207,208,209,247,310,322,478,486],f_ij:421,f_indent:209,f_int:317,f_jj:91,f_k:421,f_langevin:320,f_max:[283,288],f_msst:250,f_r:[237,444,445,446],f_sigma:369,f_solid:318,f_ss:6,f_temp:237,face:[3,6,57,59,71,153,163,167,199,207,208,325,327,328,329,330,351,390,410,425,460,463],face_threshold:163,facet:163,facil:[0,12],facilit:[6,13],fact:[6,8,16,230,308,318,391,431,472],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,116,118,140,159,164,167,171,182,188,190,191,195,196,204,211,215,217,218,228,233,236,238,239,250,252,253,256,276,280,292,296,298,300,308,312,316,323,324,325,329,339,349,351,357,363,365,366,369,370,372,374,379,380,381,383,387,391,394,398,399,410,413,415,417,418,424,426,433,442,447,457,460,463,464,469,472,474,475,478,481,485,486],factori:[3,458],factoriz:348,fail:[3,11,12,59,169,215,218,348,356,358,381,424,458],failur:[121,428,459,486],fairli:[11,415,469,474],faken:73,falcon:233,fall:[3,6,191,206,279,458,486],fals:[86,331,333,431,486],fame:8,famili:[449,457],familiar:[0,11],fan:421,far:[3,6,12,17,57,59,61,86,188,191,192,211,212,213,215,218,252,274,292,293,308,325,336,339,354,358,359,448,458,460,465,478],farago:236,farrel:[444,446],farther:188,fashion:[6,8,41,71,165,191,194,195,196,201,207,211,213,218,228,230,234,249,250,252,254,255,256,257,258,266,269,270,271,272,282,283,285,293,297,301,307,310,318,320,324,325,326,328,330,358,394,408,463,472,486,489],fasolino:396,fast:[6,7,9,12,13,17,39,188,261,283,321,348,349,371,408,409,413,441,443,462,467,469,478,487,490],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,143,152,171,172,174,175,176,177,179,180,182,183,185,188,191,194,197,210,211,217,224,227,231,235,236,252,254,255,256,257,258,259,267,269,270,272,280,284,285,293,295,296,308,311,313,315,317,320,324,328,334,336,337,338,339,342,344,348,349,360,361,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,382,383,385,386,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,411,416,417,418,420,425,426,433,441,442,443,444,445,446,448,449,451,452,453,455,469,473,481],fastest:[1,6,14,17,153,207,320,321,363,457],fatal:[3,477],fault:[70,424],faulti:12,fava:390,favor:214,favorit:7,fbmc:315,fcc:[],fcm:[266,486],fdirect:221,fdotr:395,fdti:87,fe2:164,fe3:164,fe_md_boundari:200,featu:8,featur:[],fecr:385,feedback:[7,233],feel:[7,233,234,242,274,329,331,358,415],felling:412,felt:329,femtosecond:485,fene:[],fennel:[379,399],fep:[],ferguson:[6,171,472],fermi:[1,12,15,151,363,446],fermion:[9,387],ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,192,202,203,204,206,207,208,209,237,252,279,282,284,296,322,348,356,357,358,365,431,457,460,465,469,471,479,486,488],fewer:[1,3,11,15,16,61,242,469],fewest:3,fextern:226,feynman:276,fff:458,ffield:[378,388,423,424,431],ffmpeg:[3,12,190],ffplai:190,fft:[1,3,7,12,14,15,88,109,110,141,275,348,349,469],fft_inc:[12,349],fft_lib:12,fft_path:12,fftbench:[348,479],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:440,fictiti:[6,197,198,223,226,230,276,292,379,399,403,440],field1:[461,465],field2:461,field:[],fifth:[305,417],figur:[1,3,8,11,12,283,457,458],fij:382,file0:274,file1:[11,13,274,319,333,357,465,467,471],file2:[11,13,319,333,357,465,467,471],file:[],file_from:189,filen:357,filenam:[3,12,13,38,41,56,185,188,190,191,192,200,203,204,205,206,207,208,209,211,216,274,278,281,284,285,286,289,290,293,294,319,320,345,346,347,357,358,364,365,369,379,385,386,388,396,410,411,412,417,421,422,423,424,431,432,442,443,444,445,446,449,456,457,458,461,462,467,471,478,486,488,489,490],filennam:467,filep:[3,188,191,462,467,490],filepo:290,fill:[7,9,165,190,279,320,351,359,369,413,424,463],filter:[191,200],final_integr:8,final_integrate_respa:8,finchham:[6,147,381],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,168,185,192,201,214,215,225,228,251,274,280,288,292,354,356,358,359,379,394,399,403,410,431,441,443,481,486],find_custom:8,fine:[16,17,169,197,223,318,359,363,486],finer:[140,165,486],finest:348,finger:[165,187,249,463],finish:[6,11,41,211,333,345,347,348,360,362,363,448,465,486,487],finit:[],finni:[7,385,441],finvers:221,fiorin:[9,216],fire:[354,355,356,358,474],firebrick:191,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,150,153,159,161,163,164,166,167,168,172,185,188,189,190,191,192,194,195,203,204,206,207,208,209,211,214,217,228,229,234,239,249,250,251,252,274,276,281,282,283,285,290,293,296,297,305,306,308,309,310,317,318,319,320,322,326,331,333,334,340,351,356,357,358,359,362,363,364,365,368,369,370,372,374,376,378,379,385,387,388,391,392,394,395,396,398,399,403,408,409,410,412,413,415,417,421,423,424,431,432,440,442,443,444,445,446,449,453,455,456,457,458,460,461,462,465,467,469,472,473,474,477,478,481,486,487,488,490],fischer:[6,9,19,20,171,374,472],fit:[3,6,9,12,38,56,185,292,308,365,369,396,410,415,436,443,445,468,486],five:[73,151,283,357,369,411,460,474],fix:[],fix_adapt:[159,196,407],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,201,279],fix_evapor:201,fix_flux:200,fix_gcmc:[201,357],fix_gl:230,fix_gld:230,fix_grav:279,fix_id:[3,215,250,252,254,255,256,257,258,280,283],fix_modifi:[],fix_mov:[187,326],fix_nh:8,fix_npt:230,fix_nvt:[201,228],fix_poem:[3,6],fix_pour:[3,218],fix_qbmsst:9,fix_qeq:[3,378],fix_rattl:296,fix_reax_bond:423,fix_rigid:[242,368],fix_saed_vtk:294,fix_setforc:8,fix_shak:296,fix_srd:3,fix_styl:256,fix_temp_rescal:314,fixedpoint:[215,252],fixextern:226,fixid:200,fji:382,flag1:[220,361],flag2:[220,361],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,93,103,104,106,118,160,164,168,188,190,191,192,209,214,216,220,233,236,240,242,248,249,275,282,293,305,307,308,315,319,328,331,346,349,357,361,362,363,365,393,398,410,413,440,455,457,458,460,461,462,464,465,466,470,486],flag_buck:373,flag_coul:[373,382,403],flag_lj:[382,403],flagfld:[371,408,409],flaghi:[3,371,408,409],flaglog:[371,408,409],flagn:220,flagvf:[371,408,409],flat:[6,320,325,326,330],flavor:[2,7,12],fld:[9,325,371,408,409],flen:366,flex_press:366,flexibl:[3,6,8,166,190,203,207,216,230,253,316,323,387,445,478],flip:[3,6,217,252,327,328],floor:486,flop:12,floralwhit:191,flow:[],fluctuat:[6,64,87,215,228,229,236,239,252,256,274,275,318,320,342],fluid:[],fluid_veloc:243,flush:[3,191,477],flux:[],flv:190,fly:[7,9,12,41,190,194,200,205,218,221,293,296,321,369,413,478,481],fmackai:9,fmag:219,fmass:276,fmax:[356,478],fmomentum:221,fmsec:[2,191,236,237,249,252,280,293,311,312,469,480,485,487],fname:347,fno:[12,16],fnorm:[356,478],fnpt:221,fnvt:221,foce:394,fock:366,focu:296,fogarti:[9,286,424],foil:[140,274,432],fold:[306,469],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,144,145,151,153,158,161,163,165,166,171,174,175,176,177,179,180,182,183,185,188,189,190,191,194,200,201,202,203,204,205,206,207,208,209,211,216,217,218,221,222,226,228,229,230,233,235,236,237,239,242,250,252,256,257,258,269,270,272,275,276,278,281,282,283,284,286,288,290,292,293,294,296,310,311,312,313,316,317,318,319,320,322,323,331,332,336,337,338,339,342,344,346,351,353,356,357,358,363,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,420,421,422,423,424,425,426,428,430,431,432,433,434,435,436,437,438,439,440,442,443,444,445,446,447,448,449,451,452,453,455,457,458,460,461,462,463,465,467,468,469,472,474,475,476,481,486,487,489],foo:[4,8,11,12,188,190,226,458,471,486],foot:6,footprint:[12,363],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:242,forcefield:[292,393],forcegroup:239,forcezero:354,ford:382,forestgreen:191,forev:71,forget:[237,481],forgiv:252,fork:[12,188],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,87,89,90,93,103,104,106,116,140,141,159,160,169,173,191,194,195,196,213,229,230,236,238,242,249,270,275,286,288,292,293,320,325,329,334,335,342,353,355,357,358,365,366,369,376,385,387,389,393,394,398,410,412,413,417,418,421,423,424,425,431,432,433,441,443,444,445,446,452,454,457,458,460,465,470,477,481,486],formal:[6,78,80,91,229,230,236,252,276,308,316,431],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,173,185,188,189,190,191,192,203,206,207,208,209,211,213,275,278,282,284,286,289,293,294,304,319,320,331,332,335,353,357,358,364,365,369,376,385,388,398,410,412,422,423,424,426,432,443,449,450,457,458,460,461,462,465,476,477,478,486,488],former:[6,12,16,39,41,191,211,320,324,369,371,466,472,486],formerli:[7,13],formul:[1,40,64,141,197,223,236,252,270,284,286,292,296,319,348,365,369,385,387,390,410,420],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,94,96,97,106,112,118,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,164,165,170,172,173,184,188,195,196,197,198,203,204,205,206,209,210,217,223,231,232,234,236,237,249,274,275,281,290,295,302,306,308,311,312,313,322,325,328,330,331,333,334,335,337,343,351,357,365,366,368,369,374,375,376,377,382,383,385,386,390,391,392,393,395,398,399,401,402,403,405,406,408,409,410,414,415,416,425,426,433,441,442,444,445,446,449,451,452,456,460,463,470,477,478,485,486,487],forth:[1,6,11,12,13,14,15,362,458,463,467],fortran:[3,6,9,11,12,13,226,385,394,410,423,424],fortun:8,forward:[3,8,87,347,358,363],foster:[369,420,421],foul:168,found:[3,6,9,12,73,159,188,214,216,228,233,239,275,315,321,333,347,359,376,379,382,455,461,462,477],four:[6,11,54,81,103,104,140,161,250,320,342,357,358,413,455],fourier:[],fourth:[6,105,292,305,315,374,417,431],fox:[6,118,171,439,472],fphi:[38,56,443],fpic:12,fplo:[38,56,443],fprime:443,fqdn:235,fqq:382,frac:[221,237,447,481],fraction:[1,3,6,8,12,16,39,41,80,109,141,168,187,190,191,201,212,213,214,215,250,279,283,290,291,308,313,314,351,358,363,369,371,391,408,409,465,470],fragment:[42,233,290],frame:[83,140,191,200,250,283,327,390],framer:[190,191],framework:[5,230,364,432],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,87,159,196,274,308,317,318,319,320,355,358,366,387,407,413,421,452,457],freedom:[3,6,8,94,96,97,99,101,102,112,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,203,214,221,228,230,236,237,242,252,253,256,257,258,269,270,272,276,278,293,296,311,312,313,318,356,382,478,481,487],freeli:[0,6,7,12,144,158,163,190],freez:[],frenkel:[228,318],freq:199,frequenc:[3,6,16,39,191,205,264,275,276,283,288,346,383,387,424,431,455,469,474,486,489],frequent:[3,64,67,70,72,73,77,88,140,191,212,213,225,316,323,415,467],fri:[250,283],friction:[4,5,6,10,42,194,230,236,283,288,293,320,324,326,391,470],friedrich:298,from:[],front:[250,283,327],frontend:[190,287],frozen:[6,112,169,227,229,237,359,389],fs2:[6,91],fscale:233,fstr:486,fstring:458,ftol:[356,358,455,474],fuchsia:191,fuction:379,fudg:296,fugac:228,fugacity_coeff:228,fulfil:6,full:[1,2,6,9,12,17,38,39,40,91,190,204,205,216,239,274,348,349,363,369,385,387,388,390,447,460,462,467,468,472,474,479,481,489],full_energi:[3,228],fuller:356,fulli:[3,6,9,78,230,235,274,356,358,379,421,422,488],fulton:385,fumi:370,func:[458,486],funcfl:385,functino:[],functionaliri:216,fund:[0,7],fundament:[308,485],funnel_flow:304,funrol:413,further:[3,6,8,12,13,61,63,71,86,105,107,116,190,191,194,203,206,207,208,209,212,218,222,239,243,276,284,294,298,308,320,322,331,349,354,356,357,358,359,364,368,378,413,431,455,474,475,486],furthermor:[27,174,387],furthest:61,futher:3,futur:[],g_ewald:3,g_ewald_6:3,g_ewald_disp:3,g_jik:421,g_p:320,ga3:164,gaa:36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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":212,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,145,153,154,158,164,165,168,170,184,186,187,188,190,191,192,193,195,196,197,199,200,201,203,207,208,209,212,213,215,216,217,218,222,225,228,229,234,236,237,238,239,240,242,247,250,252,253,256,270,271,275,276,279,280,281,282,283,285,288,290,291,293,294,308,310,315,316,317,318,321,323,325,327,331,343,346,348,349,351,352,354,355,357,359,360,361,363,366,369,371,387,408,409,413,415,423,424,440,441,455,456,457,460,461,463,465,467,468,469,472,474,476,477,478,479,480,485,487,488,489],"function":486,"long":[205,370,372,373,374,375,379,381,382,399,403,407,418,426],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[195,196],addforc:197,addit:[12,13],addtorqu:198,adiabat:6,adjust_dt:298,adp:364,airebo:365,alloi:385,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:199,arrai:6,aspher:[6,82,144,254,257,260,261,269],atc:[9,200],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,163,199,201,202,282,486],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:210,awpmd:[9,366],balanc:[41,211],barostat:6,basal:67,beck:367,berendsen:[280,311],between:6,binary2txt:13,bodi:[6,8,42,68,262,368],bond:[8,13,69,212,213,214,289],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:369,born:[370,381],boundari:[7,57],box:[6,58,215],brownian:371,buck:[372,373,381],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,171,374,407],chunk:[6,66,71,75,90,93,104,106,114,145,160,162,203],citat:7,class2:[21,43,172,334,375],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[325,377,452],colvar:[9,13,216],com:[74,75,146],comb3:378,comb:[285,378],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,484,485,486,487,488,489,490],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,486],compute_modifi:102,condit:7,conduct:[6,316],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:[204,205],cosin:[23,24,25,26,27,28,174],cossq:336,coul:[370,372,373,374,375,379,380,381,392,399,403,407,418,426],coupl:6,creat:213,create_atom:165,create_bond:166,create_box:167,createatom:13,creation:7,csld:312,csvr:312,cubic:401,cuda:[9,14,109,112,143,152,197,210,224,227,231,252,259,295,296,311,313,324,370,372,374,375,385,391,392,399,400,402,405,416,442,444],custom:8,cut:[49,366,372,375,379,382,387,389,399,400,407,414,418],cvff:337,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[379,399],deform:[148,149,217],delete_atom:168,delete_bond:169,delta:24,deposit:218,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,7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\ No newline at end of file From a165a3c430517eb4ccc1dc875be2deecd6649c31 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 23 Oct 2015 00:30:30 +0000 Subject: [PATCH 23/31] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14185 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/doc2/Section_packages.html | 27 ++++++++++++++++++++++++++- doc/doc2/genindex.html | 4 ++++ 2 files changed, 30 insertions(+), 1 deletion(-) diff --git a/doc/doc2/Section_packages.html b/doc/doc2/Section_packages.html index f6197d0145..56f1eb3435 100644 --- a/doc/doc2/Section_packages.html +++ b/doc/doc2/Section_packages.html @@ -216,7 +216,7 @@ serial.
    - + @@ -226,6 +226,7 @@ serial. + - + @@ -964,7 +965,21 @@ serial.

    - + + + + + + + + + @@ -975,7 +990,7 @@ serial.

    - + @@ -989,7 +1004,7 @@ serial.

    - + @@ -1009,6 +1024,8 @@ Jerome Henin (LISM, Marseille, France).

    (3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua (U Blaise Pascal).

    +

    (4) The SMTBQ package was created by Nicolas Salles, Emile Maras, +Olivier Politano, and Robert Tetot (LAAS-CNRS, France).

    If the Library is not listed as lib/package, then it is a third-party library not included in the LAMMPS distribution. See the src/package/Makefile.lammps file for info on where to download the @@ -1462,8 +1479,23 @@ Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if you have questions.

    +
    +
    +

    4.35. USER-SMTBQ package¶

    +

    This package implements the Second Moment Tight Binding - QEq (SMTB-Q) +potential for the description of ionocovalent bonds in oxides.

    +

    There are example scripts for using this package in +examples/USER/smtbq.

    +

    See this doc page to get started:

    +

    pair_style smtbq

    +

    The persons who created the USER-SMTBQ package are Nicolas Salles, +Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at +these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact +them directly if you have any questions.

    +
    +
    -

    4.35. USER-SPH package¶

    +

    4.36. USER-SPH package¶

    This package implements smoothed particle hydrodynamics (SPH) in LAMMPS. Currently, the package has the following features:

      diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt index b53ef54c45..251bfa33b3 100644 --- a/doc/Section_packages.txt +++ b/doc/Section_packages.txt @@ -207,7 +207,7 @@ USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferra USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, - USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, - -USER-MGPT, Fast MGPT multi-ion potentials, Tomas Oppelstrup & John Moriarty (LLNL), "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -, - +USER-MGPT, fast MGPT multi-ion potentials, Tomas Oppelstrup & John Moriarty (LLNL), "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -, - USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, - USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_accelerate_omp.html, -, -, - @@ -217,6 +217,7 @@ USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html USER-QUIP, QUIP/libatoms interface, Albert Bartok-Partay (U Cambridge), "pair_style quip"_pair_quip.html, USER/quip, -, lib/quip USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, - USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, - +USER-SMTBQ, Second Moment Tight Binding - QEq potential, Salles & Maras & Politano & Tetot (4), "pair_style smtbq"_pair_smtbq.html, USER/smtbq, -, - USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, - USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute <...>/tally"_compute_tally.html, USER/tally, -, - :tb(ea=c) @@ -241,6 +242,9 @@ Jerome Henin (LISM, Marseille, France). Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua (U Blaise Pascal). +(4) The SMTBQ package was created by Nicolas Salles, Emile Maras, +Olivier Politano, and Robert Tetot (LAAS-CNRS, France). + If the Library is not listed as lib/package, then it is a third-party library not included in the LAMMPS distribution. See the src/package/Makefile.lammps file for info on where to download the @@ -805,6 +809,27 @@ Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if you have questions. +:line + +USER-SMTBQ package :h4 + +This package implements the Second Moment Tight Binding - QEq (SMTB-Q) +potential for the description of ionocovalent bonds in oxides. + +There are example scripts for using this package in +examples/USER/smtbq. + +See this doc page to get started: + +"pair_style smtbq"_pair_smtbq.html + +The persons who created the USER-SMTBQ package are Nicolas Salles, +Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at +these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact +them directly if you have any questions. + +:line + USER-SPH package :h4 This package implements smoothed particle hydrodynamics (SPH) in diff --git a/doc/searchindex.js b/doc/searchindex.js index 64b464ec73..8ed78e9198 100644 --- a/doc/searchindex.js +++ b/doc/searchindex.js @@ -1 +1 @@ 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187,188,189,190,191,192,194,195,196,200,201,203,204,211,212,213,214,215,217,221,228,239,240,241,242,243,248,249,250,252,257,258,264,269,270,272,275,279,283,291,293,296,304,309,311,312,313,315,316,317,318,319,323,325,327,331,334,335,340,347,353,354,356,357,359,361,362,363,364,365,369,376,378,385,386,387,388,394,395,396,407,408,409,410,411,412,413,417,421,423,424,431,432,442,444,445,446,449,455,457,459,460,461,462,463,465,466,468,470,472,474,477,478,481,485,486,487,488,489,490],afterrun:468,afterward:3,afterword:41,ag1:164,ag2:164,again:[6,11,12,16,17,62,140,145,151,159,188,191,217,232,279,334,347,358,408,409,455,457,458,460,462,467,474,476,486,488],against:[11,12,13,64,218,358,423,424],aggreg:[6,12,65,68,69,79,92,108,115,232,248,291,293,306,455,487],aggress:[232,474],agilio:[9,13],agre:[3,8,185,356,365,396,424],agreement:[5,7],ahd:393,ahead:327,aidan:[0,5,7,9,13,351],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:190,akohlmei:[7,9,13,192,233],aktulga:[7,9,286,424],al2o3:431,al2o3_001:[118,294],al3:164,ala:[239,431],alain:9,alat:[274,410],alb:[421,444,446],albeit:292,albert:9,alchem:[87,159],alcohol:323,alcu:[364,369],alcu_eam:421,alderton:382,alejandr:[252,253],alessandro:13,algebra:413,algorithm:[0,1,6,7,8,9,41,61,191,200,211,214,217,239,241,242,264,276,293,296,315,316,320,323,328,354,355,356,360,363,387,409,413,428,430,455,457,474],alia:[12,16],alias:[1,349],aliceblu:191,align:[6,12,29,41,71,167,185,207,211,234,351,460,463,481],alkali:387,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,153,158,159,160,161,162,163,164,165,166,167,168,169,171,173,178,184,185,188,189,190,191,192,194,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,245,247,248,250,252,253,254,255,256,257,258,259,260,261,262,263,264,265,267,268,269,270,271,272,273,274,275,276,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,304,305,307,308,309,310,311,312,315,316,317,318,319,320,321,322,323,325,326,327,328,329,330,331,332,333,334,335,338,343,346,347,348,349,350,351,353,356,357,358,359,360,362,363,364,365,366,368,369,370,372,373,374,375,376,378,379,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,403,407,408,409,410,411,412,413,414,415,416,417,418,420,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,454,455,457,458,459,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,477,478,479,481,485,486,487,488,489,490],allen:[29,87,382,390],allentildeslei:87,allign:3,allindex:332,alloc:[3,5,6,8,9,11,12,60,226,322,357,359,363,419,424,460,468],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,142,144,145,158,163,164,165,167,173,184,185,188,190,191,192,194,195,197,199,200,201,203,204,205,206,207,208,209,211,213,214,215,216,217,218,222,223,226,228,229,230,231,233,236,239,242,243,247,249,252,253,274,278,280,281,282,283,287,293,294,296,297,299,300,304,308,315,316,317,318,320,321,322,323,324,325,331,333,335,343,348,349,351,356,357,358,359,362,363,366,369,370,371,372,373,374,379,385,387,391,392,393,394,399,403,408,409,413,415,421,424,425,428,430,431,440,450,452,455,458,460,462,463,464,465,466,467,470,472,473,474,477,478,486,487],almost:[2,3,12,60,234,283,320,349,360,363,440],alo:379,alon:[6,7,214,289,423,424,458],alond:13,along:[6,8,9,12,29,40,87,118,164,165,187,188,190,214,234,239,240,244,249,251,283,293,296,297,301,305,306,315,319,320,326,329,331,351,354,355,356,358,379,382,391,394,397,399,403,410,423,424,443,460,463,470,471,486],alonso:[411,412],alpha:[6,12,51,195,239,275,283,288,356,364,367,370,379,383,385,386,388,393,398,399,410,416,420,445,447,478,481],alpha_:447,alpha_c:407,alpha_i:[432,447],alpha_ialpha_j:447,alpha_lj:407,alphabet:[2,3,22,37,44,55,63,173,184,194,335,343,357,376,441,460],alphanumer:[3,63,194,282,290,333,357,486],alreadi:[3,7,8,9,12,16,17,18,42,165,166,168,189,199,203,207,208,211,213,217,243,281,283,308,331,357,358,383,392,394,401,409,440,450,453,456,460,461,465,470,486],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,149,151,152,153,154,155,157,158,159,160,161,162,163,165,166,167,168,169,171,173,184,185,186,188,189,190,191,192,194,195,196,197,199,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,223,226,227,228,229,230,232,233,236,237,238,239,249,250,252,253,254,255,256,257,258,263,266,267,2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6],clariti:333,clark:418,class2:[],classic:[0,3,5,6,7,8,9,226,276,283,288,320,344,387],classifi:[9,441,449],claus:458,clean:[6,12,14,15,17,468],cleanli:[459,489],clear:[],clearli:7,clebsch:140,clermont:[9,13],clever:464,click:[2,11,22,37,44,55,165,173,184,190,233,335,343,358,376,441],client:[233,235],climb:[251,358,474],clinic:[7,13],clo:[154,187,487],clock:[12,455,474],clockwis:326,close:[3,6,11,12,13,39,41,67,141,168,188,213,214,215,230,237,239,252,270,293,296,326,329,347,349,352,354,355,358,363,365,369,379,380,410,415,427,429,446,464,470,481,483],closer:[3,41,116,163,187,188,211,215,219,317,358],closest:[213,274,293,323,390,425,440,450],cloud:[431,481],clovertown:18,clsuter:72,clump1:[278,293],clump2:[278,293],clump3:[278,293],clump:293,cluster:[],clutter:[3,9],cmap:460,cmatrix:230,cmax:410,cmd:[11,12,276,471],cmin:410,cmm:[],cn1:204,cn2:204,cna:[],cnn:204,cnr:[9,13],cnt:[394,464],co2:[40,164,296,357],coars:[7,9,29,36,40,54,177,278,293,308,392,426,472],coarser:[349,486],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,171,172,173,178,334,335,340,376,394,398,415,428,430,433,460,462],coeffcient:460,coeffici:[],coefficienct:383,coefficient0:385,coefficient1:385,coeffieci:[6,367],coeffincientn:385,coexist:[9,228,387],cohes:[6,388,410],coincid:[122,329,374,408,409,455],colberg:189,cold:[6,150,228,232,359,481],coldest:316,coleman8:9,coleman:[9,118,164,294],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,145,153,160,162,165,188,191,203,216,242,248,278,288,291,293,331,348,357,359,377,397,460,467,473,479,490],collid:[222,308,330],colliex:164,collinear:[3,278],collis:[3,239,308,326,330,384,391,453],colllis:308,colloid:[],colombo:39,colon:[192,331,461],color1:191,color2:191,color:[3,9,41,188,190,191,211,229,283,288],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,145,153,160,162,163,164,185,188,191,194,202,203,204,206,207,208,209,242,249,250,283,293,309,310,320,330,389,393,423,424,461,475,477,486],colvar:[],colvarmodul:12,com:[],comamnd:217,comand:[214,462],comannd:363,comb3:[],comb:[],comb_1:285,comb_2:285,combiant:380,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,144,158,188,190,200,206,233,242,252,276,282,312,321,329,332,334,348,349,351,355,363,377,379,380,387,388,394,406,407,432,442,444,446,449,452,463,468,473,481,486],come:[],comfort:[12,13],comm:[0,3,12,61,73,189,233,235,236,349,358,363,383,415,420,443],comm_modifi:[],comm_modift:61,comm_styl:[],command:[],comment:[2,7,11,12,38,56,171,185,188,237,293,320,357,358,364,385,386,388,398,410,417,424,431,432,442,443,444,445,446,449,457,458,460,481,486],commerci:7,commmand:[3,6,12,59,107,271,454,455,457,474,489],common:[],commonli:[3,6,12,17,25,57,59,105,167,188,190,192,344,392,401,432,444,446,460,463,472],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,169,190,191,211,212,213,215,216,217,233,235,239,241,242,243,252,275,282,284,285,286,293,308,320,331,346,348,359,360,361,363,384,419,457,458,462,469,470,486,488,490],communc:348,comp:[7,189,235,236,296,349,358,387,415,420,425,439,443,445],compact:[63,194,376,441],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,148,163,164,173,184,191,221,284,331,333,348,349,356,358,410,431,455,474,475,481,485],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,172,173,184,334,335,343,375,441],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,176,188,192,196,202,203,204,206,207,208,209,211,275,287,312,315,322,325,328,348,363,395,413,415,443,457,458,486],compens:[6,212,213,291,359,387],compet:319,competit:349,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,163,188,189,190,192,233,319,349,363,413,460,461,465,486],compl:17,complain:[12,17],complement:410,complementari:[7,379,399],complet:[3,6,9,12,15,41,59,71,191,207,211,216,242,276,279,282,308,319,321,333,347,358,363,388,428,430,448,455,460,465,468,472,474,477,481,486],complex:[6,8,11,12,13,25,40,42,62,140,142,153,165,166,239,304,329,346,358,387,413,443,458,460,463,486],compli:[315,319],complic:[6,7,9,12,13,201,228,458],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,160,161,162,188,190,191,197,198,202,203,204,205,206,207,208,209,210,214,215,217,218,223,226,231,235,236,239,242,244,248,249,251,252,253,256,257,258,269,270,272,273,275,276,277,280,291,293,295,296,297,301,302,305,308,311,312,313,315,322,323,328,329,330,348,351,355,356,357,358,363,383,387,391,408,409,428,430,431,432,460,461,470,478,486,487],componenet:6,composit:[6,201,239,385],compound:[378,387,388,449],compres:[71,114,203],compress:[3,59,71,114,168,188,190,191,203,217,250,256,280,283],compris:[40,329,397,425,448],compton:[118,164],comptu:3,compuat:349,comput:[],computation:[3,6,212,213,320,369],computational:481,compute_arrai:8,compute_fep:[196,407],compute_group_group:228,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,294],compute_scalar:8,compute_temp:8,compute_ti:196,compute_vector:8,compute_xrd:164,concaten:[2,3,489],concav:329,concentr:385,concept:[6,145,155,203,469],conceptu:[3,6,71,153,215,217,358,379,394,410,465],concern:[6,73,87,189,229],concis:[11,319],conclud:12,concret:8,concurr:[9,16,349,486],conden:[320,444,446],condens:[6,147,320,365,381,385,399,449],condit:[],conducit:6,conduct:[],cone:463,confer:413,confid:[3,474],config:[12,188,457],configfil:216,configur:[1,2,6,12,15,17,38,59,122,167,185,187,188,190,194,215,216,217,218,222,228,235,236,264,276,284,319,346,356,358,365,369,386,410,413,442,444,446,449,455,460,462,463,474],confin:[460,474],conflict:[3,12,40,415,458],conform:[3,6,13,59,214,215,251,292,297,319,342,358,387,472],confus:[3,449],conjuct:383,conjug:[7,8,236,355,387,423,424],conjunct:[6,7,71,86,87,114,148,153,159,165,169,191,195,196,236,239,243,264,279,280,284,285,286,288,293,308,316,323,328,348,349,358,370,372,376,379,383,387,393,399,415,418,426,447,460,463,467,481,490],connect:[3,6,87,150,168,214,233,278,293,296,305,358,380,391,440,446,457,458,464,481],conput:3,consecut:[3,11,12,39,71,165,191,195,196,218,233,234,379,399,403,455,461,463],consequ:[1,6,201,320,398,474],conserv:[3,194,201,214,221,222,229,232,236,238,239,243,248,250,252,264,293,296,311,312,316,323,324,328,358,382,383,391,405,431,469,474],consid:[6,9,70,71,78,87,115,147,150,151,168,188,191,195,196,202,204,207,211,213,214,218,240,253,275,293,315,316,319,320,323,349,376,387,394,424,425,431,440,455,456,458,461,462,463,465,468,470,478,481,486],consider:[6,8,236,237,311,312,313,363,469],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,145,148,150,165,177,187,192,197,198,203,217,218,221,223,226,229,236,237,238,249,252,254,255,256,257,258,259,260,262,263,264,265,267,268,269,270,271,272,280,283,288,290,292,293,311,312,313,314,324,348,349,351,357,358,363,365,369,371,377,379,387,390,394,408,409,410,413,415,425,428,430,431,443,450,458,460,461,463,464,465,472,481,486],consistent_fe_initi:200,consit:293,constant:[],constitu:[3,6,242,293,325,329,377,425],constitut:[428,430],constrain:[3,6,8,143,144,145,146,148,151,152,153,154,155,157,158,194,203,218,228,229,234,242,246,278,279,291,293,296,306,316,323,356,357,387,465,472,481],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,118,140,164,215,252,275,292,329,359,363,382,413,415,440,442,443,463,464,479,486],constructor:8,consult:424,consum:[1,288,419,486],consumpt:346,contact:[],contact_stiff:[427,429],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,145,153,163,164,165,167,171,173,184,185,188,190,191,192,194,195,196,200,202,203,204,206,207,208,209,211,216,218,223,230,234,235,236,237,239,250,264,274,275,278,279,281,283,286,290,293,294,298,308,315,319,320,329,330,333,347,349,357,358,361,362,364,365,366,369,378,379,382,385,386,387,394,395,410,413,417,421,422,423,424,432,442,443,444,445,446,447,449,455,456,457,458,460,461,462,463,465,467,469,472,474,477,478,481,486,488,490],content:[12,18,424,476,478],context:[3,6,8,12,17,117,191,212,213,218,278,290,324,355,452,460,467,476,485,486,487],contibut:70,contigu:457,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,161,191,194,195,196,201,203,204,205,206,207,208,209,211,214,215,216,217,218,228,229,230,232,233,234,236,237,238,244,249,250,252,254,255,256,257,258,269,270,271,272,277,279,282,283,293,294,297,307,308,310,317,318,320,326,329,333,347,362,363,369,383,384,401,404,423,424,425,428,430,445,455,458,460,462,463,468,474,477,478,486,488],continuum:[6,7,9,200,320,428,430],contour_integr:200,contract:[59,215,217,252,280,293],contradictori:3,contrain:296,contraint:264,contrari:[230,237],contrast:[1,6,42,55,64,147,150,217,331,428,430,452,489],contrib:320,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,196,201,202,203,204,206,207,208,209,215,228,236,239,242,243,247,253,270,271,278,279,287,290,293,294,296,322,348,356,358,366,383,384,385,387,394,408,409,413,415,423,424,431,472,478,481],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,174,188,190,194,200,201,211,215,216,217,232,233,236,237,252,254,255,256,257,258,280,285,293,299,300,311,312,313,320,324,346,348,360,387,390,413,423,424,427,429,442,446,455,457,469,475,476],control_typ:200,controlfil:424,convect:91,conveni:[6,12,29,188,192,209,294,351,432,486],convent:[3,8,9,29,176,183,184,191,292,305,332,385,387,486],converg:[3,6,41,88,188,190,192,197,211,214,215,223,226,256,283,285,288,292,296,354,355,356,358,378,379,399,431,455,467,474],convers:[3,8,140,190,191,201,204,280,348,379,380,381,387,399,403,407,418,458,474,485],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,165,172,188,190,191,209,250,331,334,336,339,342,351,358,364,385,413,444,446,453,458,460,461,462,467,477,481,485,486,488,490],convex:329,convinc:[7,12],cook:9,cooki:7,cool:[7,155,232,291],cooordin:188,cooper:[5,7],coord123:114,coord1:[3,114,203,207,208],coord2:[3,114,203,207,208],coord3:[3,114,203,207,208],coord:[],coordb:431,coordbb:431,coordiat:356,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,148,154,160,162,163,165,169,187,188,189,190,191,192,194,197,202,203,206,207,208,211,212,213,214,215,216,217,218,221,223,224,226,228,231,232,233,234,235,236,237,249,251,252,254,255,257,258,270,273,274,275,278,279,280,290,291,293,295,296,297,302,305,306,307,308,310,318,319,320,327,328,330,331,351,356,357,358,363,364,365,368,386,431,455,460,461,463,465,468,470,474,481,486,487],coordn:[114,203],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,190,320,358,376,423,458],copper:453,coproccesor:16,coprocessor:[1,4,7,9,16,17,363,473],coproprocessor:17,copy_arrai:8,copyright:[7,8,278],coral:191,core:[],core_shel:147,coreshel:[6,9,372,379,381],cornel:[6,171,472],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,190,329,330,351,448,460],cornflowerblu:191,cornsilk:191,corpor:16,corr:378,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,147,152,159,190,217,228,230,236,252,253,270,278,280,283,319,325,329,348,358,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,451,452,453,460,475,478,481],correction_max_iter:200,correctli:[3,8,9,11,17,71,81,102,103,143,144,146,148,150,151,152,153,154,157,158,161,188,191,197,218,223,226,237,246,252,253,286,293,296,305,307,326,329,358,359,363,381,409,413,457,458,460,470,485,487],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,143,144,152,159,164,171,172,173,174,175,176,177,179,180,182,183,185,188,190,191,195,196,197,203,205,206,207,208,210,213,215,217,224,226,227,231,236,239,240,248,249,250,252,254,255,256,257,258,259,264,267,269,270,272,275,276,280,285,293,295,296,311,313,315,324,325,326,328,329,330,332,334,335,336,337,338,339,342,344,349,353,355,357,358,364,365,367,370,371,372,373,374,375,376,377,378,379,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,413,415,416,417,418,420,421,423,424,425,426,431,432,433,442,443,444,445,446,448,449,451,452,453,455,457,458,460,461,463,473,474,475,477,478,481,486],correspondingli:[408,409,469],cosin:[],cosineshift:27,cosmo:[230,235],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,164,190,191,203,207,208,211,212,213,225,252,285,320,348,349,361,379,399,403,413,415,442,457,469],costheta0:[442,444,446,449],costheta:421,costli:[11,88,230,359],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,145,155,160,162,178,188,190,191,195,196,203,204,207,211,217,226,235,282,283,284,288,291,293,295,308,309,315,319,320,321,325,329,331,333,340,345,347,354,356,359,363,366,389,393,394,423,424,456,457,458,460,462,464,467,468,476,481,486,487],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,116,141,166,170,284,286,321,348,349,356,363,370,372,373,374,375,378,379,380,381,382,387,391,392,394,399,403,407,415,418,423,424,426,431,441,446,447,449,452,465,472,478,481,485],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,114,116,117,153,163,169,197,198,201,203,206,207,208,210,211,218,223,225,228,234,252,264,279,296,311,312,329,349,356,357,358,360,363,389,393,415,478,486],counter:[326,455,466,468,474],counteract:228,counterbal:232,counterpart:[188,293,455],counterproduct:18,coupl:[],courant:298,cours:[3,8,126,128,159,188,195,196,229,292,305,319,325,327,328,330,331,349,408,433,457,460,473,481,486,488],courtesi:351,cov:431,coval:[6,29,387,410,431,481],covari:230,cover:[6,71,185,191,200,239,387,397,448],coverag:[71,207],cpc:235,cpp:[1,3,6,8,9,11,12,13,87,188,195,196,226,296],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,191,194,205,221,237,321,346,349,363,376,441,455,473,474,477,478,479,486],cpuremain:478,cr2:164,cr3:164,crack:[4,359],crada:[5,7],crai:[5,7,13,18,188],crash:[3,12,359,481],craympi:363,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:200,create_faceset:200,create_group:189,create_nodeset:200,createatom:[],creation:[],crimson:191,critchlei:278,criteria:[3,116,166,190,191,212,213,214,247,356,420,448,462,465,486],criterion:[12,41,121,163,165,168,201,211,214,228,264,285,298,326,331,356,358,378,387,391,431,465,474,475],criterioni:474,critic:[6,48,49,250,315,320,356],cross:[3,12,22,71,89,144,173,188,190,202,207,213,217,249,251,270,293,301,305,307,316,323,335,351,358,374,383,384,385,392,393,394,399,401,403,421,426,428,430,444,446,453,460,464,470,488],crossov:1,crossterm:460,crozier:[0,7,13],crucial:283,crystal:[4,6,13,73,274,275,318,351,359,464,478,481],crystallin:[6,275,351,445,481],crystallis:315,crystallogr:[118,164],crystallograph:[351,478],crystallographi:[118,164,351],cs1:164,cs_chunk:6,cs_im:[40,460],cs_re:[40,460],csanyi:[140,422,432],cscl:410,csequ:6,csh:[11,12,376],cshrc:[11,12],csic:[386,442,444,446,449],csinfo:6,csisi:[386,442,444,446,449],csld:[],cst:385,cstherm:6,cstyle:457,csvr:[],ctcm:[364,385],ctemp_cor:221,cterm:297,ctr:9,ctype:11,cu1:164,cu2:164,cu3au:410,cube:[6,41,163,168,211,221,329,351,481],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:369,cummul:[3,6,209,212,213,214,216,225,230,236,238,308,311,312,313,314,316,323,393,478],cumul:[6,201,203,206,207,208,222,228,236,250,252,256,264,293,294,358],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,145,153,155,161,163,166,169,188,189,190,191,192,195,196,200,203,207,208,209,211,212,213,214,215,216,217,218,222,223,226,228,230,233,234,236,242,249,252,253,257,258,264,269,270,272,278,284,285,287,290,291,292,293,296,297,298,299,300,301,302,304,306,307,308,311,312,313,319,320,323,324,325,326,327,328,330,331,333,346,347,348,349,352,353,355,356,357,358,363,369,376,378,382,385,387,388,391,394,395,398,408,409,410,411,412,415,421,423,424,427,428,429,430,433,444,446,447,450,455,456,457,458,460,461,462,463,464,466,467,468,470,472,474,475,477,478,486,487,488,489,490],curv:[6,165,228,275],curvatur:[390,425,453],custom:[],cut0:458,cut1:469,cut2:469,cut:[],cuthi:[274,286],cutinn:[371,408,409],cutlo:[274,286],cutmax:421,cutoff1:[375,382,399,403,407,418,426],cutoff2:[370,372,373,375,381,382,399,403,407,418,426],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,163,166,168,213,214,219,274,283,284,286,288,290,293,308,321,325,329,331,346,348,349,356,359,360,361,363,364,365,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,383,384,385,386,387,388,389,390,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,431,432,433,434,435,436,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,458,462,465,469,481,486],cutoffa:386,cutoffc:386,cuu3:385,cval:164