From 00062205b993295e888824f1f480f4dca0daffca Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Wed, 2 Sep 2020 17:51:53 -0400 Subject: [PATCH 01/39] bond/react: rename variable used for possible reaction create->attempt, to avoid clashing with create-atoms variables --- src/USER-REACTION/fix_bond_react.cpp | 64 ++++++++++++++-------------- src/USER-REACTION/fix_bond_react.h | 8 ++-- 2 files changed, 36 insertions(+), 36 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 99d016f1a0..79967e49a1 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -474,10 +474,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : partner = finalpartner = NULL; distsq = NULL; probability = NULL; - maxcreate = 0; - created = NULL; - ncreate = NULL; - allncreate = 0; + maxattempt = 0; + attempt = NULL; + nattempt = NULL; + allnattempt = 0; local_num_mega = 0; ghostly_num_mega = 0; restore = NULL; @@ -519,10 +519,10 @@ FixBondReact::~FixBondReact() memory->destroy(partner); memory->destroy(finalpartner); - memory->destroy(ncreate); + memory->destroy(nattempt); memory->destroy(distsq); memory->destroy(probability); - memory->destroy(created); + memory->destroy(attempt); memory->destroy(edge); memory->destroy(equivalences); memory->destroy(reverse_equiv); @@ -815,19 +815,19 @@ void FixBondReact::post_integrate() memory->destroy(partner); memory->destroy(finalpartner); memory->destroy(distsq); - memory->destroy(ncreate); + memory->destroy(nattempt); memory->destroy(probability); nmax = atom->nmax; memory->create(partner,nmax,"bond/react:partner"); memory->create(finalpartner,nmax,"bond/react:finalpartner"); memory->create(distsq,nmax,2,"bond/react:distsq"); - memory->create(ncreate,nreacts,"bond/react:ncreate"); + memory->create(nattempt,nreacts,"bond/react:nattempt"); memory->create(probability,nmax,"bond/react:probability"); } // reset create counts for (int i = 0; i < nreacts; i++) { - ncreate[i] = 0; + nattempt[i] = 0; } int nlocal = atom->nlocal; @@ -909,7 +909,7 @@ void FixBondReact::post_integrate() // and probability constraint is satisfied // if other atom is owned by another proc, it should do same thing - int temp_ncreate = 0; + int temp_nattempt = 0; for (int i = 0; i < nlocal; i++) { if (partner[i] == 0) { continue; @@ -930,17 +930,17 @@ void FixBondReact::post_integrate() } } - // store final created bond partners and count the rxn possibility once + // store final bond partners and count the rxn possibility once finalpartner[i] = tag[j]; finalpartner[j] = tag[i]; - if (tag[i] < tag[j]) temp_ncreate++; + if (tag[i] < tag[j]) temp_nattempt++; } // cycle loop if no even eligible bonding atoms were found (on any proc) int some_chance; - MPI_Allreduce(&temp_ncreate,&some_chance,1,MPI_INT,MPI_SUM,world); + MPI_Allreduce(&temp_nattempt,&some_chance,1,MPI_INT,MPI_SUM,world); if (!some_chance) continue; // communicate final partner @@ -948,7 +948,7 @@ void FixBondReact::post_integrate() commflag = 3; comm->forward_comm_fix(this); - // add instance to 'created' only if this processor + // add instance to 'attempt' only if this processor // owns the atoms with smaller global ID // NOTE: we no longer care about ghost-ghost instances as bond/create did // this is because we take care of updating topology later (and differently) @@ -959,21 +959,21 @@ void FixBondReact::post_integrate() j = atom->map(finalpartner[i]); // if (j < 0 || tag[i] < tag[j]) { if (tag[i] < tag[j]) { //atom->map(std::min(tag[i],tag[j])) <= nlocal && - if (ncreate[rxnID] == maxcreate) { - maxcreate += DELTA; - // third column of 'created': bond/react integer ID - memory->grow(created,maxcreate,2,nreacts,"bond/react:created"); + if (nattempt[rxnID] == maxattempt) { + maxattempt += DELTA; + // third column of 'attempt': bond/react integer ID + memory->grow(attempt,maxattempt,2,nreacts,"bond/react:attempt"); } // to ensure types remain in same order // unnecessary now taken from reaction map file if (iatomtype[rxnID] == type[i]) { - created[ncreate[rxnID]][0][rxnID] = tag[i]; - created[ncreate[rxnID]][1][rxnID] = finalpartner[i]; + attempt[nattempt[rxnID]][0][rxnID] = tag[i]; + attempt[nattempt[rxnID]][1][rxnID] = finalpartner[i]; } else { - created[ncreate[rxnID]][0][rxnID] = finalpartner[i]; - created[ncreate[rxnID]][1][rxnID] = tag[i]; + attempt[nattempt[rxnID]][0][rxnID] = finalpartner[i]; + attempt[nattempt[rxnID]][1][rxnID] = tag[i]; } - ncreate[rxnID]++; + nattempt[rxnID]++; } } } @@ -981,11 +981,11 @@ void FixBondReact::post_integrate() // break loop if no even eligible bonding atoms were found (on any proc) int some_chance; - allncreate = 0; + allnattempt = 0; for (int i = 0; i < nreacts; i++) - allncreate += ncreate[i]; + allnattempt += nattempt[i]; - MPI_Allreduce(&allncreate,&some_chance,1,MPI_INT,MPI_SUM,world); + MPI_Allreduce(&allnattempt,&some_chance,1,MPI_INT,MPI_SUM,world); if (!some_chance) { unlimit_bond(); return; @@ -1201,13 +1201,13 @@ void FixBondReact::superimpose_algorithm() memory->create(restore_pt,MAXGUESS,4,"bond/react:restore_pt"); memory->create(pioneers,max_natoms,"bond/react:pioneers"); memory->create(restore,max_natoms,MAXGUESS,"bond/react:restore"); - memory->create(local_mega_glove,max_natoms+1,allncreate,"bond/react:local_mega_glove"); - memory->create(ghostly_mega_glove,max_natoms+1,allncreate,"bond/react:ghostly_mega_glove"); + memory->create(local_mega_glove,max_natoms+1,allnattempt,"bond/react:local_mega_glove"); + memory->create(ghostly_mega_glove,max_natoms+1,allnattempt,"bond/react:ghostly_mega_glove"); attempted_rxn = 1; for (int i = 0; i < max_natoms+1; i++) { - for (int j = 0; j < allncreate; j++) { + for (int j = 0; j < allnattempt; j++) { local_mega_glove[i][j] = 0; ghostly_mega_glove[i][j] = 0; } @@ -1215,7 +1215,7 @@ void FixBondReact::superimpose_algorithm() // let's finally begin the superimpose loop for (rxnID = 0; rxnID < nreacts; rxnID++) { - for (lcl_inst = 0; lcl_inst < ncreate[rxnID]; lcl_inst++) { + for (lcl_inst = 0; lcl_inst < nattempt[rxnID]; lcl_inst++) { onemol = atom->molecules[unreacted_mol[rxnID]]; twomol = atom->molecules[reacted_mol[rxnID]]; @@ -1238,10 +1238,10 @@ void FixBondReact::superimpose_algorithm() int myjbonding = jbonding[rxnID]; glove[myibonding-1][0] = myibonding; - glove[myibonding-1][1] = created[lcl_inst][0][rxnID]; + glove[myibonding-1][1] = attempt[lcl_inst][0][rxnID]; glove_counter++; glove[myjbonding-1][0] = myjbonding; - glove[myjbonding-1][1] = created[lcl_inst][1][rxnID]; + glove[myjbonding-1][1] = attempt[lcl_inst][1][rxnID]; glove_counter++; // special case, only two atoms in reaction templates diff --git a/src/USER-REACTION/fix_bond_react.h b/src/USER-REACTION/fix_bond_react.h index 61a1bd4213..bb7ed7fe9f 100644 --- a/src/USER-REACTION/fix_bond_react.h +++ b/src/USER-REACTION/fix_bond_react.h @@ -80,10 +80,10 @@ class FixBondReact : public Fix { int max_natoms; // max natoms in a molecule template tagint *partner,*finalpartner; double **distsq,*probability; - int *ncreate; - int maxcreate; - int allncreate; - tagint ***created; + int *nattempt; + int maxattempt; + int allnattempt; + tagint ***attempt; class Molecule *onemol; // pre-reacted molecule template class Molecule *twomol; // post-reacted molecule template From e01a926c878eff6cd155ae6e7809b43ec53e7430 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Wed, 2 Sep 2020 19:16:18 -0400 Subject: [PATCH 02/39] bond/react: add create_atoms section to map file --- src/USER-REACTION/fix_bond_react.cpp | 101 ++++++++++++++++++--------- src/USER-REACTION/fix_bond_react.h | 4 +- 2 files changed, 70 insertions(+), 35 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 79967e49a1..fd1448e859 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -390,6 +390,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms"); memory->create(custom_edges,max_natoms,nreacts,"bond/react:custom_edges"); memory->create(delete_atoms,max_natoms,nreacts,"bond/react:delete_atoms"); + memory->create(create_atoms,max_natoms,nreacts,"bond/react:create_atoms"); memory->create(chiral_atoms,max_natoms,6,nreacts,"bond/react:chiral_atoms"); for (int j = 0; j < nreacts; j++) @@ -398,6 +399,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : if (update_edges_flag[j] == 1) custom_edges[i][j] = 1; else custom_edges[i][j] = 0; delete_atoms[i][j] = 0; + create_atoms[i][j] = 0; for (int k = 0; k < 6; k++) { chiral_atoms[i][k][j] = 0; } @@ -410,11 +412,13 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : twomol = atom->molecules[reacted_mol[i]]; onemol->check_attributes(0); twomol->check_attributes(0); - if (onemol->natoms != twomol->natoms) - error->all(FLERR,"Bond/react: Reaction templates must contain the same number of atoms"); get_molxspecials(); read(i); fclose(fp); + if (ncreate == 0 && onemol->natoms != twomol->natoms) + error->all(FLERR,"Bond/react: Reaction templates must contain the same number of atoms"); + else if (ncreate > 0 && onemol->natoms + ncreate != twomol->natoms) + error->all(FLERR,"Bond/react: Incorrect number of created atoms"); iatomtype[i] = onemol->type[ibonding[i]-1]; jatomtype[i] = onemol->type[jbonding[i]-1]; find_landlocked_atoms(i); @@ -529,6 +533,7 @@ FixBondReact::~FixBondReact() memory->destroy(landlocked_atoms); memory->destroy(custom_edges); memory->destroy(delete_atoms); + memory->destroy(create_atoms); memory->destroy(chiral_atoms); memory->destroy(nevery); @@ -2090,7 +2095,8 @@ void FixBondReact::find_landlocked_atoms(int myrxn) // always remove edge atoms from landlocked list for (int i = 0; i < twomol->natoms; i++) { - if (edge[equivalences[i][1][myrxn]-1][myrxn] == 1) landlocked_atoms[i][myrxn] = 0; + if (create_atoms[i][myrxn] == 0 && edge[equivalences[i][1][myrxn]-1][myrxn] == 1) + landlocked_atoms[i][myrxn] = 0; else landlocked_atoms[i][myrxn] = 1; } int nspecial_limit = -1; @@ -2114,44 +2120,48 @@ void FixBondReact::find_landlocked_atoms(int myrxn) // bad molecule templates check // if atoms change types, but aren't landlocked, that's bad for (int i = 0; i < twomol->natoms; i++) { - if (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1] && landlocked_atoms[i][myrxn] == 0) { - char str[128]; - snprintf(str,128,"Bond/react: Atom type affected by reaction %s too close to template edge",rxn_name[myrxn]); - error->all(FLERR,str); + if (create_atoms[i][myrxn] == 0) { + if (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1] && landlocked_atoms[i][myrxn] == 0) { + char str[128]; + snprintf(str,128,"Bond/react: Atom type affected by reaction %s too close to template edge",rxn_name[myrxn]); + error->all(FLERR,str); + } } } // additionally, if a bond changes type, but neither involved atom is landlocked, bad // would someone want to change an angle type but not bond or atom types? (etc.) ...hopefully not yet for (int i = 0; i < twomol->natoms; i++) { - if (landlocked_atoms[i][myrxn] == 0) { - for (int j = 0; j < twomol->num_bond[i]; j++) { - int twomol_atomj = twomol->bond_atom[i][j]; - if (landlocked_atoms[twomol_atomj-1][myrxn] == 0) { - int onemol_atomi = equivalences[i][1][myrxn]; - int onemol_batom; - for (int m = 0; m < onemol->num_bond[onemol_atomi-1]; m++) { - onemol_batom = onemol->bond_atom[onemol_atomi-1][m]; - if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) { - if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) { - char str[128]; - snprintf(str,128,"Bond/react: Bond type affected by reaction %s too close to template edge",rxn_name[myrxn]); - error->all(FLERR,str); - } - } - } - if (newton_bond) { - int onemol_atomj = equivalences[twomol_atomj-1][1][myrxn]; - for (int m = 0; m < onemol->num_bond[onemol_atomj-1]; m++) { - onemol_batom = onemol->bond_atom[onemol_atomj-1][m]; - if (onemol_batom == equivalences[i][1][myrxn]) { - if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) { + if (create_atoms[i][myrxn] == 0) { + if (landlocked_atoms[i][myrxn] == 0) { + for (int j = 0; j < twomol->num_bond[i]; j++) { + int twomol_atomj = twomol->bond_atom[i][j]; + if (landlocked_atoms[twomol_atomj-1][myrxn] == 0) { + int onemol_atomi = equivalences[i][1][myrxn]; + int onemol_batom; + for (int m = 0; m < onemol->num_bond[onemol_atomi-1]; m++) { + onemol_batom = onemol->bond_atom[onemol_atomi-1][m]; + if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) { + if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) { char