,cvd:315,cvel:297,cvff:[],cwiggl:[3,249,325,328,330,486],cyan:[2,190,191],cycl:[3,228,250,252,253,256],cyclic:[3,185],cygwin:12,cylind:[3,4,190,234,279,326,329,463],cylindr:[6,234,305,326],cypress:363,cyrot:369,cyrstal:275,d3q15:239,d3q19:239,d_double_doubl:15,d_e:320,d_flag2:282,d_flag:282,d_name:[113,188,282,310,470],d_single_doubl:15,d_single_singl:15,d_sx:282,d_sy:282,d_sz:282,daan:318,dai:12,daili:12,daivi:270,damag:[],dammak:288,damp:[3,6,194,199,236,237,238,243,252,253,256,280,283,288,293,311,312,324,326,327,355,356,358,370,372,374,379,382,387,391,399,407,418,426,441,447,474,481],damp_com:237,damp_drud:237,dampen:[293,481],dampflag:[326,391],dan:17,danger:[3,12,228,331,383,478],dangl:168,daniel:9,darden:[349,382],darkblu:191,darkcyan:191,darken:190,darkgoldenrod:191,darkgrai:191,darkgreen:191,darkkhaki:191,darkmagenta:191,darkolivegreen:191,darkorang:191,darkorchid:191,darkr:191,darksalmon:191,darkseagreen:191,darkslateblu:191,darkslategrai:191,darkturquois:191,darkviolet:191,dasgupta:284,dash:[391,477],dat:[6,91,185,200,456],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,294],dataset:294,datatyp:3,date:[0,6,12,13,423,424,486],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,188,204],davi:325,david:[9,19,348,349,444,446],daw:[385,421],dbg:14,dcd:[3,6,7,188,189,190,191,192,276,461,465],ddim:187,deactiv:407,dealt:235,debug:[6,7,11,12,13,14,17,118,122,164,165,276,281,346,348,363,395,415,450,458,459,462,467,470,477,486],deby:[],decai:[379,453],decid:[3,6,12,16,71,249,282,293,321,475],decipher:351,declar:189,declin:308,decod:190,decompos:[87,432],decomposit:[3,5,7,18,62,200,276],decoupl:[6,481],decreas:[3,188,197,198,205,214,217,223,226,228,236,319,348],decrement:297,deepli:345,deeppink:191,deepskyblu:191,def:[12,13,458],defaul:61,defect:[6,70,163,413],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,171,172,173,174,175,176,177,179,180,182,183,184,185,186,187,188,189,190,191,194,195,196,197,198,199,200,201,202,203,204,206,207,208,209,210,211,212,213,214,215,217,218,221,222,223,226,227,228,231,234,235,236,237,238,239,247,249,251,252,253,254,255,256,257,258,260,261,262,265,267,268,269,270,271,272,274,275,276,278,279,280,282,284,286,291,293,294,295,296,298,302,306,308,310,311,312,313,314,316,317,318,320,322,323,325,326,327,328,329,330,331,333,334,335,336,337,338,339,342,343,344,346,348,349,351,353,355,356,357,358,359,360,361,362,363,365,366,367,368,370,371,372,373,374,375,376,377,379,380,382,383,384,386,387,389,390,391,392,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,413,414,415,416,417,418,420,421,423,424,425,426,427,428,429,430,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,457,458,460,461,463,464,465,466,469,470,471,472,474,475,477,478,481,482,483,484,485,486,487],definit:[2,3,6,8,12,13,78,80,116,140,191,203,204,205,206,207,208,209,217,234,256,294,310,322,325,328,330,332,343,346,357,366,369,377,387,397,421,428,430,432,448,458,460,462,469,471,485,486],defint:478,deform:[],deg2theta:164,deg:481,degener:[3,278],degrad:[8,18,275,349,469],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,164,165,171,172,175,176,183,185,187,190,203,214,221,228,230,231,236,237,242,252,253,256,257,258,269,270,272,276,278,292,293,296,311,312,313,318,334,336,339,342,344,356,382,385,393,470,478,481,487],degress:[145,203],del:474,delai:[3,6,12,359,384,478],deleg:394,delet:[2,3,7,8,12,54,57,60,63,163,168,169,194,203,204,206,207,208,209,212,214,225,228,252,294,311,312,331,333,347,357,359,362,415,460,461,463,471,472,477,482,484,486,487],delete_atom:[],delete_bond:[],delete_el:200,deli:187,delimit:[458,486],deloc:[253,387,431],delr:410,delt_lo:474,delta:[],delta_1:369,delta_3:369,delta_7:369,delta_conf:3,delta_ij:[410,421],delta_mu:3,delta_pi:369,delta_r:421,delta_sigma:369,delx:187,delz:187,demand:288,demo:11,demon:273,demonstr:[283,410],den:279,dendrim:393,denniston:[9,239,241,242,243,275],denomin:[7,170],denot:[118,221,237,275,286,288,379,392,394,424,428,430],dens:[71,214,387],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,151,163,165,195,196,200,203,207,208,211,217,226,239,242,245,246,275,279,280,284,320,325,351,353,357,364,369,385,410,411,412,421,425,431,435,437,438,439,460,469,470,478,485],density_continu:430,density_summ:430,depart:[0,7],departur:[250,283],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,143,148,152,153,159,165,166,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,190,191,194,195,196,197,198,201,203,205,206,207,209,210,211,213,215,217,223,224,227,230,231,232,234,236,237,239,241,242,249,252,254,255,256,257,258,259,267,269,270,272,274,285,288,290,293,295,296,302,308,311,312,313,315,317,319,320,322,324,325,328,329,330,331,333,334,335,336,337,338,339,342,344,349,351,356,357,359,360,361,363,364,365,367,368,369,370,371,372,373,374,375,376,377,378,379,380,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,413,414,416,417,418,420,421,423,424,425,426,431,432,433,441,442,443,444,445,446,447,448,449,451,452,453,455,457,460,462,463,466,470,472,474,477,478,480,486,487],dependend:6,depflag:12,dephas:[455,474],depos:218,deposit:[],deprec:[284,423],depth:[51,144,190,320,390,425],dequidt:9,der:[87,107,377,378,407,423,424,452,481],deriv:[6,7,8,9,38,56,63,87,140,159,185,204,215,217,228,236,249,252,254,255,256,257,258,274,280,284,288,317,318,320,325,326,329,355,357,365,369,377,382,387,388,392,401,405,406,410,413,423,424,441,443,452,481],derjagin:452,derlet:274,descend:191,descent:[7,355],descib:[40,284],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,144,145,149,150,153,156,158,159,163,164,165,167,168,177,182,185,188,189,194,195,196,203,204,205,206,207,208,209,211,214,215,216,217,218,220,221,229,230,233,234,235,236,237,238,239,241,242,243,247,251,252,253,256,263,271,274,276,281,282,283,284,285,286,293,297,305,308,309,310,311,312,313,314,315,316,317,318,323,325,326,328,333,348,349,351,354,355,356,357,358,362,365,366,368,370,371,372,374,375,376,377,378,379,382,385,387,388,390,391,392,394,399,400,401,402,403,404,405,406,407,408,409,410,413,414,420,421,422,423,424,425,426,431,432,433,440,441,442,443,444,445,446,447,449,451,452,453,455,457,458,460,461,463,464,470,473,474,477,486,487,488],descript:[],descriptor:[140,188,395],deserno:349,design:[0,3,6,7,8,9,11,13,14,15,17,118,147,150,164,200,214,220,221,252,253,274,275,294,315,320,366,367,368,371,374,379,381,387,407,408,409,411,412,421,424,443,469],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,112,117,141,147,165,178,187,203,209,215,217,226,228,229,236,237,238,242,252,270,278,279,280,281,284,288,293,296,308,311,312,313,314,319,326,340,345,348,349,351,354,356,357,358,383,385,393,408,409,442,444,446,456,457,458,460,464,469,474,475,477,478,486,487,488],desk:7,desktop:[4,6,7,10,12,190],despit:481,destabil:369,destre:342,destroi:[11,39,212,213],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,143,144,145,148,158,159,160,162,165,166,169,170,173,184,188,190,191,194,195,196,200,203,204,205,206,207,209,211,213,214,215,216,217,218,226,228,229,230,231,233,234,236,238,239,243,249,250,251,252,253,254,255,256,257,258,262,264,269,270,271,272,275,278,279,280,282,283,285,286,287,293,296,308,311,312,313,314,315,316,318,319,320,321,322,323,324,331,333,335,343,348,349,352,356,357,359,360,363,364,365,366,368,369,371,373,374,375,376,377,378,379,382,383,387,388,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,410,414,415,420,423,424,425,431,432,433,441,448,451,452,458,460,461,462,463,465,466,469,470,472,475,478,479,486,487,490],detect:[2,3,12,61,63,86,227,279,319,358,378,393,398,455,457,460,471,474,486],determ:363,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,153,154,163,164,165,187,188,190,191,192,193,197,198,199,202,203,204,205,206,207,208,209,210,211,215,217,218,221,223,228,231,232,234,236,237,242,247,249,250,252,257,258,269,270,272,274,276,280,283,290,291,292,293,294,295,298,300,302,308,311,312,313,315,321,322,325,326,327,328,329,330,331,343,348,349,351,357,359,360,363,365,366,373,378,382,384,385,389,391,394,395,403,410,413,415,424,425,431,440,443,447,452,457,460,461,463,465,467,470,474,476,477,479,485,486,487],detil:108,devan:[9,426],devanathan:446,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,233,256,278,283,284,287,365,369,387,412,413,431,449,462],devemi:9,deviat:[250,256,274,389],deviator:9,devic:[1,3,12,15,17,233,363],device_typ:363,devin:[285,378],devis:412,dfactor:190,dff:481,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,349],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,287,413],dhi:[59,187,217,279],dhug:[250,283],dhugoniot:[250,283],dia:410,diagnost:[],diagon:[3,6,83,140,141,142,215,252,280,293,323,428,430],diagonalstyl:432,diagram:[41,118,164,184,211,276],diallo:393,diam:[190,191,279,357],diamet:[3,6,40,113,165,188,190,191,195,196,236,279,293,308,324,326,357,377,390,391,397,401,425,448,452,460,461,470],diamond:[351,387,410],diamter:[40,279],dick:6,dicsuss:249,dictat:[201,250],did:[3,12,356,383,384,385,391,415,444,446,468],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,161,322,348],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,143,144,145,146,148,151,152,153,154,155,157,158,159,165,166,168,173,184,185,187,188,190,191,194,196,199,201,203,206,211,212,213,214,215,216,217,221,227,228,229,230,231,232,233,236,237,239,249,252,253,254,255,257,258,260,262,265,267,268,269,272,274,276,278,280,283,284,285,288,291,293,296,297,305,306,308,311,312,313,316,317,318,320,323,324,325,326,329,333,334,343,345,347,348,349,351,352,354,355,357,358,360,361,362,363,364,365,369,373,374,376,377,378,383,385,387,390,391,392,394,397,399,400,402,403,410,411,412,414,415,417,421,423,424,425,426,427,428,430,431,432,433,441,442,443,444,446,448,449,452,454,455,457,458,460,462,463,464,465,468,469,470,472,474,475,477,478,479,481,485,486,487,488],differenti:[1,3,6,29,185,348,379,421,445],difficult:[215,276,363,393,469],difficulti:[296,423],diffract:[],diffus:[],digit:[2,3,191,333,413],dih_table1:185,dih_table2:185,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:213,dihydrid:387,dij:296,dilat:[],dim1:3,dim2:3,dim:[3,59,71,143,146,147,148,151,152,153,154,155,157,165,187,207,217,234,326,351,410,463,485,486,487],dimdim:486,dimems:275,dimens:[],dimension:[3,39,112,118,140,143,145,146,147,148,151,152,153,154,155,157,164,186,203,207,251,275,320,351,354,358,421,460,470],dimensionless:[105,121,122,124,127,129,131,136,140,320,349,432,452],dimentionless:135,dimer:[6,293,410],dimgrai:191,dimstr:[41,211],dinola:[280,311],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,188,310,481],dir1:471,dir2:471,dir:[1,3,4,8,9,11,12,250,274,283,307,421,423,424,458,471,486],dirac:140,direc:421,direct:[],directli:[3,6,8,9,11,12,87,113,140,142,188,189,190,197,223,230,234,239,275,294,312,324,326,327,328,329,351,355,363,364,365,370,372,373,379,382,385,387,399,403,415,418,426,440,458,470,471,472,478,486],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,192,216,235,278,284,287,304,308,317,318,358,362,364,365,369,376,378,379,385,386,388,395,396,407,410,411,412,413,417,421,422,423,424,431,432,442,444,445,446,449,458,460,461,462,471,486],disabl:[3,12,16,320,398,458,473,486],disadvantag:[6,211],disallow:[188,217,252],disappear:462,discard:[2,3,41,71,205,207,211,321,329,457,462,463],discontinu:[9,185,356,405],discourag:410,discov:[13,321],discret:[6,8,40,42,190,191,236,239],discuss:[],disk:[6,84,85,158,186,218,228,279,458],disloc:[70,413],disord:[39,70,413],disp:[],dispar:425,disperion:[382,403],dispers:[3,6,7,9,163,275,348,349,373,382,403,408,415,424,443,449],displac:[],displace_atom:[],displace_box:59,displacemet:463,displai:[11,13,22,37,44,55,173,184,188,190,335,343,376,441],dispters:3,disregard:413,dissip:[6,229,236,275,317,318,371,383,391,408,409,441],dissolut:212,dist:[6,69,91,108,117,188,276,292,384,440,455,487],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,154,160,163,165,166,167,168,172,187,188,190,191,199,203,207,208,212,213,214,215,217,218,219,222,228,234,239,249,250,251,252,256,264,274,275,279,283,284,291,292,293,296,297,301,305,306,307,308,315,316,318,319,320,323,325,326,327,328,329,330,334,348,349,351,354,356,358,359,360,363,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,383,384,385,386,387,389,390,391,392,393,397,398,399,400,401,402,403,404,405,406,407,408,409,410,413,414,415,416,417,418,419,420,421,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,455,458,460,463,469,470,474,478,481,485,487],distinct:[6,221,290,348,425],distinguish:[6,86,140,242,387,459],distort:364,distrbut:364,distribut:[],distro:[111,376,420,421],ditto:[8,11,12,14,15,16,17,18,115,213,453,458],div:8,divd:117,diverg:[3,12,39,293,318,462,481,488],divid:[3,6,16,41,91,112,117,126,128,141,162,163,173,184,191,203,204,206,211,217,274,316,323,328,348,356,358,388,424,431,449,469,477,486],divis:[6,239,369,397,407,457,460,478,486],dl_poli:[6,7],dlambda:159,dlammps_async_imd:233,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,190],dlammps_gzip:[3,12,188,190,319,460,461,465],dlammps_jpeg:[3,12,190],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,190],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,188],dlen:470,dlmp_intel_offload:[12,16],dlo:[59,187,217,279],dlopen:6,dlvo:[7,377,452],dm_lb:239,dmax:[308,354],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,141,144,145,158,160,162,165,166,167,173,184,188,189,190,191,192,194,195,196,201,202,203,204,205,206,207,208,209,218,228,236,237,247,252,253,257,258,262,269,270,271,272,279,282,293,305,308,311,312,313,322,326,329,331,333,335,343,347,356,357,358,363,364,365,368,376,378,379,385,386,388,393,394,396,397,410,411,412,415,417,420,421,422,432,441,442,444,446,448,449,458,460,461,462,463,465,468,469,470,477,478,486,487,488,489],docuement:425,dodgerblu:191,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,116,117,118,142,144,145,147,148,153,155,159,164,165,166,167,169,171,173,178,184,185,187,188,189,190,191,194,200,201,203,207,210,211,213,214,215,217,221,223,225,228,229,232,234,236,237,239,242,248,252,253,254,255,257,258,269,270,271,272,280,281,282,286,288,291,293,308,311,313,315,316,320,323,324,325,328,329,330,331,336,337,339,340,342,347,348,349,350,351,357,358,359,364,365,366,367,368,369,371,373,374,375,377,378,379,380,382,383,384,385,386,387,389,390,391,392,394,395,396,397,398,401,402,404,405,406,408,409,410,411,412,413,415,421,422,423,424,425,427,428,429,430,431,432,433,434,435,436,437,438,439,440,442,443,444,445,446,447,448,449,451,452,453,455,456,457,458,460,461,462,463,464,467,468,470,471,472,473,474,477,478,481,486,490],doegenomestolif:7,doesn:[3,7,8,12,165,188,201,207,208,305,357,359,363,365,378,386,396,423,424,442,444,445,446,449,460,462],dof:[3,8,112,144,145,158,203,293,487],dof_per_atom:[145,203],dof_per_chunk:[145,203],doff:[357,460],doi:[6,216],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,154,164,167,187,189,190,191,194,201,211,215,217,218,232,235,239,252,253,276,288,293,320,325,326,348,349,358,363,384,415,455,457,460,464,477],domin:[1,387,474],don:[0,8,11,12,13,116,168,197,223,237,282,329,410,431,458,460],donadio:312,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,159,162,165,168,185,188,190,191,200,201,203,205,206,207,208,209,211,212,213,214,215,217,218,226,228,233,234,236,237,244,252,257,258,269,270,272,273,275,276,277,282,290,293,294,296,308,311,312,313,315,317,318,331,333,347,348,349,356,358,359,362,363,365,373,385,394,395,396,403,409,410,415,423,440,443,448,455,456,457,458,461,464,465,468,478,479,481,486,487],donor:393,dot:[141,161,197,223,231,251],doti:[369,421],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,217,226,281,329,333,347,349,362,363,369,388,392,413,423,424,456,460,464,468,473,486,487],dover:200,down:[3,6,7,8,11,39,71,215,228,236,308,324,363,387,415,431,459,479],downhil:[354,355],download:[5,7,8,9,11,12,13,17,233,395,422],downsid:6,downward:290,dozen:[8,12,107,194,423,424],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:245,dproduct:366,dr_ewald:[118,294],drag:[],dragforc:239,drai:[250,283],drain:[232,324,356],dramat:[59,187,212,213,214,215,217,252,308,311,312,349,363,415,431,457],drautz:369,draw:190,drawback:282,drawn:[188,190,191,229,455],drayleigh:[250,283],dreid:[],drfourth:105,drho:[113,364,385],drift:[6,103,105,229,230,236,237,248,291,308,469,477,4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228,236,252,270,280,292,293,328,383,387,431,444,446,460,463,468,469,478,481],equlibrium:6,equliibr:[284,286],er3:164,eradiu:[40,113,387,460],eras:[295,317],erat:[217,409],erc:379,erfc:[379,399,415],erforc:113,erg:485,erhart:[201,385,444,446],ermscal:366,ernst:9,eror:3,eros:410,erose_form:410,erot:[],errata:[444,446],erratum:325,erron:3,error:[],erta:391,ervel:[113,460],escap:[218,481],especi:[8,11,16,153,165,194,201,211,228,283,288,291,292,363,457],espresso:[9,287],essenti:[8,11,12,27,88,128,146,147,148,151,152,153,154,155,157,174,204,256,275,324,349,365,379,399,446,465,478],essex:29,establish:[87,232],estim:[1,3,6,10,12,38,41,56,91,141,200,211,222,250,308,315,348,349,354,415,424,443,474,478],esu:485,esub:410,eta:[6,239,252,283,284,286,324,386,388,390,421,445,449,485],eta_dot:252,eta_ij:421,eta_ji:388,etag:[40,460],etail:478,etap:252,etap_dot:252,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,143,145,146,147,148,149,151,152,153,154,155,157,159,165,167,168,169,178,188,190,191,194,195,200,201,202,203,206,207,208,209,212,213,217,218,226,228,229,236,252,279,290,294,320,321,329,333,347,348,356,357,358,359,361,385,386,394,407,409,413,419,423,424,442,444,446,449,455,458,460,461,462,467,469,470,474,476,477,478,479,481,485,486,488,490],ethernet:18,etol:[356,358,455,474],etot0:283,etot:[6,94,96,97,110,141,151,191,221,237,250,283,477,478],eu2:164,eu3:164,euler:[356,358],eulerian:200,euqat:434,europhi:239,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,87,88,91,107,117,140,142,145,155,163,165,188,190,191,195,196,197,198,200,202,203,204,205,206,207,208,209,210,217,223,229,231,232,234,235,236,237,275,281,284,295,298,302,311,312,313,322,325,328,330,331,333,348,349,354,356,363,413,415,421,427,429,431,443,455,456,458,462,463,465,467,468,469,470,474,476,478,486,487],evalut:[333,458],evan:[153,270],evanseck:[6,20,171,374,472],evapor:[],evaul:[8,356],evdwl:[107,423,424,478],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,119,166,167,181,185,188,191,194,195,196,201,202,203,206,207,208,209,211,212,213,215,217,218,221,234,237,250,252,253,275,288,290,293,294,304,308,316,320,323,325,329,331,341,348,354,356,358,363,368,387,388,391,394,415,425,449,450,460,461,463,465,466,467,469,470,472,475,477,478,479,481,490],evenli:[3,41,141,185,211,239,397,450,460],event:[],eventu:[3,6,12,15,167,284,474],ever:[54,56,235,308],evera:[377,390,425,441],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,113,119,128,153,168,188,189,190,191,192,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,222,225,226,228,230,232,233,234,239,240,248,252,253,256,273,274,275,279,280,281,282,283,284,285,286,288,290,291,293,294,296,297,308,310,311,312,313,314,315,316,319,320,321,322,323,331,333,347,349,358,359,360,363,383,384,394,407,423,424,431,437,454,455,456,460,462,464,465,467,468,469,474,475,476,478,486,490],everyth:[8,107],everywher:[116,401],eviri:387,evolut:[230,239,276,455],evolv:[239,276,321],ewald:[2,3,5,6,7,8,12,88,110,118,141,321,348,349,356,370,372,373,379,382,387,399,403,418,426,441,443,462],ewald_disp:382,ewalddisp:3,exact:[22,41,44,71,122,159,168,173,211,214,229,230,236,237,238,279,288,289,308,320,335,348,376,462,467,474,486,488,490],exactli:[3,6,12,14,17,38,41,56,59,71,91,116,144,149,156,165,185,195,196,206,211,217,222,229,236,237,238,253,263,264,271,275,283,308,313,314,327,363,376,383,385,391,394,397,408,415,443,462,463,470,474,486],exager:481,examin:[6,8,9,17,214,275],examp:[458,486],exampl:[],exce:[3,6,16,17,18,41,58,71,167,203,207,208,211,215,217,222,225,252,275,299,300,308,356,363,460,486],exceed:[3,41,59,211,217,252,308,468],excel:387,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,191,194,197,203,204,206,210,211,215,217,224,227,228,231,234,236,238,252,253,254,255,256,257,258,259,263,264,267,269,270,271,272,276,285,286,293,295,296,305,308,311,313,314,320,324,328,331,333,334,335,336,337,338,339,342,343,344,348,349,351,353,357,358,359,361,362,363,364,365,367,370,371,372,373,374,375,376,377,378,379,381,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,411,416,417,418,420,423,424,425,426,433,441,442,443,444,445,446,448,449,451,452,453,455,457,458,460,462,463,465,468,469,470,471,472,474,478,481,485,486,487,489],excess:[205,387],exchang:[2,3,6,8,9,61,62,194,200,201,228,236,285,293,316,320,323,348,363,387,475],exchange:348,excit:[9,387],exclud:[3,6,9,12,16,17,63,71,112,140,145,152,153,169,188,203,207,212,213,240,248,278,291,293,315,326,331,356,357,359,371,391,394,408,409,415,440,472],exclus:[1,3,9,12,16,87,363,378,413,415,469,479],excurs:455,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,166,190,233,287,333,347,350,362,456,458,468,471,474,486],exempl:431,exemplari:229,exemplifi:387,exert:[6,234,237,288,327,328,329,349],exhaust:[200,362,486],exhibit:[252,355,387,469],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,122,165,166,184,189,190,191,194,199,210,213,215,218,228,278,279,281,331,334,336,337,339,343,352,357,363,394,423,450,456,458,460,461,462,471,472,473,486,487,488],exit:[2,3,11,12,41,57,188,211,347,362,458,459,468,477,486],exlanatori:3,exp:[],expand:[],expans:[12,140,188,471,486],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,146,157,163,185,211,223,228,230,249,274,280,282,283,288,293,331,349,359,376,410,413,415,455,458,460,462,465,469,474,486],expens:[6,10,71,191,274,278,293,320,331,348,349,359,363,458],experi:[6,13,15,17,210,218,233,242,251,280,292,293,354,358,383,415,469,474],experienc:[6,12,241,242],experiment:[228,348,363,474],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,145,153,185,188,190,191,194,203,204,209,211,213,215,217,252,274,282,293,305,331,333,347,348,351,357,358,362,368,385,397,431,433,448,458,461,462,465,467,470,481,486,490],explan:[3,6,59,113,140,188,203,251,274,394,454,457,458,460,469],explanatori:[3,8,117,188,202,203,206,207,208,293,357,457,486],explantori:[3,289],explic:414,explicit:[6,9,11,22,44,77,87,113,116,159,173,195,196,217,299,300,335,353,365,366,369,374,376,385,387,398,408,447,454,457,461,464],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,143,152,155,163,165,171,172,174,175,176,177,179,180,182,183,185,188,191,197,207,210,217,224,227,229,231,236,252,254,255,256,257,258,259,267,269,270,272,282,283,285,293,295,296,311,313,314,320,324,328,334,336,337,338,339,342,344,357,363,364,365,367,370,371,372,373,374,375,376,377,378,379,380,382,383,384,385,386,388,389,390,391,392,393,394,397,398,399,400,401,402,403,404,405,406,407,408,411,413,415,416,417,418,420,425,426,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,451,452,453,460,462,469,470,472,473,479,481],explictli:[16,473],exploit:[9,15,17,276],explor:[118,164],expon:[3,284,286,385,390,393,407,414,426],exponenti:[87,421,442,449,453,474,486],expos:11,exposit:[200,383,384],express:[6,140,151,165,195,196,215,249,274,284,320,326,333,369,385,387,401,410,431,432,441,486],expressiont:369,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,194,197,198,201,209,210,216,219,223,226,227,228,230,231,232,234,236,238,250,252,256,264,274,275,291,292,293,295,297,302,305,307,311,312,313,314,315,317,318,320,322,325,329,330,390,410,413,424,425,432,477,478],extent:[1,3,41,45,57,71,163,167,188,199,207,211,234,327,330,348,351,365,427,429,443,457,460,463],exterior:[3,6,329],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,143,144,146,148,151,152,153,154,155,157,158,164,165,166,167,171,191,206,211,213,252,281,282,283,293,308,356,357,360,361,382,391,394,397,410,415,457,458,460,463,472,481,486],extract:[3,6,11,13,36,63,87,107,115,117,119,195,196,286,358,379,388,410,432,458,465,477],extract_atom:11,extract_comput:[11,458],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,190,205,215,217,252,318,387,445,481],extrema:407,extrins:200,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[161,322],f_a:[444,445,446],f_ave:117,f_c:445,f_f:446,f_fix_id:283,f_harm:318,f_i:421,f_id:[6,71,117,119,188,194,202,203,204,205,206,207,208,209,247,310,322,478,486],f_ij:421,f_indent:209,f_int:317,f_jj:91,f_k:421,f_langevin:320,f_max:[283,288],f_msst:250,f_r:[237,444,445,446],f_sigma:369,f_solid:318,f_ss:6,f_temp:237,face:[3,6,57,59,71,153,163,167,199,207,208,325,327,328,329,330,351,390,410,425,460,463],face_threshold:163,facet:163,facil:[0,12],facilit:[6,13],fact:[6,8,16,230,308,318,391,431,472],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,116,118,140,159,164,167,171,182,188,190,191,195,196,204,211,215,217,218,228,233,236,238,239,250,252,253,256,276,280,292,296,298,300,308,312,316,323,324,325,329,339,349,351,357,363,365,366,369,370,372,374,379,380,381,383,387,391,394,398,399,410,413,415,417,418,424,426,433,442,447,457,460,463,464,469,472,474,475,478,481,485,486],factori:[3,458],factoriz:348,fail:[3,11,12,59,169,215,218,348,356,358,381,424,458],failur:[121,428,459,486],fairli:[11,415,469,474],faken:73,falcon:233,fall:[3,6,191,206,279,458,486],fals:[86,331,333,431,486],fame:8,famili:[449,457],familiar:[0,11],fan:421,far:[3,6,12,17,57,59,61,86,188,191,192,211,212,213,215,218,252,274,292,293,308,325,336,339,354,358,359,448,458,460,465,478],farago:236,farrel:[444,446],farther:188,fashion:[6,8,41,71,165,191,194,195,196,201,207,211,213,218,228,230,234,249,250,252,254,255,256,257,258,266,269,270,271,272,282,283,285,293,297,301,307,310,318,320,324,325,326,328,330,358,394,408,463,472,486,489],fasolino:396,fast:[6,7,9,12,13,17,39,188,261,283,321,348,349,371,408,409,413,441,443,462,467,469,478,487,490],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,143,152,171,172,174,175,176,177,179,180,182,183,185,188,191,194,197,210,211,217,224,227,231,235,236,252,254,255,256,257,258,259,267,269,270,272,280,284,285,293,295,296,308,311,313,315,317,320,324,328,334,336,337,338,339,342,344,348,349,360,361,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,382,383,385,386,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,411,416,417,418,420,425,426,433,441,442,443,444,445,446,448,449,451,452,453,455,469,473,481],fastest:[1,6,14,17,153,207,320,321,363,457],fatal:[3,477],fault:[70,424],faulti:12,fava:390,favor:214,favorit:7,fbmc:315,fcc:[],fcm:[266,486],fdirect:221,fdotr:395,fdti:87,fe2:164,fe3:164,fe_md_boundari:200,featu:8,featur:[],fecr:385,feedback:[7,233],feel:[7,233,234,242,274,329,331,358,415],felling:412,felt:329,femtosecond:485,fene:[],fennel:[379,399],fep:[],ferguson:[6,171,472],fermi:[1,12,15,151,363,446],fermion:[9,387],ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,192,202,203,204,206,207,208,209,237,252,279,282,284,296,322,348,356,357,358,365,431,457,460,465,469,471,479,486,488],fewer:[1,3,11,15,16,61,242,469],fewest:3,fextern:226,feynman:276,fff:458,ffield:[378,388,423,424,431],ffmpeg:[3,12,190],ffplai:190,fft:[1,3,7,12,14,15,88,109,110,141,275,348,349,469],fft_inc:[12,349],fft_lib:12,fft_path:12,fftbench:[348,479],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:440,fictiti:[6,197,198,223,226,230,276,292,379,399,403,440],field1:[461,465],field2:461,field:[],fifth:[305,417],figur:[1,3,8,11,12,283,457,458],fij:382,file0:274,file1:[11,13,274,319,333,357,465,467,471],file2:[11,13,319,333,357,465,467,471],file:[],file_from:189,filen:357,filenam:[3,12,13,38,41,56,185,188,190,191,192,200,203,204,205,206,207,208,209,211,216,274,278,281,284,285,286,289,290,293,294,319,320,345,346,347,357,358,364,365,369,379,385,386,388,396,410,411,412,417,421,422,423,424,431,432,442,443,444,445,446,449,456,457,458,461,462,467,471,478,486,488,489,490],filennam:467,filep:[3,188,191,462,467,490],filepo:290,fill:[7,9,165,190,279,320,351,359,369,413,424,463],filter:[191,200],final_integr:8,final_integrate_respa:8,finchham:[6,147,381],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,168,185,192,201,214,215,225,228,251,274,280,288,292,354,356,358,359,379,394,399,403,410,431,441,443,481,486],find_custom:8,fine:[16,17,169,197,223,318,359,363,486],finer:[140,165,486],finest:348,finger:[165,187,249,463],finish:[6,11,41,211,333,345,347,348,360,362,363,448,465,486,487],finit:[],finni:[7,385,441],finvers:221,fiorin:[9,216],fire:[354,355,356,358,474],firebrick:191,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,150,153,159,161,163,164,166,167,168,172,185,188,189,190,191,192,194,195,203,204,206,207,208,209,211,214,217,228,229,234,239,249,250,251,252,274,276,281,282,283,285,290,293,296,297,305,306,308,309,310,317,318,319,320,322,326,331,333,334,340,351,356,357,358,359,362,363,364,365,368,369,370,372,374,376,378,379,385,387,388,391,392,394,395,396,398,399,403,408,409,410,412,413,415,417,421,423,424,431,432,440,442,443,444,445,446,449,453,455,456,457,458,460,461,462,465,467,469,472,473,474,477,478,481,486,487,488,490],fischer:[6,9,19,20,171,374,472],fit:[3,6,9,12,38,56,185,292,308,365,369,396,410,415,436,443,445,468,486],five:[73,151,283,357,369,411,460,474],fix:[],fix_adapt:[159,196,407],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,201,279],fix_evapor:201,fix_flux:200,fix_gcmc:[201,357],fix_gl:230,fix_gld:230,fix_grav:279,fix_id:[3,215,250,252,254,255,256,257,258,280,283],fix_modifi:[],fix_mov:[187,326],fix_nh:8,fix_npt:230,fix_nvt:[201,228],fix_poem:[3,6],fix_pour:[3,218],fix_qbmsst:9,fix_qeq:[3,378],fix_rattl:296,fix_reax_bond:423,fix_rigid:[242,368],fix_saed_vtk:294,fix_setforc:8,fix_shak:296,fix_srd:3,fix_styl:256,fix_temp_rescal:314,fixedpoint:[215,252],fixextern:226,fixid:200,fji:382,flag1:[220,361],flag2:[220,361],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,93,103,104,106,118,160,164,168,188,190,191,192,209,214,216,220,233,236,240,242,248,249,275,282,293,305,307,308,315,319,328,331,346,349,357,361,362,363,365,393,398,410,413,440,455,457,458,460,461,462,464,465,466,470,486],flag_buck:373,flag_coul:[373,382,403],flag_lj:[382,403],flagfld:[371,408,409],flaghi:[3,371,408,409],flaglog:[371,408,409],flagn:220,flagvf:[371,408,409],flat:[6,320,325,326,330],flavor:[2,7,12],fld:[9,325,371,408,409],flen:366,flex_press:366,flexibl:[3,6,8,166,190,203,207,216,230,253,316,323,387,445,478],flip:[3,6,217,252,327,328],floor:486,flop:12,floralwhit:191,flow:[],fluctuat:[6,64,87,215,228,229,236,239,252,256,274,275,318,320,342],fluid:[],fluid_veloc:243,flush:[3,191,477],flux:[],flv:190,fly:[7,9,12,41,190,194,200,205,218,221,293,296,321,369,413,478,481],fmackai:9,fmag:219,fmass:276,fmax:[356,478],fmomentum:221,fmsec:[2,191,236,237,249,252,280,293,311,312,469,480,485,487],fname:347,fno:[12,16],fnorm:[356,478],fnpt:221,fnvt:221,foce:394,fock:366,focu:296,fogarti:[9,286,424],foil:[140,274,432],fold:[306,469],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,144,145,151,153,158,161,163,165,166,171,174,175,176,177,179,180,182,183,185,188,189,190,191,194,200,201,202,203,204,205,206,207,208,209,211,216,217,218,221,222,226,228,229,230,233,235,236,237,239,242,250,252,256,257,258,269,270,272,275,276,278,281,282,283,284,286,288,290,292,293,294,296,310,311,312,313,316,317,318,319,320,322,323,331,332,336,337,338,339,342,344,346,351,353,356,357,358,363,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,420,421,422,423,424,425,426,428,430,431,432,433,434,435,436,437,438,439,440,442,443,444,445,446,447,448,449,451,452,453,455,457,458,460,461,462,463,465,467,468,469,472,474,475,476,481,486,487,489],foo:[4,8,11,12,188,190,226,458,471,486],foot:6,footprint:[12,363],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:242,forcefield:[292,393],forcegroup:239,forcezero:354,ford:382,forestgreen:191,forev:71,forget:[237,481],forgiv:252,fork:[12,188],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,87,89,90,93,103,104,106,116,140,141,159,160,169,173,191,194,195,196,213,229,230,236,238,242,249,270,275,286,288,292,293,320,325,329,334,335,342,353,355,357,358,365,366,369,376,385,387,389,393,394,398,410,412,413,417,418,421,423,424,425,431,432,433,441,443,444,445,446,452,454,457,458,460,465,470,477,481,486],formal:[6,78,80,91,229,230,236,252,276,308,316,431],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,173,185,188,189,190,191,192,203,206,207,208,209,211,213,275,278,282,284,286,289,293,294,304,319,320,331,332,335,353,357,358,364,365,369,376,385,388,398,410,412,422,423,424,426,432,443,449,450,457,458,460,461,462,465,476,477,478,486,488],former:[6,12,16,39,41,191,211,320,324,369,371,466,472,486],formerli:[7,13],formul:[1,40,64,141,197,223,236,252,270,284,286,292,296,319,348,365,369,385,387,390,410,420],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,94,96,97,106,112,118,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,164,165,170,172,173,184,188,195,196,197,198,203,204,205,206,209,210,217,223,231,232,234,236,237,249,274,275,281,290,295,302,306,308,311,312,313,322,325,328,330,331,333,334,335,337,343,351,357,365,366,368,369,374,375,376,377,382,383,385,386,390,391,392,393,395,398,399,401,402,403,405,406,408,409,410,414,415,416,425,426,433,441,442,444,445,446,449,451,452,456,460,463,470,477,478,485,486,487],forth:[1,6,11,12,13,14,15,362,458,463,467],fortran:[3,6,9,11,12,13,226,385,394,410,423,424],fortun:8,forward:[3,8,87,347,358,363],foster:[369,420,421],foul:168,found:[3,6,9,12,73,159,188,214,216,228,233,239,275,315,321,333,347,359,376,379,382,455,461,462,477],four:[6,11,54,81,103,104,140,161,250,320,342,357,358,413,455],fourier:[],fourth:[6,105,292,305,315,374,417,431],fox:[6,118,171,439,472],fphi:[38,56,443],fpic:12,fplo:[38,56,443],fprime:443,fqdn:235,fqq:382,frac:[221,237,447,481],fraction:[1,3,6,8,12,16,39,41,80,109,141,168,187,190,191,201,212,213,214,215,250,279,283,290,291,308,313,314,351,358,363,369,371,391,408,409,465,470],fragment:[42,233,290],frame:[83,140,191,200,250,283,327,390],framer:[190,191],framework:[5,230,364,432],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,87,159,196,274,308,317,318,319,320,355,358,366,387,407,413,421,452,457],freedom:[3,6,8,94,96,97,99,101,102,112,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,203,214,221,228,230,236,237,242,252,253,256,257,258,269,270,272,276,278,293,296,311,312,313,318,356,382,478,481,487],freeli:[0,6,7,12,144,158,163,190],freez:[],frenkel:[228,318],freq:199,frequenc:[3,6,16,39,191,205,264,275,276,283,288,346,383,387,424,431,455,469,474,486,489],frequent:[3,64,67,70,72,73,77,88,140,191,212,213,225,316,323,415,467],fri:[250,283],friction:[4,5,6,10,42,194,230,236,283,288,293,320,324,326,391,470],friedrich:298,from:[],front:[250,283,327],frontend:[190,287],frozen:[6,112,169,227,229,237,359,389],fs2:[6,91],fscale:233,fstr:486,fstring:458,ftol:[356,358,455,474],fuchsia:191,fuction:379,fudg:296,fugac:228,fugacity_coeff:228,fulfil:6,full:[1,2,6,9,12,17,38,39,40,91,190,204,205,216,239,274,348,349,363,369,385,387,388,390,447,460,462,467,468,472,474,479,481,489],full_energi:[3,228],fuller:356,fulli:[3,6,9,78,230,235,274,356,358,379,421,422,488],fulton:385,fumi:370,func:[458,486],funcfl:385,functino:[],functionaliri:216,fund:[0,7],fundament:[308,485],funnel_flow:304,funrol:413,further:[3,6,8,12,13,61,63,71,86,105,107,116,190,191,194,203,206,207,208,209,212,218,222,239,243,276,284,294,298,308,320,322,331,349,354,356,357,358,359,364,368,378,413,431,455,474,475,486],furthermor:[27,174,387],furthest:61,futher:3,futur:[],g_ewald:3,g_ewald_6:3,g_ewald_disp:3,g_jik:421,g_p:320,ga3:164,gaa:36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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":212,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,145,153,154,158,164,165,168,170,184,186,187,188,190,191,192,193,195,196,197,199,200,201,203,207,208,209,212,213,215,216,217,218,222,225,228,229,234,236,237,238,239,240,242,247,250,252,253,256,270,271,275,276,279,280,281,282,283,285,288,290,291,293,294,308,310,315,316,317,318,321,323,325,327,331,343,346,348,349,351,352,354,355,357,359,360,361,363,366,369,371,387,408,409,413,415,423,424,440,441,455,456,457,460,461,463,465,467,468,469,472,474,476,477,478,479,480,485,487,488,489],"function":486,"long":[205,370,372,373,374,375,379,381,382,399,403,407,418,426],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[195,196],addforc:197,addit:[12,13],addtorqu:198,adiabat:6,adjust_dt:298,adp:364,airebo:365,alloi:385,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:199,arrai:6,aspher:[6,82,144,254,257,260,261,269],atc:[9,200],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,163,199,201,202,282,486],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:210,awpmd:[9,366],balanc:[41,211],barostat:6,basal:67,beck:367,berendsen:[280,311],between:6,binary2txt:13,bodi:[6,8,42,68,262,368],bond:[8,13,69,212,213,214,289],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:369,born:[370,381],boundari:[7,57],box:[6,58,215],brownian:371,buck:[372,373,381],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,171,374,407],chunk:[6,66,71,75,90,93,104,106,114,145,160,162,203],citat:7,class2:[21,43,172,334,375],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[325,377,452],colvar:[9,13,216],com:[74,75,146],comb3:378,comb:[285,378],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,484,485,486,487,488,489,490],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,486],compute_modifi:102,condit:7,conduct:[6,316],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:[204,205],cosin:[23,24,25,26,27,28,174],cossq:336,coul:[370,372,373,374,375,379,380,381,392,399,403,407,418,426],coupl:6,creat:213,create_atom:165,create_bond:166,create_box:167,createatom:13,creation:7,csld:312,csvr:312,cubic:401,cuda:[9,14,109,112,143,152,197,210,224,227,231,252,259,295,296,311,313,324,370,372,374,375,385,391,392,399,400,402,405,416,442,444],custom:8,cut:[49,366,372,375,379,382,387,389,399,400,407,414,418],cvff:337,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[379,399],deform:[148,149,217],delete_atom:168,delete_bond:169,delta:24,deposit:218,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,7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7,438,439,440,441,442,443,444,445,446,447,448,449,451,452,453],pair_writ:450,pairwis:8,parallel:11,paramet:6,pars:2,partial:152,particl:[6,7,42],partit:454,past:5,per:6,perform:[1,10],peri:420,period:25,phonon:[9,13,275],pimd:276,piston:327,planeforc:277,plastic:111,plastic_strain:124,plastic_strain_r:125,pmb:420,poem:[9,278],point:284,polariz:6,poli:[371,408,409],polym:13,polymorph:421,post:7,potenti:[2,6,8],pour:279,pppm:6,prd:455,pre:7,press:280,pressur:112,previou:12,print:[281,456],problem:[3,4],process:[6,7],processor:457,profil:153,properti:[6,113,114,115,282],pymol_aspher:13,python:[9,11,13,458],qbmsst:283,qeq:[284,285,286],qmmm:[9,287],qtb:[9,288],quadrat:183,quantiti:6,quartic:[35,54],quip:422,quit:459,ramp:154,rattl:296,rdf:116,read_data:460,read_dump:461,read_restart:462,reax:[9,13,286,289,290,423,424],reaxc:9,rebo:365,recent:291,reduc:117,refer:486,reflect:328,region:[8,117,155,156,329,463,486],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,182,183,184,185,186,187,188,189,190,191,192,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,227,228,229,230,231,232,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,288,289,290,291,293,294,295,297,298,299,300,301,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,342,343,344,345,346,347,348,349,351,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,465,466,467,468,469,470,472,473,474,475,476,477,478,479,480,482,483,484,486,487,488,489,490],relax:215,replic:464,replica:[6,7],report:3,requir:12,rerun:465,rescal:[313,314],reset:222,reset_timestep:466,resquar:425,restart2data:13,restart:[6,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,467],restrain:292,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,484,485,486,487,488,489,490],rho:126,rhosum:437,rigid:[6,83,98,242,293],ring:342,rotat:157,rule:2,run:[6,11,12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,468],run_styl:469,scalabl:10,scalar:6,screen:12,script:[2,6,8,11],sdk:[36,426],self:307,serial:11,set:[6,470],setforc:295,setvel:302,shake:296,share:[11,12],shell:[6,471],shield:284,shift:[26,27,48,49,174],simpl:31,simul:6,size:6,slater:284,slice:119,sllod:[270,271],small:293,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,297,298,299,300,301,302,304,427,428,429,430],smooth:[405,406],smtbq:431,sna:140,snad:140,snap:432,snapshot:6,snav:140,soft:[407,433],solver:2,sourc:7,spatial:[207,208],spc:6,speci:290,special:[7,415,486],special_bond:472,sph:[9,434,435,436,437,438,439],sphere:[84,85,158,208,242,255,258,267,272],spheric:6,spline:[411,412],spring:[305,306,307,318],squar:28,srd:[308,330],srp:440,standard:9,start:[12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330],state:310,stationari:246,stop:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330],store:[309,310],strategi:1,streitz:379,stress:[141,142],structur:2,style:[1,2,6,8],submit:8,suffix:473,summari:6,swap:[201,214],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,484,485,486,487,488,489,490],system:6,tabl:[0,6,38,56,185,443,444],tad:474,taitwat:[438,439],talli:142,temp:[143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,311,312,313,314],temper:475,temperatur:6,tersoff:[444,445,446],test:11,tfmc:315,thermal:[6,316],thermo:[6,476],thermo_modifi:477,thermo_styl:478,thermodynam:[6,8],thermostat:6,thole:447,time:[6,209],timer:479,timestep:480,tip3p:6,tip4p:[6,379,399,403,407],tip:12,tlsph:428,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:319,tool:[12,13],torqu:1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\ No newline at end of file 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:[16,245,282,320,391,424],cart:[3,457],carter:[9,17],cartesian:[3,62,364,457],carv:168,cascad:[222,320],cash:7,cast:[230,486],cat:[15,190],catastroph:284,cate:239,categori:[],cation:[388,431],cauchi:[133,138],caus:[1,2,3,6,8,12,16,17,165,167,168,169,188,191,199,215,222,228,264,274,291,293,296,325,327,328,329,330,333,347,349,356,358,362,393,399,405,408,409,415,454,458,459,460,461,464,465,467,468,486,490],caution:[1,349],cautiou:[212,213],cautious:365,caveat:[365,469],cbecker:[364,385],cc1:[6,14,66,75,90,93,104,106,114,145,160,162,203,207],cc2:14,ccc:[386,442,444,446,449],ccflag:[12,16,17,18,19,188],ccm6:385,ccsi:[386,442,444,446,449],ccu:369,cd2:164,cdeam:385,cdennist:9,cdll:11,cdof:[6,145,203],cdte:369,cdte_bop:369,cdtese:369,cdzn:369,cdznte:369,ce3:164,ce4:164,ceas:355,ceil:486,cell:[3,6,59,88,116,118,163,164,165,188,199,215,216,228,233,250,252,253,256,275,283,286,320,348,349,351,384,387,413,478],cella:[6,478],cellalpha:[6,478],cellb:[6,478],cellbeta:[6,478],cellc:[6,478],cellgamma:[6,478],center:[3,6,25,42,63,66,71,74,75,86,89,90,98,103,104,105,114,116,118,145,146,147,150,153,157,160,162,165,190,191,194,195,196,198,203,206,207,208,215,217,218,219,221,228,229,234,236,237,242,248,252,257,258,269,270,272,275,279,284,290,291,293,294,297,305,306,308,310,311,312,313,315,316,318,325,329,334,351,357,368,386,387,390,391,397,408,409,410,411,412,442,444,445,446,448,449,463,470,481,486],centimet:485,central:[3,61,70,76,77,116,122,140,242,274,296,306,357,413,417,423,424,449,460],centro:[],centroid:[3,276,448,470],cerda:348,ceriotti2:230,ceriotti:[13,230,235],certain:[1,2,3,6,8,12,17,39,71,113,117,119,169,188,190,202,203,204,206,207,208,209,214,226,227,293,295,309,322,333,340,347,359,394,415,424,447,462,466,481,486],certainli:234,cerutti:349,cfg:[3,6,7,13,188,189,190,191,192],cfile:424,cfl:[128,298],cfor:297,cg_type:426,cgiko:2,cgikot:2,cgkio:2,cgko:2,cgkot:2,cgo:2,cgot:2,ch2:296,ch2lmp:[],ch3:296,ch5md:189,chain3:359,chain:[],challeng:[6,297],chalopin:288,champaign:[233,348,349,408],chan:413,chandler:[364,385],chandrasekhar:[6,399],chang:[1,2,3,6,8,9,11,12,14,15,16,17,39,40,41,46,55,57,59,62,71,80,87,116,126,128,147,148,149,165,166,167,169,185,187,188,189,190,191,192,194,195,196,197,198,200,201,207,208,210,211,212,213,214,215,216,217,218,222,223,225,227,228,230,232,233,234,236,238,239,240,242,248,249,250,252,253,254,255,256,257,258,264,269,270,271,272,274,275,279,280,282,283,287,290,291,292,293,295,296,297,308,311,312,313,314,316,317,318,319,320,321,323,326,329,331,349,354,356,358,361,363,383,387,391,394,408,409,410,413,415,423,424,431,441,455,456,457,458,460,461,462,463,464,465,466,468,469,470,471,472,475,478,482,484,485,486,487,488],change_box:[],changeabl:188,channel:[4,197],chapter:[276,349],charact:[2,3,6,12,38,41,56,63,185,188,190,191,192,194,211,282,290,333,357,362,387,398,421,423,424,431,443,457,458,462,467,468,486,488,489,490],character:[6,67,70,116,140,432,455,474],characterist:[237,308,317],charg:[1,3,4,5,6,7,9,11,15,40,87,88,113,118,164,165,188,192,194,195,196,201,218,223,228,282,284,285,286,290,310,323,348,349,357,370,372,378,379,381,382,385,387,388,394,399,403,407,418,423,424,431,441,446,447,449,450,452,453,460,461,465,470,472,481,485,486],charmm2lammp:13,charmm:[],chartreus:191,cheap:308,cheaper:[222,390,425],check:[3,6,8,11,12,15,17,39,41,71,91,185,201,207,211,212,213,218,225,228,234,235,292,296,308,316,318,323,331,333,347,356,357,358,359,360,363,384,395,398,415,424,455,457,458,460,468,474,477,478,486],checkf:185,checkqeq:424,checku:185,chem:[6,13,20,21,25,39,40,43,45,46,87,88,112,141,171,172,182,205,216,221,229,230,237,239,251,252,253,270,271,276,280,283,285,293,297,308,311,312,315,316,317,318,325,334,342,344,348,349,355,358,365,370,374,375,378,379,380,382,383,387,389,390,392,393,399,403,404,407,410,414,415,418,431,440,447,469,472,474,481],chemic:[9,118,159,164,188,200,201,228,284,289,290,315,349,423,424,436],chemistri:[9,283,284,286,369,387,423,424],chen:320,cheng:378,chenoweth:[423,424],chenoweth_2008:[423,424],chi:[92,154,187,274,284,286,388,390,487],chiefli:422,child:8,chip:[7,12,17,18,363,473],chipot:216,chiral:342,chmod:[11,12],cho:410,chocol:[7,191],choic:[3,6,12,15,16,18,40,41,54,87,141,144,158,169,185,203,207,208,211,214,217,218,230,236,239,250,252,276,284,293,315,343,349,354,355,358,360,363,394,407,415,419,460,469,470,473,474,480,481,485],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,117,155,156,190,212,213,214,215,218,225,236,239,250,252,254,255,256,257,258,280,308,312,326,348,349,355,450,455,457,469,475],chose:[444,446],chosen:[2,3,6,12,17,140,165,168,177,185,190,196,201,215,218,225,228,229,237,239,250,252,256,276,279,290,308,312,315,316,321,323,324,330,349,350,355,363,387,391,397,398,401,426,444,455,469,474,481],chri:163,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,93,104,106,114,145,160,162,203],chute:[4,10,231],ciccotti:296,cieplak:[6,171,472],cii:204,cij:204,circl:304,circular:[3,6,144,186],circumst:18,circumv:288,citat:[],cite:[3,7,8,12,236,431],cko:2,cl1:164,clarendon:[29,382],clarifi:[7,444,446],clariti:333,clark:418,class2:[],classic:[0,3,5,6,7,8,9,226,276,283,288,320,344,387],classifi:[9,441,449],claus:458,clean:[6,12,14,15,17,468],cleanli:[459,489],clear:[],clearli:7,clebsch:140,clermont:[9,13],clever:464,click:[2,11,22,37,44,55,165,173,184,190,233,335,343,358,376,441],client:[233,235],climb:[251,358,474],clinic:[7,13],clo:[154,187,487],clock:[12,455,474],clockwis:326,close:[3,6,11,12,13,39,41,67,141,168,188,213,214,215,230,237,239,252,270,293,296,326,329,347,349,352,354,355,358,363,365,369,379,380,410,415,427,429,446,464,470,481,483],closer:[3,41,116,163,187,188,211,215,219,317,358],closest:[213,274,293,323,390,425,440,450],cloud:[431,481],clovertown:18,clsuter:72,clump1:[278,293],clump2:[278,293],clump3:[278,293],clump:293,cluster:[],clutter:[3,9],cmap:460,cmatrix:230,cmax:410,cmd:[11,12,276,471],cmin:410,cmm:[],cn1:204,cn2:204,cna:[],cnn:204,cnr:[9,13],cnt:[394,464],co2:[40,164,296,357],coars:[7,9,29,36,40,54,177,278,293,308,392,426,472],coarser:[349,486],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,171,172,173,178,334,335,340,376,394,398,415,428,430,433,460,462],coeffcient:460,coeffici:[],coefficienct:383,coefficient0:385,coefficient1:385,coeffieci:[6,367],coeffincientn:385,coexist:[9,228,387],cohes:[6,388,410],coincid:[122,329,374,408,409,455],colberg:189,cold:[6,150,228,232,359,481],coldest:316,coleman8:9,coleman:[9,118,164,294],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,145,153,160,162,165,188,191,203,216,242,248,278,288,291,293,331,348,357,359,377,397,460,467,473,479,490],collid:[222,308,330],colliex:164,collinear:[3,278],collis:[3,239,308,326,330,384,391,453],colllis:308,colloid:[],colombo:39,colon:[192,331,461],color1:191,color2:191,color:[3,9,41,188,190,191,211,229,283,288],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,145,153,160,162,163,164,185,188,191,194,202,203,204,206,207,208,209,242,249,250,283,293,309,310,320,330,389,393,423,424,461,475,477,486],colvar:[],colvarmodul:12,com:[],comamnd:217,comand:[214,462],comannd:363,comb3:[],comb:[],comb_1:285,comb_2:285,combiant:380,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,144,158,188,190,200,206,233,242,252,276,282,312,321,329,332,334,348,349,351,355,363,377,379,380,387,388,394,406,407,432,442,444,446,449,452,463,468,473,481,486],come:[],comfort:[12,13],comm:[0,3,12,61,73,189,233,235,236,349,358,363,383,415,420,443],comm_modifi:[],comm_modift:61,comm_styl:[],command:[],comment:[2,7,11,12,38,56,171,185,188,237,293,320,357,358,364,385,386,388,398,410,417,424,431,432,442,443,444,445,446,449,457,458,460,481,486],commerci:7,commmand:[3,6,12,59,107,271,454,455,457,474,489],common:[],commonli:[3,6,12,17,25,57,59,105,167,188,190,192,344,392,401,432,444,446,460,463,472],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,169,190,191,211,212,213,215,216,217,233,235,239,241,242,243,252,275,282,284,285,286,293,308,320,331,346,348,359,360,361,363,384,419,457,458,462,469,470,486,488,490],communc:348,comp:[7,189,235,236,296,349,358,387,415,420,425,439,443,445],compact:[63,194,376,441],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,148,163,164,173,184,191,221,284,331,333,348,349,356,358,410,431,455,474,475,481,485],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,172,173,184,334,335,343,375,441],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,176,188,192,196,202,203,204,206,207,208,209,211,275,287,312,315,322,325,328,348,363,395,413,415,443,457,458,486],compens:[6,212,213,291,359,387],compet:319,competit:349,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,163,188,189,190,192,233,319,349,363,413,460,461,465,486],compl:17,complain:[12,17],complement:410,complementari:[7,379,399],complet:[3,6,9,12,15,41,59,71,191,207,211,216,242,276,279,282,308,319,321,333,347,358,363,388,428,430,448,455,460,465,468,472,474,477,481,486],complex:[6,8,11,12,13,25,40,42,62,140,142,153,165,166,239,304,329,346,358,387,413,443,458,460,463,486],compli:[315,319],complic:[6,7,9,12,13,201,228,458],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,160,161,162,188,190,191,197,198,202,203,204,205,206,207,208,209,210,214,215,217,218,223,226,231,235,236,239,242,244,248,249,251,252,253,256,257,258,269,270,272,273,275,276,277,280,291,293,295,296,297,301,302,305,308,311,312,313,315,322,323,328,329,330,348,351,355,356,357,358,363,383,387,391,408,409,428,430,431,432,460,461,470,478,486,487],componenet:6,composit:[6,201,239,385],compound:[378,387,388,449],compres:[71,114,203],compress:[3,59,71,114,168,188,190,191,203,217,250,256,280,283],compris:[40,329,397,425,448],compton:[118,164],comptu:3,compuat:349,comput:[],computation:[3,6,212,213,320,369],computational:481,compute_arrai:8,compute_fep:[196,407],compute_group_group:228,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,294],compute_scalar:8,compute_temp:8,compute_ti:196,compute_vector:8,compute_xrd:164,concaten:[2,3,489],concav:329,concentr:385,concept:[6,145,155,203,469],conceptu:[3,6,71,153,215,217,358,379,394,410,465],concern:[6,73,87,189,229],concis:[11,319],conclud:12,concret:8,concurr:[9,16,349,486],conden:[320,444,446],condens:[6,147,320,365,381,385,399,449],condit:[],conducit:6,conduct:[],cone:463,confer:413,confid:[3,474],config:[12,188,457],configfil:216,configur:[1,2,6,12,15,17,38,59,122,167,185,187,188,190,194,215,216,217,218,222,228,235,236,264,276,284,319,346,356,358,365,369,386,410,413,442,444,446,449,455,460,462,463,474],confin:[460,474],conflict:[3,12,40,415,458],conform:[3,6,13,59,214,215,251,292,297,319,342,358,387,472],confus:[3,449],conjuct:383,conjug:[7,8,236,355,387,423,424],conjunct:[6,7,71,86,87,114,148,153,159,165,169,191,195,196,236,239,243,264,279,280,284,285,286,288,293,308,316,323,328,348,349,358,370,372,376,379,383,387,393,399,415,418,426,447,460,463,467,481,490],connect:[3,6,87,150,168,214,233,278,293,296,305,358,380,391,440,446,457,458,464,481],conput:3,consecut:[3,11,12,39,71,165,191,195,196,218,233,234,379,399,403,455,461,463],consequ:[1,6,201,320,398,474],conserv:[3,194,201,214,221,222,229,232,236,238,239,243,248,250,252,264,293,296,311,312,316,323,324,328,358,382,383,391,405,431,469,474],consid:[6,9,70,71,78,87,115,147,150,151,168,188,191,195,196,202,204,207,211,213,214,218,240,253,275,293,315,316,319,320,323,349,376,387,394,424,425,431,440,455,456,458,461,462,463,465,468,470,478,481,486],consider:[6,8,236,237,311,312,313,363,469],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,145,148,150,165,177,187,192,197,198,203,217,218,221,223,226,229,236,237,238,249,252,254,255,256,257,258,259,260,262,263,264,265,267,268,269,270,271,272,280,283,288,290,292,293,311,312,313,314,324,348,349,351,357,358,363,365,369,371,377,379,387,390,394,408,409,410,413,415,425,428,430,431,443,450,458,460,461,463,464,465,472,481,486],consistent_fe_initi:200,consit:293,constant:[],constitu:[3,6,242,293,325,329,377,425],constitut:[428,430],constrain:[3,6,8,143,144,145,146,148,151,152,153,154,155,157,158,194,203,218,228,229,234,242,246,278,279,291,293,296,306,316,323,356,357,387,465,472,481],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,118,140,164,215,252,275,292,329,359,363,382,413,415,440,442,443,463,464,479,486],constructor:8,consult:424,consum:[1,288,419,486],consumpt:346,contact:[],contact_stiff:[427,429],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,145,153,163,164,165,167,171,173,184,185,188,190,191,192,194,195,196,200,202,203,204,206,207,208,209,211,216,218,223,230,234,235,236,237,239,250,264,274,275,278,279,281,283,286,290,293,294,298,308,315,319,320,329,330,333,347,349,357,358,361,362,364,365,366,369,378,379,382,385,386,387,394,395,410,413,417,421,422,423,424,432,442,443,444,445,446,447,449,455,456,457,458,460,461,462,463,465,467,469,472,474,477,478,481,486,488,490],content:[12,18,424,476,478],context:[3,6,8,12,17,117,191,212,213,218,278,290,324,355,452,460,467,476,485,486,487],contibut:70,contigu:457,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,161,191,194,195,196,201,203,204,205,206,207,208,209,211,214,215,216,217,218,228,229,230,232,233,234,236,237,238,244,249,250,252,254,255,256,257,258,269,270,271,272,277,279,282,283,293,294,297,307,308,310,317,318,320,326,329,333,347,362,363,369,383,384,401,404,423,424,425,428,430,445,455,458,460,462,463,468,474,477,478,486,488],continuum:[6,7,9,200,320,428,430],contour_integr:200,contract:[59,215,217,252,280,293],contradictori:3,contrain:296,contraint:264,contrari:[230,237],contrast:[1,6,42,55,64,147,150,217,331,428,430,452,489],contrib:320,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,196,201,202,203,204,206,207,208,209,215,228,236,239,242,243,247,253,270,271,278,279,287,290,293,294,296,322,348,356,358,366,383,384,385,387,394,408,409,413,415,423,424,431,472,478,481],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,174,188,190,194,200,201,211,215,216,217,232,233,236,237,252,254,255,256,257,258,280,285,293,299,300,311,312,313,320,324,346,348,360,387,390,413,423,424,427,429,442,446,455,457,469,475,476],control_typ:200,controlfil:424,convect:91,conveni:[6,12,29,188,192,209,294,351,432,486],convent:[3,8,9,29,176,183,184,191,292,305,332,385,387,486],converg:[3,6,41,88,188,190,192,197,211,214,215,223,226,256,283,285,288,292,296,354,355,356,358,378,379,399,431,455,467,474],convers:[3,8,140,190,191,201,204,280,348,379,380,381,387,399,403,407,418,458,474,485],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,165,172,188,190,191,209,250,331,334,336,339,342,351,358,364,385,413,444,446,453,458,460,461,462,467,477,481,485,486,488,490],convex:329,convinc:[7,12],cook:9,cooki:7,cool:[7,155,232,291],cooordin:188,cooper:[5,7],coord123:114,coord1:[3,114,203,207,208],coord2:[3,114,203,207,208],coord3:[3,114,203,207,208],coord:[],coordb:431,coordbb:431,coordiat:356,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,148,154,160,162,163,165,169,187,188,189,190,191,192,194,197,202,203,206,207,208,211,212,213,214,215,216,217,218,221,223,224,226,228,231,232,233,234,235,236,237,249,251,252,254,255,257,258,270,273,274,275,278,279,280,290,291,293,295,296,297,302,305,306,307,308,310,318,319,320,327,328,330,331,351,356,357,358,363,364,365,368,386,431,455,460,461,463,465,468,470,474,481,486,487],coordn:[114,203],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,190,320,358,376,423,458],copper:453,coproccesor:16,coprocessor:[1,4,7,9,16,17,363,473],coproprocessor:17,copy_arrai:8,copyright:[7,8,278],coral:191,core:[],core_shel:147,coreshel:[6,9,372,379,381],cornel:[6,171,472],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,190,329,330,351,448,460],cornflowerblu:191,cornsilk:191,corpor:16,corr:378,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,147,152,159,190,217,228,230,236,252,253,270,278,280,283,319,325,329,348,358,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,451,452,453,460,475,478,481],correction_max_iter:200,correctli:[3,8,9,11,17,71,81,102,103,143,144,146,148,150,151,152,153,154,157,158,161,188,191,197,218,223,226,237,246,252,253,286,293,296,305,307,326,329,358,359,363,381,409,413,457,458,460,470,485,487],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,143,144,152,159,164,171,172,173,174,175,176,177,179,180,182,183,185,188,190,191,195,196,197,203,205,206,207,208,210,213,215,217,224,226,227,231,236,239,240,248,249,250,252,254,255,256,257,258,259,264,267,269,270,272,275,276,280,285,293,295,296,311,313,315,324,325,326,328,329,330,332,334,335,336,337,338,339,342,344,349,353,355,357,358,364,365,367,370,371,372,373,374,375,376,377,378,379,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,413,415,416,417,418,420,421,423,424,425,426,431,432,433,442,443,444,445,446,448,449,451,452,453,455,457,458,460,461,463,473,474,475,477,478,481,486],correspondingli:[408,409,469],cosin:[],cosineshift:27,cosmo:[230,235],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,164,190,191,203,207,208,211,212,213,225,252,285,320,348,349,361,379,399,403,413,415,442,457,469],costheta0:[442,444,446,449],costheta:421,costli:[11,88,230,359],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,145,155,160,162,178,188,190,191,195,196,203,204,207,211,217,226,235,282,283,284,288,291,293,295,308,309,315,319,320,321,325,329,331,333,340,345,347,354,356,359,363,366,389,393,394,423,424,456,457,458,460,462,464,467,468,476,481,486,487],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,116,141,166,170,284,286,321,348,349,356,363,370,372,373,374,375,378,379,380,381,382,387,391,392,394,399,403,407,415,418,423,424,426,431,441,446,447,449,452,465,472,478,481,485],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,114,116,117,153,163,169,197,198,201,203,206,207,208,210,211,218,223,225,228,234,252,264,279,296,311,312,329,349,356,357,358,360,363,389,393,415,478,486],counter:[326,455,466,468,474],counteract:228,counterbal:232,counterpart:[188,293,455],counterproduct:18,coupl:[],courant:298,cours:[3,8,126,128,159,188,195,196,229,292,305,319,325,327,328,330,331,349,408,433,457,460,473,481,486,488],courtesi:351,cov:431,coval:[6,29,387,410,431,481],covari:230,cover:[6,71,185,191,200,239,387,397,448],coverag:[71,207],cpc:235,cpp:[1,3,6,8,9,11,12,13,87,188,195,196,226,296],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,191,194,205,221,237,321,346,349,363,376,441,455,473,474,477,478,479,486],cpuremain:478,cr2:164,cr3:164,crack:[4,359],crada:[5,7],crai:[5,7,13,18,188],crash:[3,12,359,481],craympi:363,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:200,create_faceset:200,create_group:189,create_nodeset:200,createatom:[],creation:[],crimson:191,critchlei:278,criteria:[3,116,166,190,191,212,213,214,247,356,420,448,462,465,486],criterion:[12,41,121,163,165,168,201,211,214,228,264,285,298,326,331,356,358,378,387,391,431,465,474,475],criterioni:474,critic:[6,48,49,250,315,320,356],cross:[3,12,22,71,89,144,173,188,190,202,207,213,217,249,251,270,293,301,305,307,316,323,335,351,358,374,383,384,385,392,393,394,399,401,403,421,426,428,430,444,446,453,460,464,470,488],crossov:1,crossterm:460,crozier:[0,7,13],crucial:283,crystal:[4,6,13,73,274,275,318,351,359,464,478,481],crystallin:[6,275,351,445,481],crystallis:315,crystallogr:[118,164],crystallograph:[351,478],crystallographi:[118,164,351],cs1:164,cs_chunk:6,cs_im:[40,460],cs_re:[40,460],csanyi:[140,422,432],cscl:410,csequ:6,csh:[11,12,376],cshrc:[11,12],csic:[386,442,444,446,449],csinfo:6,csisi:[386,442,444,446,449],csld:[],cst:385,cstherm:6,cstyle:457,csvr:[],ctcm:[364,385],ctemp_cor:221,cterm:297,ctr:9,ctype:11,cu1:164,cu2:164,cu3au:410,cube:[6,41,163,168,211,221,329,351,481],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:369,cummul:[3,6,209,212,213,214,216,225,230,236,238,308,311,312,313,314,316,323,393,478],cumul:[6,201,203,206,207,208,222,228,236,250,252,256,264,293,294,358],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,145,153,155,161,163,166,169,188,189,190,191,192,195,196,200,203,207,208,209,211,212,213,214,215,216,217,218,222,223,226,228,230,233,234,236,242,249,252,253,257,258,264,269,270,272,278,284,285,287,290,291,292,293,296,297,298,299,300,301,302,304,306,307,308,311,312,313,319,320,323,324,325,326,327,328,330,331,333,346,347,348,349,352,353,355,356,357,358,363,369,376,378,382,385,387,388,391,394,395,398,408,409,410,411,412,415,421,423,424,427,428,429,430,433,444,446,447,450,455,456,457,458,460,461,462,463,464,466,467,468,470,472,474,475,477,478,486,487,488,489,490],curv:[6,165,228,275],curvatur:[390,425,453],custom:[],cut0:458,cut1:469,cut2:469,cut:[],cuthi:[274,286],cutinn:[371,408,409],cutlo:[274,286],cutmax:421,cutoff1:[375,382,399,403,407,418,426],cutoff2:[370,372,373,375,381,382,399,403,407,418,426],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,163,166,168,213,214,219,274,283,284,286,288,290,293,308,321,325,329,331,346,348,349,356,359,360,361,363,364,365,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,383,384,385,386,387,388,389,390,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,431,432,433,434,435,436,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,458,462,465,469,481,486],cutoffa:386,cutoffc:386,cuu3:385,cval:164,cvd:315,cvel:297,cvff:[],cwiggl:[3,249,325,328,330,486],cyan:[2,190,191],cycl:[3,228,250,252,253,256],cyclic:[3,185],cygwin:12,cylind:[3,4,190,234,279,326,329,463],cylindr:[6,234,305,326],cypress:363,cyrot:369,cyrstal:275,d3q15:239,d3q19:239,d_double_doubl:15,d_e:320,d_flag2:282,d_flag:282,d_name:[113,188,282,310,470],d_single_doubl:15,d_single_singl:15,d_sx:282,d_sy:282,d_sz:282,daan:318,dai:12,daili:12,daivi:270,damag:[],dammak:288,damp:[3,6,194,199,236,237,238,243,252,253,256,280,283,288,293,311,312,324,326,327,355,356,358,370,372,374,379,382,387,391,399,407,418,426,441,447,474,481],damp_com:237,damp_drud:237,dampen:[293,481],dampflag:[326,391],dan:17,danger:[3,12,228,331,383,478],dangl:168,daniel:9,darden:[349,382],darkblu:191,darkcyan:191,darken:190,darkgoldenrod:191,darkgrai:191,darkgreen:191,darkkhaki:191,darkmagenta:191,darkolivegreen:191,darkorang:191,darkorchid:191,darkr:191,darksalmon:191,darkseagreen:191,darkslateblu:191,darkslategrai:191,darkturquois:191,darkviolet:191,dasgupta:284,dash:[391,477],dat:[6,91,185,200,456],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,294],dataset:294,datatyp:3,date:[0,6,12,13,423,424,486],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,188,204],davi:325,david:[9,19,348,349,444,446],daw:[385,421],dbg:14,dcd:[3,6,7,188,189,190,191,192,276,461,465],ddim:187,deactiv:407,dealt:235,debug:[6,7,11,12,13,14,17,118,122,164,165,276,281,346,348,363,395,415,450,458,459,462,467,470,477,486],deby:[],decai:[379,453],decid:[3,6,12,16,71,249,282,293,321,475],decipher:351,declar:189,declin:308,decod:190,decompos:[87,432],decomposit:[3,5,7,18,62,200,276],decoupl:[6,481],decreas:[3,188,197,198,205,214,217,223,226,228,236,319,348],decrement:297,deepli:345,deeppink:191,deepskyblu:191,def:[12,13,458],defaul:61,defect:[6,70,163,413],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,171,172,173,174,175,176,177,179,180,182,183,184,185,186,187,188,189,190,191,194,195,196,197,198,199,200,201,202,203,204,206,207,208,209,210,211,212,213,214,215,217,218,221,222,223,226,227,228,231,234,235,236,237,238,239,247,249,251,252,253,254,255,256,257,258,260,261,262,265,267,268,269,270,271,272,274,275,276,278,279,280,282,284,286,291,293,294,295,296,298,302,306,308,310,311,312,313,314,316,317,318,320,322,323,325,326,327,328,329,330,331,333,334,335,336,337,338,339,342,343,344,346,348,349,351,353,355,356,357,358,359,360,361,362,363,365,366,367,368,370,371,372,373,374,375,376,377,379,380,382,383,384,386,387,389,390,391,392,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,413,414,415,416,417,418,420,421,423,424,425,426,427,428,429,430,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,457,458,460,461,463,464,465,466,469,470,471,472,474,475,477,478,481,482,483,484,485,486,487],definit:[2,3,6,8,12,13,78,80,116,140,191,203,204,205,206,207,208,209,217,234,256,294,310,322,325,328,330,332,343,346,357,366,369,377,387,397,421,428,430,432,448,458,460,462,469,471,485,486],defint:478,deform:[],deg2theta:164,deg:481,degener:[3,278],degrad:[8,18,275,349,469],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,164,165,171,172,175,176,183,185,187,190,203,214,221,228,230,231,236,237,242,252,253,256,257,258,269,270,272,276,278,292,293,296,311,312,313,318,334,336,339,342,344,356,382,385,393,470,478,481,487],degress:[145,203],del:474,delai:[3,6,12,359,384,478],deleg:394,delet:[2,3,7,8,12,54,57,60,63,163,168,169,194,203,204,206,207,208,209,212,214,225,228,252,294,311,312,331,333,347,357,359,362,415,460,461,463,471,472,477,482,484,486,487],delete_atom:[],delete_bond:[],delete_el:200,deli:187,delimit:[458,486],deloc:[253,387,431],delr:410,delt_lo:474,delta:[],delta_1:369,delta_3:369,delta_7:369,delta_conf:3,delta_ij:[410,421],delta_mu:3,delta_pi:369,delta_r:421,delta_sigma:369,delx:187,delz:187,demand:288,demo:11,demon:273,demonstr:[283,410],den:279,dendrim:393,denniston:[9,239,241,242,243,275],denomin:[7,170],denot:[118,221,237,275,286,288,379,392,394,424,428,430],dens:[71,214,387],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,151,163,165,195,196,200,203,207,208,211,217,226,239,242,245,246,275,279,280,284,320,325,351,353,357,364,369,385,410,411,412,421,425,431,435,437,438,439,460,469,470,478,485],density_continu:430,density_summ:430,depart:[0,7],departur:[250,283],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,143,148,152,153,159,165,166,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,190,191,194,195,196,197,198,201,203,205,206,207,209,210,211,213,215,217,223,224,227,230,231,232,234,236,237,239,241,242,249,252,254,255,256,257,258,259,267,269,270,272,274,285,288,290,293,295,296,302,308,311,312,313,315,317,319,320,322,324,325,328,329,330,331,333,334,335,336,337,338,339,342,344,349,351,356,357,359,360,361,363,364,365,367,368,369,370,371,372,373,374,375,376,377,378,379,380,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,413,414,416,417,418,420,421,423,424,425,426,431,432,433,441,442,443,444,445,446,447,448,449,451,452,453,455,457,460,462,463,466,470,472,474,477,478,480,486,487],dependend:6,depflag:12,dephas:[455,474],depos:218,deposit:[],deprec:[284,423],depth:[51,144,190,320,390,425],dequidt:9,der:[87,107,377,378,407,423,424,452,481],deriv:[6,7,8,9,38,56,63,87,140,159,185,204,215,217,228,236,249,252,254,255,256,257,258,274,280,284,288,317,318,320,325,326,329,355,357,365,369,377,382,387,388,392,401,405,406,410,413,423,424,441,443,452,481],derjagin:452,derlet:274,descend:191,descent:[7,355],descib:[40,284],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,144,145,149,150,153,156,158,159,163,164,165,167,168,177,182,185,188,189,194,195,196,203,204,205,206,207,208,209,211,214,215,216,217,218,220,221,229,230,233,234,235,236,237,238,239,241,242,243,247,251,252,253,256,263,271,274,276,281,282,283,284,285,286,293,297,305,308,309,310,311,312,313,314,315,316,317,318,323,325,326,328,333,348,349,351,354,355,356,357,358,362,365,366,368,370,371,372,374,375,376,377,378,379,382,385,387,388,390,391,392,394,399,400,401,402,403,404,405,406,407,408,409,410,413,414,420,421,422,423,424,425,426,431,432,433,440,441,442,443,444,445,446,447,449,451,452,453,455,457,458,460,461,463,464,470,473,474,477,486,487,488],descript:[],descriptor:[140,188,395],deserno:349,design:[0,3,6,7,8,9,11,13,14,15,17,118,147,150,164,200,214,220,221,252,253,274,275,294,315,320,366,367,368,371,374,379,381,387,407,408,409,411,412,421,424,443,469],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,112,117,141,147,165,178,187,203,209,215,217,226,228,229,236,237,238,242,252,270,278,279,280,281,284,288,293,296,308,311,312,313,314,319,326,340,345,348,349,351,354,356,357,358,383,385,393,408,409,442,444,446,456,457,458,460,464,469,474,475,477,478,486,487,488],desk:7,desktop:[4,6,7,10,12,190],despit:481,destabil:369,destre:342,destroi:[11,39,212,213],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,143,144,145,148,158,159,160,162,165,166,169,170,173,184,188,190,191,194,195,196,200,203,204,205,206,207,209,211,213,214,215,216,217,218,226,228,229,230,231,233,234,236,238,239,243,249,250,251,252,253,254,255,256,257,258,262,264,269,270,271,272,275,278,279,280,282,283,285,286,287,293,296,308,311,312,313,314,315,316,318,319,320,321,322,323,324,331,333,335,343,348,349,352,356,357,359,360,363,364,365,366,368,369,371,373,374,375,376,377,378,379,382,383,387,388,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,410,414,415,420,423,424,425,431,432,433,441,448,451,452,458,460,461,462,463,465,466,469,470,472,475,478,479,486,487,490],detect:[2,3,12,61,63,86,227,279,319,358,378,393,398,455,457,460,471,474,486],determ:363,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,153,154,163,164,165,187,188,190,191,192,193,197,198,199,202,203,204,205,206,207,208,209,210,211,215,217,218,221,223,228,231,232,234,236,237,242,247,249,250,252,257,258,269,270,272,274,276,280,283,290,291,292,293,294,295,298,300,302,308,311,312,313,315,321,322,325,326,327,328,329,330,331,343,348,349,351,357,359,360,363,365,366,373,378,382,384,385,389,391,394,395,403,410,413,415,424,425,431,440,443,447,452,457,460,461,463,465,467,470,474,476,477,479,485,486,487],detil:108,devan:[9,426],devanathan:446,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,233,256,278,283,284,287,365,369,387,412,413,431,449,462],devemi:9,deviat:[250,256,274,389],deviator:9,devic:[1,3,12,15,17,233,363],device_typ:363,devin:[285,378],devis:412,dfactor:190,dff:481,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,349],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,287,413],dhi:[59,187,217,279],dhug:[250,283],dhugoniot:[250,283],dia:410,diagnost:[],diagon:[3,6,83,140,141,142,215,252,280,293,323,428,430],diagonalstyl:432,diagram:[41,118,164,184,211,276],diallo:393,diam:[190,191,279,357],diamet:[3,6,40,113,165,188,190,191,195,196,236,279,293,308,324,326,357,377,390,391,397,401,425,448,452,460,461,470],diamond:[351,387,410],diamter:[40,279],dick:6,dicsuss:249,dictat:[201,250],did:[3,12,356,383,384,385,391,415,444,446,468],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,161,322,348],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,143,144,145,146,148,151,152,153,154,155,157,158,159,165,166,168,173,184,185,187,188,190,191,194,196,199,201,203,206,211,212,213,214,215,216,217,221,227,228,229,230,231,232,233,236,237,239,249,252,253,254,255,257,258,260,262,265,267,268,269,272,274,276,278,280,283,284,285,288,291,293,296,297,305,306,308,311,312,313,316,317,318,320,323,324,325,326,329,333,334,343,345,347,348,349,351,352,354,355,357,358,360,361,362,363,364,365,369,373,374,376,377,378,383,385,387,390,391,392,394,397,399,400,402,403,410,411,412,414,415,417,421,423,424,425,426,427,428,430,431,432,433,441,442,443,444,446,448,449,452,454,455,457,458,460,462,463,464,465,468,469,470,472,474,475,477,478,479,481,485,486,487,488],differenti:[1,3,6,29,185,348,379,421,445],difficult:[215,276,363,393,469],difficulti:[296,423],diffract:[],diffus:[],digit:[2,3,191,333,413],dih_table1:185,dih_table2:185,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:213,dihydrid:387,dij:296,dilat:[],dim1:3,dim2:3,dim:[3,59,71,143,146,147,148,151,152,153,154,155,157,165,187,207,217,234,326,351,410,463,485,486,487],dimdim:486,dimems:275,dimens:[],dimension:[3,39,112,118,140,143,145,146,147,148,151,152,153,154,155,157,164,186,203,207,251,275,320,351,354,358,421,460,470],dimensionless:[105,121,122,124,127,129,131,136,140,320,349,432,452],dimentionless:135,dimer:[6,293,410],dimgrai:191,dimstr:[41,211],dinola:[280,311],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,188,310,481],dir1:471,dir2:471,dir:[1,3,4,8,9,11,12,250,274,283,307,421,423,424,458,471,486],dirac:140,direc:421,direct:[],directli:[3,6,8,9,11,12,87,113,140,142,188,189,190,197,223,230,234,239,275,294,312,324,326,327,328,329,351,355,363,364,365,370,372,373,379,382,385,387,399,403,415,418,426,440,458,470,471,472,478,486],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,192,216,235,278,284,287,304,308,317,318,358,362,364,365,369,376,378,379,385,386,388,395,396,407,410,411,412,413,417,421,422,423,424,431,432,442,444,445,446,449,458,460,461,462,471,486],disabl:[3,12,16,320,398,458,473,486],disadvantag:[6,211],disallow:[188,217,252],disappear:462,discard:[2,3,41,71,205,207,211,321,329,457,462,463],discontinu:[9,185,356,405],discourag:410,discov:[13,321],discret:[6,8,40,42,190,191,236,239],discuss:[],disk:[6,84,85,158,186,218,228,279,458],disloc:[70,413],disord:[39,70,413],disp:[],dispar:425,disperion:[382,403],dispers:[3,6,7,9,163,275,348,349,373,382,403,408,415,424,443,449],displac:[],displace_atom:[],displace_box:59,displacemet:463,displai:[11,13,22,37,44,55,173,184,188,190,335,343,376,441],dispters:3,disregard:413,dissip:[6,229,236,275,317,318,371,383,391,408,409,441],dissolut:212,dist:[6,69,91,108,117,188,276,292,384,440,455,487],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,154,160,163,165,166,167,168,172,187,188,190,191,199,203,207,208,212,213,214,215,217,218,219,222,228,234,239,249,250,251,252,256,264,274,275,279,283,284,291,292,293,296,297,301,305,306,307,308,315,316,318,319,320,323,325,326,327,328,329,330,334,348,349,351,354,356,358,359,360,363,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,383,384,385,386,387,389,390,391,392,393,397,398,399,400,401,402,403,404,405,406,407,408,409,410,413,414,415,416,417,418,419,420,421,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,455,458,460,463,469,470,474,478,481,485,487],distinct:[6,221,290,348,425],distinguish:[6,86,140,242,387,459],distort:364,distrbut:364,distribut:[],distro:[111,376,420,421],ditto:[8,11,12,14,15,16,17,18,115,213,453,458],div:8,divd:117,diverg:[3,12,39,293,318,462,481,488],divid:[3,6,16,41,91,112,117,126,128,141,162,163,173,184,191,203,204,206,211,217,274,316,323,328,348,356,358,388,424,431,449,469,477,486],divis:[6,239,369,397,407,457,460,478,486],dl_poli:[6,7],dlambda:159,dlammps_async_imd:233,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,190],dlammps_gzip:[3,12,188,190,319,460,461,465],dlammps_jpeg:[3,12,190],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,190],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,188],dlen:470,dlmp_intel_offload:[12,16],dlo:[59,187,217,279],dlopen:6,dlvo:[7,377,452],dm_lb:239,dmax:[308,354],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,141,144,145,158,160,162,165,166,167,173,184,188,189,190,191,192,194,195,196,201,202,203,204,205,206,207,208,209,218,228,236,237,247,252,253,257,258,262,269,270,271,272,279,282,293,305,308,311,312,313,322,326,329,331,333,335,343,347,356,357,358,363,364,365,368,376,378,379,385,386,388,393,394,396,397,410,411,412,415,417,420,421,422,432,441,442,444,446,448,449,458,460,461,462,463,465,468,469,470,477,478,486,487,488,489],docuement:425,dodgerblu:191,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,116,117,118,142,144,145,147,148,153,155,159,164,165,166,167,169,171,173,178,184,185,187,188,189,190,191,194,200,201,203,207,210,211,213,214,215,217,221,223,225,228,229,232,234,236,237,239,242,248,252,253,254,255,257,258,269,270,271,272,280,281,282,286,288,291,293,308,311,313,315,316,320,323,324,325,328,329,330,331,336,337,339,340,342,347,348,349,350,351,357,358,359,364,365,366,367,368,369,371,373,374,375,377,378,379,380,382,383,384,385,386,387,389,390,391,392,394,395,396,397,398,401,402,404,405,406,408,409,410,411,412,413,415,421,422,423,424,425,427,428,429,430,431,432,433,434,435,436,437,438,439,440,442,443,444,445,446,447,448,449,451,452,453,455,456,457,458,460,461,462,463,464,467,468,470,471,472,473,474,477,478,481,486,490],doegenomestolif:7,doesn:[3,7,8,12,165,188,201,207,208,305,357,359,363,365,378,386,396,423,424,442,444,445,446,449,460,462],dof:[3,8,112,144,145,158,203,293,487],dof_per_atom:[145,203],dof_per_chunk:[145,203],doff:[357,460],doi:[6,216],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,154,164,167,187,189,190,191,194,201,211,215,217,218,232,235,239,252,253,276,288,293,320,325,326,348,349,358,363,384,415,455,457,460,464,477],domin:[1,387,474],don:[0,8,11,12,13,116,168,197,223,237,282,329,410,431,458,460],donadio:312,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,159,162,165,168,185,188,190,191,200,201,203,205,206,207,208,209,211,212,213,214,215,217,218,226,228,233,234,236,237,244,252,257,258,269,270,272,273,275,276,277,282,290,293,294,296,308,311,312,313,315,317,318,331,333,347,348,349,356,358,359,362,363,365,373,385,394,395,396,403,409,410,415,423,440,443,448,455,456,457,458,461,464,465,468,478,479,481,486,487],donor:393,dot:[141,161,197,223,231,251],doti:[369,421],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,217,226,281,329,333,347,349,362,363,369,388,392,413,423,424,456,460,464,468,473,486,487],dover:200,down:[3,6,7,8,11,39,71,215,228,236,308,324,363,387,415,431,459,479],downhil:[354,355],download:[5,7,8,9,11,12,13,17,233,395,422],downsid:6,downward:290,dozen:[8,12,107,194,423,424],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:245,dproduct:366,dr_ewald:[118,294],drag:[],dragforc:239,drai:[250,283],drain:[232,324,356],dramat:[59,187,212,213,214,215,217,252,308,311,312,349,363,415,431,457],drautz:369,draw:190,drawback:282,drawn:[188,190,191,229,455],drayleigh:[250,283],dreid:[],drfourth:105,drho:[113,364,385],drift:[6,103,105,229,230,236,237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113,end1i:113,end1x:113,end1z:113,end2i:113,end2x:113,end2z:113,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,40,41,57,59,71,113,168,169,172,187,188,190,191,192,195,196,204,206,208,209,214,217,221,229,234,236,237,238,251,252,253,264,280,292,293,297,308,311,312,313,314,316,319,320,323,327,330,331,347,348,357,358,362,363,383,385,390,413,425,428,430,432,433,447,450,455,458,460,461,462,463,465,467,468,472,476,478,481,486,490],end_of_step:8,endbondtors:[3,172,178,460],endif:8,energet:[214,365,424],energi:[0,1,2,3,4,5,6,7,8,9,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,36,38,40,43,45,46,47,48,49,51,53,54,56,63,65,69,82,83,84,85,86,87,88,91,94,95,96,97,98,99,101,102,107,108,109,110,112,123,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,188,191,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,334,336,337,338,339,342,344,348,349,354,355,356,358,359,363,364,365,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,423,424,425,426,431,432,433,434,435,440,441,442,443,444,445,446,448,449,450,451,452,453,455,458,460,465,469,470,472,474,476,477,478,481,485,486,489],energy_compon:431,energy_update_freq:424,enforc:[6,57,58,104,187,188,189,190,192,194,201,214,217,252,273,275,285,293,296,333,348,399,457,486,487],enforce2d:[],eng:[11,65,69,108,188,226,331,333,378,412],eng_previ:333,engin:[200,217,278,297,317,385,411],engr:[423,424],enhanc:[196,200,455],enlarg:[59,190],enough:[3,40,61,86,165,166,168,211,237,279,283,288,293,321,325,326,329,359,363,379,419,460,464,465],enpub:385,enrti:[],ensembl:[],ensight:6,ensur:[3,6,140,188,201,205,215,228,229,252,298,319,349,369,384,407,442,449],enter:[57,155,388,413,449,474],enthalpi:[123,254,255,385,477,478,486],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,141,145,164,165,191,194,195,196,203,207,208,211,214,216,225,228,229,232,236,237,248,252,254,255,256,257,258,274,276,278,291,293,306,320,322,333,363,382,403,415,443,460,468,469],entireti:[397,448],entiti:[6,8,40,42,188,293],entri:[3,8,12,38,42,56,65,69,79,92,108,115,118,127,130,131,132,133,134,136,137,138,163,185,191,206,207,208,216,283,331,357,369,386,410,417,424,432,442,443,444,445,446,449,486],entropi:474,entry1:[38,56,191,376,443],entry2:191,entryn:191,enumer:[166,188],enumuer:6,env:363,environ:[1,3,6,11,12,16,17,18,190,230,235,274,363,364,369,376,378,386,387,421,444,457,471,486],epair:[107,191,389,393,423,424,478],epen:[423,424],epfl:[230,235],epp:382,epq:382,eps0:452,eps14:407,epsilon0:446,epsilon:[3,6,36,45,46,50,53,54,87,171,195,196,228,293,308,325,329,354,356,368,374,375,377,379,380,381,382,390,392,393,394,397,398,399,400,401,402,403,404,405,406,407,414,418,425,426,436,442,448,451,452,469,481,485],epsilon_0:453,epsilon_14:374,epsilon_:425,epsilon_d:380,epsilon_i:[390,415,425],epsilon_i_:425,epsilon_i_a:[390,425],epsilon_i_b:[390,425],epsilon_i_c:[390,425],epsilon_ij:415,epsilon_j:[390,415,425],epsilon_j_:425,epsilon_j_a:[390,425],epsilon_j_b:[390,425],epsilon_j_c:[390,425],epsilon_lj:425,epton:420,eqch:160,eqeq:[423,424],eqp:382,eqq:382,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,144,159,161,165,190,191,194,195,196,197,198,201,204,205,206,209,210,211,215,217,218,223,228,229,231,232,234,236,237,239,242,243,249,250,256,266,274,276,279,281,283,284,285,288,290,292,293,295,297,302,304,311,312,313,316,317,318,320,322,323,325,328,330,331,333,347,351,356,358,359,360,362,363,378,383,389,390,393,408,413,414,421,423,424,425,427,428,429,431,432,433,443,448,449,453,456,457,458,460,462,463,467,468,471,474,476,478,486,487],equat:[3,6,7,8,9,91,112,118,164,173,184,194,215,221,222,230,236,237,239,242,250,251,252,253,256,270,274,276,283,284,288,296,308,316,320,323,325,326,328,330,342,348,349,377,382,383,387,388,391,396,408,409,410,415,425,428,430,435,436,438,439,447,453,481],equi:253,equidist:251,equil:[3,284,352,467,490],equilater:470,equilibr:[3,4,5,6,7,9,59,91,165,194,201,204,214,215,228,250,252,253,270,271,283,284,285,286,316,317,318,323,378,379,423,424,456,470],equilibria:323,equilibribum:[212,213],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,148,149,172,174,215,217,228,229,230,237,239,252,256,270,283,288,292,296,297,305,308,315,316,318,323,334,336,339,342,378,410,417,431,481],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:200,equival:[6,12,13,59,61,124,125,133,138,163,167,191,206,209,215,217,228,236,252,270,280,292,293,328,383,387,431,444,446,460,463,468,469,478,481],equlibrium:6,equliibr:[284,286],er3:164,eradiu:[40,113,387,460],eras:[295,317],erat:[217,409],erc:379,erfc:[379,399,415],erforc:113,erg:485,erhart:[201,385,444,446],ermscal:366,ernst:9,eror:3,eros:410,erose_form:410,erot:[],errata:[444,446],erratum:325,erron:3,error:[],erta:391,ervel:[113,460],escap:[218,481],especi:[8,11,16,153,165,194,201,211,228,283,288,291,292,363,457],espresso:[9,287],essenti:[8,11,12,27,88,128,146,147,148,151,152,153,154,155,157,174,204,256,275,324,349,365,379,399,446,465,478],essex:29,establish:[87,232],estim:[1,3,6,10,12,38,41,56,91,141,200,211,222,250,308,315,348,349,354,415,424,443,474,478],esu:485,esub:410,eta:[6,239,252,283,284,286,324,386,388,390,421,445,449,485],eta_dot:252,eta_ij:421,eta_ji:388,etag:[40,460],etail:478,etap:252,etap_dot:252,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,143,145,146,147,148,149,151,152,153,154,155,157,159,165,167,168,169,178,188,190,191,194,195,200,201,202,203,206,207,208,209,212,213,217,218,226,228,229,236,252,279,290,294,320,321,329,333,347,348,356,357,358,359,361,385,386,394,407,409,413,419,423,424,442,444,446,449,455,458,460,461,462,467,469,470,474,476,477,478,479,481,485,486,488,490],ethernet:18,etol:[356,358,455,474],etot0:283,etot:[6,94,96,97,110,141,151,191,221,237,250,283,477,478],eu2:164,eu3:164,euler:[356,358],eulerian:200,euqat:434,europhi:239,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,87,88,91,107,117,140,142,145,155,163,165,188,190,191,195,196,197,198,200,202,203,204,205,206,207,208,209,210,217,223,229,231,232,234,235,236,237,275,281,284,295,298,302,311,312,313,322,325,328,330,331,333,348,349,354,356,363,413,415,421,427,429,431,443,455,456,458,462,463,465,467,468,469,470,474,476,478,486,487],evalut:[333,458],evan:[153,270],evanseck:[6,20,171,374,472],evapor:[],evaul:[8,356],evdwl:[107,423,424,478],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,119,166,167,181,185,188,191,194,195,196,201,202,203,206,207,208,209,211,212,213,215,217,218,221,234,237,250,252,253,275,288,290,293,294,304,308,316,320,323,325,329,331,341,348,354,356,358,363,368,387,388,391,394,415,425,449,450,460,461,463,465,466,467,469,470,472,475,477,478,479,481,490],evenli:[3,41,141,185,211,239,397,450,460],event:[],eventu:[3,6,12,15,167,284,474],ever:[54,56,235,308],evera:[377,390,425,441],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,113,119,128,153,168,188,189,190,191,192,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,222,225,226,228,230,232,233,234,239,240,248,252,253,256,273,274,275,279,280,281,282,283,284,285,286,288,290,291,293,294,296,297,308,310,311,312,313,314,315,316,319,320,321,322,323,331,333,347,349,358,359,360,363,383,384,394,407,423,424,431,437,454,455,456,460,462,464,465,467,468,469,474,475,476,478,486,490],everyth:[8,107],everywher:[116,401],eviri:387,evolut:[230,239,276,455],evolv:[239,276,321],ewald:[2,3,5,6,7,8,12,88,110,118,141,321,348,349,356,370,372,373,379,382,387,399,403,418,426,441,443,462],ewald_disp:382,ewalddisp:3,exact:[22,41,44,71,122,159,168,173,211,214,229,230,236,237,238,279,288,289,308,320,335,348,376,462,467,474,486,488,490],exactli:[3,6,12,14,17,38,41,56,59,71,91,116,144,149,156,165,185,195,196,206,211,217,222,229,236,237,238,253,263,264,271,275,283,308,313,314,327,363,376,383,385,391,394,397,408,415,443,462,463,470,474,486],exager:481,examin:[6,8,9,17,214,275],examp:[458,486],exampl:[],exce:[3,6,16,17,18,41,58,71,167,203,207,208,211,215,217,222,225,252,275,299,300,308,356,363,460,486],exceed:[3,41,59,211,217,252,308,468],excel:387,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,191,194,197,203,204,206,210,211,215,217,224,227,228,231,234,236,238,252,253,254,255,256,257,258,259,263,264,267,269,270,271,272,276,285,286,293,295,296,305,308,311,313,314,320,324,328,331,333,334,335,336,337,338,339,342,343,344,348,349,351,353,357,358,359,361,362,363,364,365,367,370,371,372,373,374,375,376,377,378,379,381,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,411,416,417,418,420,423,424,425,426,433,441,442,443,444,445,446,448,449,451,452,453,455,457,458,460,462,463,465,468,469,470,471,472,474,478,481,485,486,487,489],excess:[205,387],exchang:[2,3,6,8,9,61,62,194,200,201,228,236,285,293,316,320,323,348,363,387,475],exchange:348,excit:[9,387],exclud:[3,6,9,12,16,17,63,71,112,140,145,152,153,169,188,203,207,212,213,240,248,278,291,293,315,326,331,356,357,359,371,391,394,408,409,415,440,472],exclus:[1,3,9,12,16,87,363,378,413,415,469,479],excurs:455,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,166,190,233,287,333,347,350,362,456,458,468,471,474,486],exempl:431,exemplari:229,exemplifi:387,exert:[6,234,237,288,327,328,329,349],exhaust:[200,362,486],exhibit:[252,355,387,469],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,122,165,166,184,189,190,191,194,199,210,213,215,218,228,278,279,281,331,334,336,337,339,343,352,357,363,394,423,450,456,458,460,461,462,471,472,473,486,487,488],exit:[2,3,11,12,41,57,188,211,347,362,458,459,468,477,486],exlanatori:3,exp:[],expand:[],expans:[12,140,188,471,486],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,146,157,163,185,211,223,228,230,249,274,280,282,283,288,293,331,349,359,376,410,413,415,455,458,460,462,465,469,474,486],expens:[6,10,71,191,274,278,293,320,331,348,349,359,363,458],experi:[6,13,15,17,210,218,233,242,251,280,292,293,354,358,383,415,469,474],experienc:[6,12,241,242],experiment:[228,348,363,474],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,145,153,185,188,190,191,194,203,204,209,211,213,215,217,252,274,282,293,305,331,333,347,348,351,357,358,362,368,385,397,431,433,448,458,461,462,465,467,470,481,486,490],explan:[3,6,59,113,140,188,203,251,274,394,454,457,458,460,469],explanatori:[3,8,117,188,202,203,206,207,208,293,357,457,486],explantori:[3,289],explic:414,explicit:[6,9,11,22,44,77,87,113,116,159,173,195,196,217,299,300,335,353,365,366,369,374,376,385,387,398,408,447,454,457,461,464],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,143,152,155,163,165,171,172,174,175,176,177,179,180,182,183,185,188,191,197,207,210,217,224,227,229,231,236,252,254,255,256,257,258,259,267,269,270,272,282,283,285,293,295,296,311,313,314,320,324,328,334,336,337,338,339,342,344,357,363,364,365,367,370,371,372,373,374,375,376,377,378,379,380,382,383,384,385,386,388,389,390,391,392,393,394,397,398,399,400,401,402,403,404,405,406,407,408,411,413,415,416,417,418,420,425,426,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,451,452,453,460,462,469,470,472,473,479,481],explictli:[16,473],exploit:[9,15,17,276],explor:[118,164],expon:[3,284,286,385,390,393,407,414,426],exponenti:[87,421,442,449,453,474,486],expos:11,exposit:[200,383,384],express:[6,140,151,165,195,196,215,249,274,284,320,326,333,369,385,387,401,410,431,432,441,486],expressiont:369,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,194,197,198,201,209,210,216,219,223,226,227,228,230,231,232,234,236,238,250,252,256,264,274,275,291,292,293,295,297,302,305,307,311,312,313,314,315,317,318,320,322,325,329,330,390,410,413,424,425,432,477,478],extent:[1,3,41,45,57,71,163,167,188,199,207,211,234,327,330,348,351,365,427,429,443,457,460,463],exterior:[3,6,329],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,143,144,146,148,151,152,153,154,155,157,158,164,165,166,167,171,191,206,211,213,252,281,282,283,293,308,356,357,360,361,382,391,394,397,410,415,457,458,460,463,472,481,486],extract:[3,6,11,13,36,63,87,107,115,117,119,195,196,286,358,379,388,410,432,458,465,477],extract_atom:11,extract_comput:[11,458],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,190,205,215,217,252,318,387,445,481],extrema:407,extrins:200,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[161,322],f_a:[444,445,446],f_ave:117,f_c:445,f_f:446,f_fix_id:283,f_harm:318,f_i:421,f_id:[6,71,117,119,188,194,202,203,204,205,206,207,208,209,247,310,322,478,486],f_ij:421,f_indent:209,f_int:317,f_jj:91,f_k:421,f_langevin:320,f_max:[283,288],f_msst:250,f_r:[237,444,445,446],f_sigma:369,f_solid:318,f_ss:6,f_temp:237,face:[3,6,57,59,71,153,163,167,199,207,208,325,327,328,329,330,351,390,410,425,460,463],face_threshold:163,facet:163,facil:[0,12],facilit:[6,13],fact:[6,8,16,230,308,318,391,431,472],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,116,118,140,159,164,167,171,182,188,190,191,195,196,204,211,215,217,218,228,233,236,238,239,250,252,253,256,276,280,292,296,298,300,308,312,316,323,324,325,329,339,349,351,357,363,365,366,369,370,372,374,379,380,381,383,387,391,394,398,399,410,413,415,417,418,424,426,433,442,447,457,460,463,464,469,472,474,475,478,481,485,486],factori:[3,458],factoriz:348,fail:[3,11,12,59,169,215,218,348,356,358,381,424,458],failur:[121,428,459,486],fairli:[11,415,469,474],faken:73,falcon:233,fall:[3,6,191,206,279,458,486],fals:[86,331,333,431,486],fame:8,famili:[449,457],familiar:[0,11],fan:421,far:[3,6,12,17,57,59,61,86,188,191,192,211,212,213,215,218,252,274,292,293,308,325,336,339,354,358,359,448,458,460,465,478],farago:236,farrel:[444,446],farther:188,fashion:[6,8,41,71,165,191,194,195,196,201,207,211,213,218,228,230,234,249,250,252,254,255,256,257,258,266,269,270,271,272,282,283,285,293,297,301,307,310,318,320,324,325,326,328,330,358,394,408,463,472,486,489],fasolino:396,fast:[6,7,9,12,13,17,39,188,261,283,321,348,349,371,408,409,413,441,443,462,467,469,478,487,490],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,143,152,171,172,174,175,176,177,179,180,182,183,185,188,191,194,197,210,211,217,224,227,231,235,236,252,254,255,256,257,258,259,267,269,270,272,280,284,285,293,295,296,308,311,313,315,317,320,324,328,334,336,337,338,339,342,344,348,349,360,361,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,382,383,385,386,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,411,416,417,418,420,425,426,433,441,442,443,444,445,446,448,449,451,452,453,455,469,473,481],fastest:[1,6,14,17,153,207,320,321,363,457],fatal:[3,477],fault:[70,424],faulti:12,fava:390,favor:214,favorit:7,fbmc:315,fcc:[],fcm:[266,486],fdirect:221,fdotr:395,fdti:87,fe2:164,fe3:164,fe_md_boundari:200,featu:8,featur:[],fecr:385,feedback:[7,233],feel:[7,233,234,242,274,329,331,358,415],felling:412,felt:329,femtosecond:485,fene:[],fennel:[379,399],fep:[],ferguson:[6,171,472],fermi:[1,12,15,151,363,446],fermion:[9,387],ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,192,202,203,204,206,207,208,209,237,252,279,282,284,296,322,348,356,357,358,365,431,457,460,465,469,471,479,486,488],fewer:[1,3,11,15,16,61,242,469],fewest:3,fextern:226,feynman:276,fff:458,ffield:[378,388,423,424,431],ffmpeg:[3,12,190],ffplai:190,fft:[1,3,7,12,14,15,88,109,110,141,275,348,349,469],fft_inc:[12,349],fft_lib:12,fft_path:12,fftbench:[348,479],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:440,fictiti:[6,197,198,223,226,230,276,292,379,399,403,440],field1:[461,465],field2:461,field:[],fifth:[305,417],figur:[1,3,8,11,12,283,457,458],fij:382,file0:274,file1:[11,13,274,319,333,357,465,467,471],file2:[11,13,319,333,357,465,467,471],file:[],file_from:189,filen:357,filenam:[3,12,13,38,41,56,185,188,190,191,192,200,203,204,205,206,207,208,209,211,216,274,278,281,284,285,286,289,290,293,294,319,320,345,346,347,357,358,364,365,369,379,385,386,388,396,410,411,412,417,421,422,423,424,431,432,442,443,444,445,446,449,456,457,458,461,462,467,471,478,486,488,489,490],filennam:467,filep:[3,188,191,462,467,490],filepo:290,fill:[7,9,165,190,279,320,351,359,369,413,424,463],filter:[191,200],final_integr:8,final_integrate_respa:8,finchham:[6,147,381],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,168,185,192,201,214,215,225,228,251,274,280,288,292,354,356,358,359,379,394,399,403,410,431,441,443,481,486],find_custom:8,fine:[16,17,169,197,223,318,359,363,486],finer:[140,165,486],finest:348,finger:[165,187,249,463],finish:[6,11,41,211,333,345,347,348,360,362,363,448,465,486,487],finit:[],finni:[7,385,441],finvers:221,fiorin:[9,216],fire:[354,355,356,358,474],firebrick:191,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,150,153,159,161,163,164,166,167,168,172,185,188,189,190,191,192,194,195,203,204,206,207,208,209,211,214,217,228,229,234,239,249,250,251,252,274,276,281,282,283,285,290,293,296,297,305,306,308,309,310,317,318,319,320,322,326,331,333,334,340,351,356,357,358,359,362,363,364,365,368,369,370,372,374,376,378,379,385,387,388,391,392,394,395,396,398,399,403,408,409,410,412,413,415,417,421,423,424,431,432,440,442,443,444,445,446,449,453,455,456,457,458,460,461,462,465,467,469,472,473,474,477,478,481,486,487,488,490],fischer:[6,9,19,20,171,374,472],fit:[3,6,9,12,38,56,185,292,308,365,369,396,410,415,436,443,445,468,486],five:[73,151,283,357,369,411,460,474],fix:[],fix_adapt:[159,196,407],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,201,279],fix_evapor:201,fix_flux:200,fix_gcmc:[201,357],fix_gl:230,fix_gld:230,fix_grav:279,fix_id:[3,215,250,252,254,255,256,257,258,280,283],fix_modifi:[],fix_mov:[187,326],fix_nh:8,fix_npt:230,fix_nvt:[201,228],fix_poem:[3,6],fix_pour:[3,218],fix_qbmsst:9,fix_qeq:[3,378],fix_rattl:296,fix_reax_bond:423,fix_rigid:[242,368],fix_saed_vtk:294,fix_setforc:8,fix_shak:296,fix_srd:3,fix_styl:256,fix_temp_rescal:314,fixedpoint:[215,252],fixextern:226,fixid:200,fji:382,flag1:[220,361],flag2:[220,361],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,93,103,104,106,118,160,164,168,188,190,191,192,209,214,216,220,233,236,240,242,248,249,275,282,293,305,307,308,315,319,328,331,346,349,357,361,362,363,365,393,398,410,413,440,455,457,458,460,461,462,464,465,466,470,486],flag_buck:373,flag_coul:[373,382,403],flag_lj:[382,403],flagfld:[371,408,409],flaghi:[3,371,408,409],flaglog:[371,408,409],flagn:220,flagvf:[371,408,409],flat:[6,320,325,326,330],flavor:[2,7,12],fld:[9,325,371,408,409],flen:366,flex_press:366,flexibl:[3,6,8,166,190,203,207,216,230,253,316,323,387,445,478],flip:[3,6,217,252,327,328],floor:486,flop:12,floralwhit:191,flow:[],fluctuat:[6,64,87,215,228,229,236,239,252,256,274,275,318,320,342],fluid:[],fluid_veloc:243,flush:[3,191,477],flux:[],flv:190,fly:[7,9,12,41,190,194,200,205,218,221,293,296,321,369,413,478,481],fmackai:9,fmag:219,fmass:276,fmax:[356,478],fmomentum:221,fmsec:[2,191,236,237,249,252,280,293,311,312,469,480,485,487],fname:347,fno:[12,16],fnorm:[356,478],fnpt:221,fnvt:221,foce:394,fock:366,focu:296,fogarti:[9,286,424],foil:[140,274,432],fold:[306,469],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,144,145,151,153,158,161,163,165,166,171,174,175,176,177,179,180,182,183,185,188,189,190,191,194,200,201,202,203,204,205,206,207,208,209,211,216,217,218,221,222,226,228,229,230,233,235,236,237,239,242,250,252,256,257,258,269,270,272,275,276,278,281,282,283,284,286,288,290,292,293,294,296,310,311,312,313,316,317,318,319,320,322,323,331,332,336,337,338,339,342,344,346,351,353,356,357,358,363,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,420,421,422,423,424,425,426,428,430,431,432,433,434,435,436,437,438,439,440,442,443,444,445,446,447,448,449,451,452,453,455,457,458,460,461,462,463,465,467,468,469,472,474,475,476,481,486,487,489],foo:[4,8,11,12,188,190,226,458,471,486],foot:6,footprint:[12,363],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:242,forcefield:[292,393],forcegroup:239,forcezero:354,ford:382,forestgreen:191,forev:71,forget:[237,481],forgiv:252,fork:[12,188],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,87,89,90,93,103,104,106,116,140,141,159,160,169,173,191,194,195,196,213,229,230,236,238,242,249,270,275,286,288,292,293,320,325,329,334,335,342,353,355,357,358,365,366,369,376,385,387,389,393,394,398,410,412,413,417,418,421,423,424,425,431,432,433,441,443,444,445,446,452,454,457,458,460,465,470,477,481,486],formal:[6,78,80,91,229,230,236,252,276,308,316,431],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,173,185,188,189,190,191,192,203,206,207,208,209,211,213,275,278,282,284,286,289,293,294,304,319,320,331,332,335,353,357,358,364,365,369,376,385,388,398,410,412,422,423,424,426,432,443,449,450,457,458,460,461,462,465,476,477,478,486,488],former:[6,12,16,39,41,191,211,320,324,369,371,466,472,486],formerli:[7,13],formul:[1,40,64,141,197,223,236,252,270,284,286,292,296,319,348,365,369,385,387,390,410,420],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,94,96,97,106,112,118,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,164,165,170,172,173,184,188,195,196,197,198,203,204,205,206,209,210,217,223,231,232,234,236,237,249,274,275,281,290,295,302,306,308,311,312,313,322,325,328,330,331,333,334,335,337,343,351,357,365,366,368,369,374,375,376,377,382,383,385,386,390,391,392,393,395,398,399,401,402,403,405,406,408,409,410,414,415,416,425,426,433,441,442,444,445,446,449,451,452,456,460,463,470,477,478,485,486,487],forth:[1,6,11,12,13,14,15,362,458,463,467],fortran:[3,6,9,11,12,13,226,385,394,410,423,424],fortun:8,forward:[3,8,87,347,358,363],foster:[369,420,421],foul:168,found:[3,6,9,12,73,159,188,214,216,228,233,239,275,315,321,333,347,359,376,379,382,455,461,462,477],four:[6,11,54,81,103,104,140,161,250,320,342,357,358,413,455],fourier:[],fourth:[6,105,292,305,315,374,417,431],fox:[6,118,171,439,472],fphi:[38,56,443],fpic:12,fplo:[38,56,443],fprime:443,fqdn:235,fqq:382,frac:[221,237,447,481],fraction:[1,3,6,8,12,16,39,41,80,109,141,168,187,190,191,201,212,213,214,215,250,279,283,290,291,308,313,314,351,358,363,369,371,391,408,409,465,470],fragment:[42,233,290],frame:[83,140,191,200,250,283,327,390],framer:[190,191],framework:[5,230,364,432],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,87,159,196,274,308,317,318,319,320,355,358,366,387,407,413,421,452,457],freedom:[3,6,8,94,96,97,99,101,102,112,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,203,214,221,228,230,236,237,242,252,253,256,257,258,269,270,272,276,278,293,296,311,312,313,318,356,382,478,481,487],freeli:[0,6,7,12,144,158,163,190],freez:[],frenkel:[228,318],freq:199,frequenc:[3,6,16,39,191,205,264,275,276,283,288,346,383,387,424,431,455,469,474,486,489],frequent:[3,64,67,70,72,73,77,88,140,191,212,213,225,316,323,415,467],fri:[250,283],friction:[4,5,6,10,42,194,230,236,283,288,293,320,324,326,391,470],friedrich:298,from:[],front:[250,283,327],frontend:[190,287],frozen:[6,112,169,227,229,237,359,389],fs2:[6,91],fscale:233,fstr:486,fstring:458,ftol:[356,358,455,474],fuchsia:191,fuction:379,fudg:296,fugac:228,fugacity_coeff:228,fulfil:6,full:[1,2,6,9,12,17,38,39,40,91,190,204,205,216,239,274,348,349,363,369,385,387,388,390,447,460,462,467,468,472,474,479,481,489],full_energi:[3,228],fuller:356,fulli:[3,6,9,78,230,235,274,356,358,379,421,422,488],fulton:385,fumi:370,func:[458,486],funcfl:385,functino:[],functionaliri:216,fund:[0,7],fundament:[308,485],funnel_flow:304,funrol:413,further:[3,6,8,12,13,61,63,71,86,105,107,116,190,191,194,203,206,207,208,209,212,218,222,239,243,276,284,294,298,308,320,322,331,349,354,356,357,358,359,364,368,378,413,431,455,474,475,486],furthermor:[27,174,387],furthest:61,futher:3,futur:[],g_ewald:3,g_ewald_6:3,g_ewald_disp:3,g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ermut:[12,386,442,444,446,449],perpendicular:[6,144,190,217,234,244,249,251,274,277,301,325,326,355,460],perram:[349,390],persepct:190,persist:[3,8,71,226,293,363,457,458,466,486],person:9,persp:[3,190],perspect:190,pertain:[376,441],perturb:[9,13,70,87,248,291,325,328,330,465],peru:191,peskin:239,pessimist:349,petersen:[308,349],pettifor:[369,441],pettifor_1:369,pettifor_2:369,pettifor_3:369,pfactor:190,pforc:458,phantom:233,pharmaceut:7,phase:[3,12,16,252,315,323,369,399,445,457],phd:422,phenol:481,phenomena:387,phi0:[183,292],phi1:172,phi2:[172,386,442],phi3:[172,386,442],phi:[1,3,4,7,9,12,16,17,79,140,184,185,190,231,275,292,337,363,364,369,385,388,410,411,412,473],phi_ij:[369,388,421],philadelphia:9,phillip:[237,383,481],phillpot:[285,378,379,431],philosoph:385,philosophi:[6,7,235],phonon:[],phophor:432,phosphid:432,phy:[6,7,13,20,21,25,39,43,45,46,64,70,73,87,88,110,112,140,141,147,153,171,172,182,189,201,205,215,216,221,229,230,235,236,237,238,239,250,251,252,253,256,270,271,275,276,280,283,285,288,293,296,297,308,311,312,315,316,317,318,320,323,325,334,342,344,348,349,355,358,365,369,370,374,375,377,378,379,380,381,382,383,385,386,387,389,390,391,392,393,396,399,401,403,404,407,408,409,410,412,414,415,418,420,421,425,431,432,440,442,443,444,445,446,447,449,455,469,472,474,481],physic:[3,6,9,12,14,16,17,18,40,53,59,120,147,159,200,217,230,236,238,239,241,242,243,250,275,284,286,319,320,349,351,358,363,365,367,373,377,385,393,394,413,422,423,424,427,435,436,438,439,455,457,469,470,475,485],physica:[408,409],physik:[7,9],pic:9,picki:8,picocoulomb:485,picogram:485,picosecond:[191,217,478,485],picosend:387,pictur:7,piec:[3,11,140,191,252,467,490],pierr:9,pieter:13,pimd:[],pin:16,pink:191,pipe:[6,188,190],pipelin:[3,6],pisarev:320,pishevar:383,piston:[],pitera:6,pixel:190,pizza:[4,6,7,11,13,41,188,190,211],pjintv:13,pka:320,place:[3,6,7,9,11,12,33,41,50,71,87,159,165,169,178,185,188,190,191,193,194,195,196,213,214,217,228,229,230,232,235,236,237,238,240,242,243,252,257,258,269,272,279,282,291,293,311,312,313,320,325,328,330,347,376,393,441,448,457,458,461,468,470,478,486],placehold:[33,178,364,365,378,385,388,395,396,410,411,412,417,421,423,424,432,440,442,444,445,446,449],placement:[351,399],plai:[190,315],plain:[9,407,458],plan:[3,5,6,17,167,460],planar:[6,40,42,234,274,326,342,344],planck:[228,276],plane:[3,6,9,41,42,57,59,67,71,190,194,200,207,211,231,234,244,274,277,287,305,307,320,326,334,336,337,338,339,344,351,409,448,463,470],planeforc:[],plasma:[9,88,253,320,387],plastic:[],plastic_strain:121,plastic_strain_r:124,platform:[1,3,7,9,12,13,15,17,188,190,192,462,467,490],plath:[6,91,194,316,323],player:190,pleas:[0,3,7,11,12,13,200,230,239,243,275,278,289,315,331,386,388,420,428,430,431],plen:366,plimpton:[0,5,7,70,112,141,214,274,308,391,420],plo:29,plog:[3,12,469],ploop:[252,253,256],plot:[7,11,13,283,405,407,443,450],plu:[3,11,12,39,59,68,96,168,191,210,215,217,218,256,293,360,387],plug:9,plugin:[9,13,192,461],plum:191,pm3:164,pmb:[],pme:349,pmf:[216,297,305],png:[3,12,188,190],pni:190,poariz:6,poem:[],point1:460,point2:460,point3:460,point:[],point_data:294,pointer:[3,7,8,11,226,458],pois:485,poiseuil:[4,197,231],poisson:[59,217,349,391],poisson_solv:200,polak:355,polar:[6,7,140,147,164,200,220,378,379,399,447,481],polar_off:378,polar_on:378,polariz:[],poli:[],politano:[9,431],pollock:[7,349],polya:331,polybond:13,polychain:293,polydispers:[3,357,371,377,391,408,409,441,452],polygon:[6,163],polym:[],polymer:7,polymorph:[],polynomi:[9,38,56,185,385,405,415,431,436,443],polytechn:278,poor:[16,17,41,211,270,271,296,363,405],poorli:[355,356],pop:[3,8],popen:12,popul:[12,288,351,384,460],popular:[12,188,386],pore:305,poros:168,porou:[239,242],port:[233,235],portabl:[7,9,12,188,189,216,423,462],portion:[1,3,9,11,12,15,16,41,54,71,88,91,107,108,110,113,141,142,155,188,191,202,203,206,207,208,209,211,215,225,239,252,254,255,257,258,285,290,291,293,294,333,347,359,363,370,372,373,374,375,379,380,382,383,387,389,390,392,393,399,403,407,418,425,426,446,450,459,460,465,469,470,479,486],poschel:391,posfreq:290,posit:[3,6,14,27,39,40,41,42,46,57,59,70,71,81,89,90,103,104,108,117,118,122,140,141,148,163,164,165,167,168,169,174,176,185,187,189,190,191,194,195,197,199,201,202,203,206,207,208,211,212,213,214,215,216,217,218,221,223,228,229,230,231,233,234,236,237,238,239,241,242,245,246,249,250,252,253,254,255,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,278,279,280,283,284,288,290,291,293,296,297,301,304,305,307,308,310,311,312,313,315,317,318,319,320,323,325,326,327,328,329,330,331,334,348,351,358,365,366,368,371,383,384,387,389,397,402,424,431,440,443,448,455,460,463,470,481,486,487],posix:233,posix_memalign:12,possibl:[1,3,6,8,9,11,12,15,38,40,41,55,59,63,70,71,87,113,115,140,141,144,158,187,188,189,191,194,196,200,201,207,211,212,213,214,218,220,230,237,274,287,288,290,293,304,308,310,320,321,338,347,349,356,359,360,363,384,393,410,424,428,430,431,443,449,458,464,473,474,475,47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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":212,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,145,153,154,158,164,165,168,170,184,186,187,188,190,191,192,193,195,196,197,199,200,201,203,207,208,209,212,213,215,216,217,218,222,225,228,229,234,236,237,238,239,240,242,247,250,252,253,256,270,271,275,276,279,280,281,282,283,285,288,290,291,293,294,308,310,315,316,317,318,321,323,325,327,331,343,346,348,349,351,352,354,355,357,359,360,361,363,366,369,371,387,408,409,413,415,423,424,440,441,455,456,457,460,461,463,465,467,468,469,472,474,476,477,478,479,480,485,487,488,489],"function":486,"long":[205,370,372,373,374,375,379,381,382,399,403,407,418,426],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[195,196],addforc:197,addit:[12,13],addtorqu:198,adiabat:6,adjust_dt:298,adp:364,airebo:365,alloi:385,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:199,arrai:6,aspher:[6,82,144,254,257,260,261,269],atc:[9,200],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,163,199,201,202,282,486],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:210,awpmd:[9,366],balanc:[41,211],barostat:6,basal:67,beck:367,berendsen:[280,311],between:6,binary2txt:13,bodi:[6,8,42,68,262,368],bond:[8,13,69,212,213,214,289],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:369,born:[370,381],boundari:[7,57],box:[6,58,215],brownian:371,buck:[372,373,381],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,171,374,407],chunk:[6,66,71,75,90,93,104,106,114,145,160,162,203],citat:7,class2:[21,43,172,334,375],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[325,377,452],colvar:[9,13,216],com:[74,75,146],comb3:378,comb:[285,378],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,484,485,486,487,488,489,490],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,486],compute_modifi:102,condit:7,conduct:[6,316],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:[204,205],cosin:[23,24,25,26,27,28,174],cossq:336,coul:[370,372,373,374,375,379,380,381,392,399,403,407,418,426],coupl:6,creat:213,create_atom:165,create_bond:166,create_box:167,createatom:13,creation:7,csld:312,csvr:312,cubic:401,cuda:[9,14,109,112,143,152,197,210,224,227,231,252,259,295,296,311,313,324,370,372,374,375,385,391,392,399,400,402,405,416,442,444],custom:8,cut:[49,366,372,375,379,382,387,389,399,400,407,414,418],cvff:337,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[379,399],deform:[148,149,217],delete_atom:168,delete_bond:169,delta:24,deposit:218,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,7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\ No newline at end of file From 9057c423506fa26447cbf35dce65bac44ba364c8 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 23 Oct 2015 00:30:53 +0000 Subject: [PATCH 25/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14187 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Manual.txt | 6 +++--- potentials/README | 1 + potentials/ffield.smtbq.Al | 2 +- src/USER-SMTBQ/README | 3 ++- 4 files changed, 7 insertions(+), 5 deletions(-) diff --git a/doc/Manual.txt b/doc/Manual.txt index b0857e6c32..f47482fdf2 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands. .. toctree:: :maxdepth: 2 - :numbered: + :numbered: // comment Section_intro Section_start @@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands. Indices and tables ================== -* :ref:`genindex` -* :ref:`search` +* :ref:`genindex` // comment +* :ref:`search` // comment END_RST --> diff --git a/potentials/README b/potentials/README index 599432ce8d..695387efc6 100644 --- a/potentials/README +++ b/potentials/README @@ -89,6 +89,7 @@ lcbop LCBOP long-range bond-order potential meam modified EAM (MEAM) library and individual elements/alloys meam.spline modified EAM (MEAM) spline potential meam.sw.spline modified EAM (MEAM) Stillinger-Weber spline potential +mgpt Moriarty generalized pseudopotential theory (GPT) potential nb3b.harmonic nonbonded 3-body harmonic potential poly polymorphic 3-body potential reax ReaxFF potential (see README.reax for more info) diff --git a/potentials/ffield.smtbq.Al b/potentials/ffield.smtbq.Al index b8fd478a09..f63b6c43ba 100755 --- a/potentials/ffield.smtbq.Al +++ b/potentials/ffield.smtbq.Al @@ -1,4 +1,4 @@ -# +# DATE: 2015-10-22 CONTRIBUTOR: Nicolas Salles, nsalles@laas.fr CITATION: N. Salles, O. Politano, E. Amzallag and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189 # SMTBQ parameter for Al-Al interaction. # Edited by N. Salles Univ. Bourgogne and E. Maras from Aalto Univ. # year: 2014 diff --git a/src/USER-SMTBQ/README b/src/USER-SMTBQ/README index c94ad47324..74b621eef1 100644 --- a/src/USER-SMTBQ/README +++ b/src/USER-SMTBQ/README @@ -1,7 +1,8 @@ This package implements the Second Moment Tight Binding - QEq (SMTB-Q) -potential for the description of the ionocovalent bond in oxides. +potential for the description of ionocovalent bonds in oxides. Authors: Nicolas Salles, Emile Maras, Olivier Politano, Robert Tetot +at LAAS-CNRS in France. Contact emails: lammps@u-bourgogne.fr, nsalles@laas.fr From 238c17e0c7b3ceb0997b481d459a4c66cc91a82a Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 23 Oct 2015 00:34:56 +0000 Subject: [PATCH 26/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14188 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- potentials/README | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/potentials/README b/potentials/README index 695387efc6..357b9291cd 100644 --- a/potentials/README +++ b/potentials/README @@ -89,11 +89,11 @@ lcbop LCBOP long-range bond-order potential meam modified EAM (MEAM) library and individual elements/alloys meam.spline modified EAM (MEAM) spline potential meam.sw.spline modified EAM (MEAM) Stillinger-Weber spline potential -mgpt Moriarty generalized pseudopotential theory (GPT) potential +mgpt model generalized pseudopotential theory (MGPT) potential nb3b.harmonic nonbonded 3-body harmonic potential poly polymorphic 3-body potential reax ReaxFF potential (see README.reax for more info) -smtbq Second Moment Tight Binding - QEq potential +smtbq second moment tight binding QEq (SMTBQ) potential snap SNAP potential snapcoeff SNAP potential snapparam SNAP potential From 8d4d51741ab2dfb07467905300fb819c26d9e307 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 23 Oct 2015 00:45:50 +0000 Subject: [PATCH 27/31] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14190 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Manual.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/Manual.txt b/doc/Manual.txt index f47482fdf2..b0857e6c32 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands. .. toctree:: :maxdepth: 2 - :numbered: // comment + :numbered: Section_intro Section_start @@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands. Indices and tables ================== -* :ref:`genindex` // comment -* :ref:`search` // comment +* :ref:`genindex` +* :ref:`search` END_RST --> From 021a327e851abb489eaabb109fa29050eab4bd37 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 23 Oct 2015 00:46:10 +0000 Subject: [PATCH 28/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14191 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/version.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/version.h b/src/version.h index 6439ed804a..d2dd60a0c9 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "23 Oct 2015" +#define LAMMPS_VERSION "24 Oct 2015" From 7a9ae37e028c427a8f6ad111461ac40f8ed5a7d2 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 23 Oct 2015 00:46:13 +0000 Subject: [PATCH 29/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14192 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Manual.html | 884 +++++++++++++++++++++++++----------------------- doc/Manual.txt | 10 +- 2 files changed, 458 insertions(+), 436 deletions(-) diff --git a/doc/Manual.html b/doc/Manual.html index 149dcb1aa6..e35e907caa 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -1,456 +1,478 @@ + + + +LAMMPS Users Manual + + + + + + + + + +
      LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
      - - - - - - - - - LAMMPS Documentation — LAMMPS 15 May 2015 version documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
      - - - - -
      - - - - -
      -
      -
      - -
      - - - -
      -
      -
      - -

      -

      LAMMPS Documentation¶

      -
      -

      10 Aug 2015 version¶

      -
      -
      -

      Version info:¶

      -

      The LAMMPS “version” is the date when it was released, such as 1 May + + +

      + +

      + +

      LAMMPS Documentation +

      +

      24 Oct 2015 version +

      +

      Version info: +

      +

      The LAMMPS "version" is the date when it was released, such as 1 May 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a -feature, we release it immediately, and post a notice on this page of the WWW site. Each dated copy of LAMMPS contains all the +feature, we release it immediately, and post a notice on this page of +the WWW site. Each dated copy of LAMMPS contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run LAMMPS. It is also in the file src/version.h and in the LAMMPS directory name created when you unpack a tarball, and at the top of -the first page of the manual (this page).

      -
        -
      • If you browse the HTML doc pages on the LAMMPS WWW site, they always -describe the most current version of LAMMPS.
        • -
      • If you browse the HTML doc pages included in your tarball, they -describe the version you have.
        • -
      • The PDF file on the WWW site or in the tarball is updated -about once per month. This is because it is large, and we don’t want -it to be part of every patch.
        • -
      • There is also a Developer.pdf file in the doc +the first page of the manual (this page). +

        +
        • If you browse the HTML doc pages on the LAMMPS WWW site, they always +describe the most current version of LAMMPS. + +
        • If you browse the HTML doc pages included in your tarball, they +describe the version you have. + +
        • The PDF file on the WWW site or in the tarball is updated +about once per month. This is because it is large, and we don't want +it to be part of every patch. + +
        • There is also a Developer.pdf file in the doc directory, which describes the internal structure and algorithms of -LAMMPS.
          • -
        -

        LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel -Simulator.

        -

        LAMMPS is a classical molecular dynamics simulation code designed to +LAMMPS. +

      +

      LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel +Simulator. +

      +

      LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely -under the terms of the GNU Public License (GPL).

      -

      The primary developers of LAMMPS are Steve Plimpton, Aidan +under the terms of the GNU Public License (GPL). +

      +

      The primary developers of LAMMPS are Steve Plimpton, Aidan Thompson, and Paul Crozier who can be contacted at -sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at -http://lammps.sandia.gov has more information about the code and its -uses.

      -
      -

      The LAMMPS documentation is organized into the following sections. If +sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at +http://lammps.sandia.gov has more information about the code and its +uses. +

      + + + + +
      + +

      The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for useful information to add, please send an email to the developers so -we can improve the LAMMPS documentation.

      -

      Once you are familiar with LAMMPS, you may want to bookmark this page at Section_commands.html#comm since -it gives quick access to documentation for all LAMMPS commands.

      -

      PDF file of the entire manual, generated by -htmldoc

      -
      - -
      -
      -
      -
      -

      Indices and tables¶

      - -
      +we can improve the LAMMPS documentation. +

      +

      Once you are familiar with LAMMPS, you may want to bookmark this +page at Section_commands.html#comm since +it gives quick access to documentation for all LAMMPS commands. +

      +

      PDF file of the entire manual, generated by +htmldoc +

      +

      +

      +
      1. +Introduction + + +
      2. Getting started + + +
      3. Commands + + +
      4. Packages + + +
      5. Accelerating LAMMPS performance + + +
      6. How-to discussions + + +
      7. Example problems + +
      8. Performance & scalability + +
      9. Additional tools + +
      10. Modifying & extending LAMMPS + + +
      11. Python interface + + +
      12. Errors + + +
      13. Future and history + + + +
      -
      -
      - - -
      -
      - -
      - -
      - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/doc/Manual.txt b/doc/Manual.txt index b0857e6c32..3b2d088b0f 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

      LAMMPS Documentation :c,h3 -10 Aug 2015 version :c,h4 +24 Oct 2015 version :c,h4 Version info: :h4 @@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands. .. toctree:: :maxdepth: 2 - :numbered: + :numbered: // comment Section_intro Section_start @@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands. Indices and tables ================== -* :ref:`genindex` -* :ref:`search` +* :ref:`genindex` // comment +* :ref:`search` // comment END_RST --> From df128b06e85b54676181d07aa0e8312f80483a63 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 23 Oct 2015 00:57:02 +0000 Subject: [PATCH 30/31] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14194 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/_images/pair_mgpt.jpg | Bin 0 -> 12874 bytes doc/_images/pair_smtbq1.jpg | Bin 0 -> 27807 bytes doc/_images/pair_smtbq2.jpg | Bin 0 -> 15544 bytes doc/_images/pair_smtbq3.jpg | Bin 0 -> 6832 bytes doc/_images/pair_vashishta.jpg | Bin 0 -> 73306 bytes doc/_images/polymorphic3.jpg | Bin 0 -> 2425 bytes 6 files changed, 0 insertions(+), 0 deletions(-) create mode 100644 doc/_images/pair_mgpt.jpg create mode 100644 doc/_images/pair_smtbq1.jpg create mode 100644 doc/_images/pair_smtbq2.jpg create mode 100644 doc/_images/pair_smtbq3.jpg create mode 100644 doc/_images/pair_vashishta.jpg create mode 100644 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z1atAKxT=ukflO8uLNGHC1@#fL$2bxGwI_7U^^0;v@(RQf8SJT?@Lsm@)*mu180FPF z$;bm(BhzIAj<>2?2i`uDpF@&QRorAQhNO`}flD^C;2=PC9 zc8R>!JC6KWKzE=0XTW%FVKL?q!Y_Rk{W0tVAy1gVFxUv&D!)`5WF`NB@Eo8U6537ek`4kcPT>eHY)p~9Urf4D^1bKQe9f@#(ZufE|r(! z82U~So9^~3<;pYWO i}^N U_{ij}^{(2)} (r_{ij}) + + \sum_i^N \sum_{j \neq i}^N \sum_{k > j, k \neq i}^N + U_{ijk}^{(3)} (r_{ij}, r_{ik}, \theta_{ijk}) + \\ + U_{ij}^{(2)} (r) & = & \frac{H_{ij}}{r^{\eta_{ij}}} + + \frac{Z_i Z_j}{r}\exp(-r/\lambda_{1,ij}) + - \frac{D_{ij}}{r^4}\exp(-r/\lambda_{4,ij}) + - \frac{W_{ij}}{r^6}, r < r_{c,{ij}} + \\ + U_{ijk}^{(3)}(r_{ij},r_{ik},\theta_{ijk}) & = & B_{ijk} + \frac{\left[ \cos \theta_{ijk} - \cos \theta_{0ijk} \right]^2} + {1+C_{ijk}\left[ \cos \theta_{ijk} - \cos \theta_{0ijk} \right]^2} \times \\ +& & \exp \left( \frac{\gamma_{ij}}{r_{ij} - r_{0,ij}} \right) + \exp \left( \frac{\gamma_{ik}}{r_{ik} - r_{0,ik}} \right), r_{ij} < r_{0,ij}, r_{ik} < r_{0,ik} +\end{eqnarray*} + +\end{document} diff --git a/doc/doc2/Eqs/polymorphic1.tex b/doc/doc2/Eqs/polymorphic1.tex new file mode 100644 index 0000000000..b4b925ccf8 --- /dev/null +++ b/doc/doc2/Eqs/polymorphic1.tex @@ -0,0 +1,9 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ +E=\frac{1}{2}\sum_{i=1}^{i=N}\sum_{j=1}^{j=N}\left[\left(1-\delta_{ij}\right)\cdot U_{IJ}\left(r_{ij}\right)-\left(1-\eta_{ij}\right)\cdot F_{IJ}\left(r_{ij}\right)\cdot V_{IJ}\left(r_{ij}\right)\right] +$$ + +\end{document} diff --git a/doc/doc2/Eqs/polymorphic2.tex b/doc/doc2/Eqs/polymorphic2.tex new file mode 100644 index 0000000000..80b1c93821 --- /dev/null +++ b/doc/doc2/Eqs/polymorphic2.tex @@ -0,0 +1,10 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ +X_{ij}=\sum_{k=i_1,k\neq i,j}^{i_N}W_{IK}\left(r_{ik}\right)\cdot G_{JIK}\left(\theta_{jik}\right)\cdot P_{IK}\left(\Delta r_{jik}\right) +\label{X_eq2} +$$ + +\end{document} diff --git a/doc/doc2/Eqs/polymorphic3.tex b/doc/doc2/Eqs/polymorphic3.tex new file mode 100644 index 0000000000..71db8d81b0 --- /dev/null +++ b/doc/doc2/Eqs/polymorphic3.tex @@ -0,0 +1,10 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ +\Delta r_{jik}=r_{ij}-\xi_{IJ}\cdot r_{ik} +\label{Dr_eq3} +$$ + +\end{document} diff --git a/doc/doc2/Eqs/polymorphic4.tex b/doc/doc2/Eqs/polymorphic4.tex new file mode 100644 index 0000000000..b792df82a0 --- /dev/null +++ b/doc/doc2/Eqs/polymorphic4.tex @@ -0,0 +1,17 @@ +\documentclass[12pt]{article} + +\begin{document} + +\begin{eqnarray*} +\left\{\begin{array}{l} +\eta_{ij}=\delta_{ij},\xi_{IJ}=0 \\ +U_{IJ}\left(r\right)=A_{IJ}\cdot\epsilon_{IJ}\cdot \left(\frac{\sigma_{IJ}}{r}\right)^q\cdot \left[B_{IJ}\cdot \left(\frac{\sigma_{IJ}}{r}\right)^{p-q}-1\right]\cdot exp\left(\frac{\sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\ +V_{IJ}\left(r\right)=\sqrt{\lambda_{IJ}\cdot \epsilon_{IJ}}\cdot exp\left(\frac{\gamma_{IJ}\cdot \sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\ +F_{IJ}\left(X\right)=-X \\ +P_{IJ}\left(\Delta r\right)=1 \\ +W_{IJ}\left(r\right)=\sqrt{\lambda_{IJ}\cdot \epsilon_{IJ}}\cdot exp\left(\frac{\gamma_{IJ}\cdot \sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\ +G_{JIK}\left(\theta\right)=\left(cos\theta+\frac{1}{3}\right)^2 +\end{array}\right. +\end{eqnarray*} + +\end{document} diff --git a/doc/doc2/Eqs/polymorphic5.tex b/doc/doc2/Eqs/polymorphic5.tex new file mode 100644 index 0000000000..a5451b98d6 --- /dev/null +++ b/doc/doc2/Eqs/polymorphic5.tex @@ -0,0 +1,17 @@ +\documentclass[12pt]{article} + +\begin{document} + +\begin{eqnarray*} +\left\{\begin{array}{l} +\eta_{ij}=\delta_{ij},\xi_{IJ}=1 \\ +U_{IJ}\left(r\right)=\frac{D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{2S_{IJ}\left(r-r_{e,IJ}\right)}\right]\cdot f_{c,IJ}\left(r\right) \\ +V_{IJ}\left(r\right)=\frac{S_{IJ}\cdot D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{\frac{2}{S_{IJ}}\left(r-r_{e,IJ}\right)}\right]\cdot f_{c,IJ}\left(r\right) \\ +F_{IJ}\left(X\right)=\left(1+X\right)^{-\frac{1}{2}} \\ +P_{IJ}\left(\Delta r\right)=exp\left(2\mu_{IK}\cdot \Delta r\right) \\ +W_{IJ}\left(r\right)=f_{c,IK}\left(r\right) \\ +G_{JIK}\left(\theta\right)=\gamma_{IK}\left[1+\frac{c_{IK}^2}{d_{IK}^2}-\frac{c_{IK}^2}{d_{IK}^2+\left(h_{IK}+cos\theta\right)^2}\right] +\end{array}\right. +\end{eqnarray*} + +\end{document} diff --git a/doc/doc2/Eqs/polymorphic6.tex b/doc/doc2/Eqs/polymorphic6.tex new file mode 100644 index 0000000000..c8f9f2f25b --- /dev/null +++ b/doc/doc2/Eqs/polymorphic6.tex @@ -0,0 +1,13 @@ +\documentclass[12pt]{article} + +\begin{document} + +\begin{eqnarray*} +f_{c,IJ}=\left\{\begin{array}{lr} +1, & r\leq r_{s,IJ} \\ +\frac{1}{2}+\frac{1}{2} cos \left[\frac{\pi \left(r-r_{s,IJ}\right)}{r_{c,IJ}-r_{s,IJ}}\right], & r_{s,IJ}
    awpmd/cutmeam/spline
    meam/sw/splinemgpt quip reax/csmd/hertz
    smd/tlsph
    smd/hertzsmd/tlsph smd/triangulated/surface smd/ulsph
    smtbq sph/heatconduction
    sph/idealgassph/idealgas sph/ljsph/rhosum
    sph/rhosum sph/taitwater
    sph/taitwater/morrissph/taitwater/morris srptersoff/table (o)thole
    tip4p/long/soft (o)  
    tersoff/table (o)tholetip4p/long/soft (o)  
    USER-H5MD dump output via HDF5 Pierre de Buyl (KU Leuven) dump h5md - - lib/h5md
    USER-INTEL Vectorized CPU and Intel(R) coprocessor styles W. Michael Brown (Intel) Section accelerate examples/intel - -
    USER-LB Lattice Boltzmann fluid Colin Denniston (U Western Ontario) fix lb/fluid USER/lb - -
    USER-MGPT Fast MGPT multi-ion potentials Tomas Oppelstrup & John Moriarty (LLNL) pair_style mgpt USER/mgpt - -
    USER-MGPT fast MGPT multi-ion potentials Tomas Oppelstrup & John Moriarty (LLNL) pair_style mgpt USER/mgpt - -
    USER-MISC single-file contributions USER-MISC/README USER-MISC/README - - -
    USER-MOLFILE VMD molfile plug-ins Axel Kohlmeyer (Temple U) dump molfile - - VMD-MOLFILE
    USER-OMP OpenMP threaded styles Axel Kohlmeyer (Temple U) Section accelerate - - -
    USER-QUIP QUIP/libatoms interface Albert Bartok-Partay (U Cambridge) pair_style quip USER/quip - lib/quip
    USER-REAXC C version of ReaxFF Metin Aktulga (LBNL) pair_style reaxc reax - -
    USER-SMD smoothed Mach dynamics Georg Ganzenmuller (EMI) userguide.pdf USER/smd - -
    USER-SMTBQ Second Moment Tight Binding - QEq potential Salles & Maras & Politano & Tetot (4) pair_style smtbq USER/smtbq - -
    USER-SPH smoothed particle hydrodynamics Georg Ganzenmuller (EMI) userguide.pdf USER/sph sph -
    USER-TALLY Pairwise tallied computes Axel Kohlmeyer (Temple U) compute <...>/tally USER/tally - -
    @@ -255,6 +256,9 @@ Jerome Henin (LISM, Marseille, France). Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua (U Blaise Pascal).

    +

    (4) The SMTBQ package was created by Nicolas Salles, Emile Maras, +Olivier Politano, and Robert Tetot (LAAS-CNRS, France). +

    If the Library is not listed as lib/package, then it is a third-party library not included in the LAMMPS distribution. See the src/package/Makefile.lammps file for info on where to download the @@ -820,6 +824,27 @@ Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if you have questions.

    +
    + +

    USER-SMTBQ package +

    +

    This package implements the Second Moment Tight Binding - QEq (SMTB-Q) +potential for the description of ionocovalent bonds in oxides. +

    +

    There are example scripts for using this package in +examples/USER/smtbq. +

    +

    See this doc page to get started: +

    +

    pair_style smtbq +

    +

    The persons who created the USER-SMTBQ package are Nicolas Salles, +Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at +these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact +them directly if you have any questions. +

    +
    +

    USER-SPH package

    This package implements smoothed particle hydrodynamics (SPH) in diff --git a/doc/doc2/genindex.html b/doc/doc2/genindex.html index 455592789c..cc20eff0fb 100644 --- a/doc/doc2/genindex.html +++ b/doc/doc2/genindex.html @@ -1882,6 +1882,10 @@ +

    pair_style smtbq +
    + +
    pair_style snap
    From 58c70ec9e461f4bc9676239fd9644be3c459dab8 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 23 Oct 2015 00:30:38 +0000 Subject: [PATCH 24/31] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14186 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Manual.html | 3 ++- doc/Section_packages.html | 44 +++++++++++++++++++++++++++++++++------ doc/Section_packages.txt | 27 +++++++++++++++++++++++- doc/searchindex.js | 2 +- 4 files changed, 67 insertions(+), 9 deletions(-) diff --git a/doc/Manual.html b/doc/Manual.html index 608f606624..149dcb1aa6 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -253,7 +253,8 @@ it gives quick access to documentation for all LAMMPS commands.

  • 4.32. USER-QTB package
  • 4.33. USER-REAXC package
  • 4.34. USER-SMD package
    • -
  • 4.35. USER-SPH package
    • +
  • 4.35. USER-SMTBQ package
    • +
  • 4.36. USER-SPH package
  • 5. Accelerating LAMMPS performance
  • 5. Accelerating LAMMPS performance
    • @@ -825,7 +826,7 @@ serial.
    USER-MGPTFast MGPT multi-ion potentialsfast MGPT multi-ion potentials Tomas Oppelstrup & John Moriarty (LLNL) pair_style mgpt USER/mgpt
    USER-SPH
    USER-SMTBQSecond Moment Tight Binding - QEq potentialSalles & Maras & Politano & Tetot (4)pair_style smtbqUSER/smtbq
      +
    • +
    +
      +
    • +
    +
    USER-SPH smoothed particle hydrodynamics Georg Ganzenmuller (EMI) userguide.pdf
    USER-TALLY
    USER-TALLY Pairwise tallied computes Axel Kohlmeyer (Temple U) compute