str[128]; snprintf(str,128,"Bond/react: Bond type affected by reaction %s too close to template edge",rxn_name[myrxn]); error->all(FLERR,str); } } } + if (newton_bond) { + int onemol_atomj = equivalences[twomol_atomj-1][1][myrxn]; + for (int m = 0; m < onemol->num_bond[onemol_atomj-1]; m++) { + onemol_batom = onemol->bond_atom[onemol_atomj-1][m]; + if (onemol_batom == equivalences[i][1][myrxn]) { + if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) { + char str[128]; + snprintf(str,128,"Bond/react: Bond type affected by reaction %s too close to template edge",rxn_name[myrxn]); + error->all(FLERR,str); + } + } + } + } } } } @@ -2173,13 +2183,22 @@ void FixBondReact::find_landlocked_atoms(int myrxn) // also, if atoms change number of bonds, but aren't landlocked, that could be bad if (me == 0) for (int i = 0; i < twomol->natoms; i++) { - if (twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0] && landlocked_atoms[i][myrxn] == 0) { - char str[128]; - snprintf(str,128,"Bond/react: Atom affected by reaction %s too close to template edge",rxn_name[myrxn]); - error->warning(FLERR,str); - break; + if (create_atoms[i][myrxn] == 0) { + if (twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0] && landlocked_atoms[i][myrxn] == 0) { + char str[128]; + snprintf(str,128,"Bond/react: Atom affected by reaction %s too close to template edge",rxn_name[myrxn]); + error->warning(FLERR,str); + break; + } } } + + // finally, if a created atom is not landlocked, bad! + for (int i = 0; i < twomol->natoms; i++) { + if (create_atoms[i][myrxn] == 1 && landlocked_atoms[i][myrxn] == 0) { + error->one(FLERR,"Bond/react: Created atom too close to template edge"); + } + } } /* ---------------------------------------------------------------------- @@ -3137,6 +3156,7 @@ void FixBondReact::read(int myrxn) // skip blank lines or lines that start with "#" // stop when read an unrecognized line + ncreate = 0; while (1) { readline(line); @@ -3156,6 +3176,7 @@ void FixBondReact::read(int myrxn) } else if (strstr(line,"customIDs")) sscanf(line,"%d",&ncustom); else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete); + else if (strstr(line,"createIDs")) sscanf(line,"%d",&ncreate); else if (strstr(line,"chiralIDs")) sscanf(line,"%d",&nchiral); else if (strstr(line,"constraints")) { sscanf(line,"%d",&nconstr); @@ -3192,6 +3213,8 @@ void FixBondReact::read(int myrxn) CustomEdges(line, myrxn); } else if (strcmp(keyword,"DeleteIDs") == 0) { DeleteAtoms(line, myrxn); + } else if (strcmp(keyword,"CreateIDs") == 0) { + CreateAtoms(line, myrxn); } else if (strcmp(keyword,"ChiralIDs") == 0) { ChiralCenters(line, myrxn); } else if (strcmp(keyword,"Constraints") == 0) { @@ -3279,6 +3302,16 @@ void FixBondReact::DeleteAtoms(char *line, int myrxn) } } +void FixBondReact::CreateAtoms(char *line, int myrxn) +{ + int tmp; + for (int i = 0; i < ncreate; i++) { + readline(line); + sscanf(line,"%d",&tmp); + create_atoms[tmp-1][myrxn] = 1; + } +} + void FixBondReact::ChiralCenters(char *line, int myrxn) { int tmp; diff --git a/src/USER-REACTION/fix_bond_react.h b/src/USER-REACTION/fix_bond_react.h index bb7ed7fe9f..4ee767e815 100644 --- a/src/USER-REACTION/fix_bond_react.h +++ b/src/USER-REACTION/fix_bond_react.h @@ -113,7 +113,7 @@ class FixBondReact : public Fix { int *ibonding,*jbonding; int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors - int nedge,nequivalent,ncustom,ndelete,nchiral,nconstr; // # edge, equivalent, custom atoms in mapping file + int nedge,nequivalent,ncustom,ndelete,ncreate,nchiral,nconstr; // # edge, equivalent, custom atoms in mapping file int attempted_rxn; // there was an attempt! int *local_rxn_count; int *ghostly_rxn_count; @@ -129,6 +129,7 @@ class FixBondReact : public Fix { int **landlocked_atoms; // all atoms at least three bonds away from edge atoms int **custom_edges; // atoms in molecule templates with incorrect valences int **delete_atoms; // atoms in pre-reacted templates to delete + int **create_atoms; // atoms in post-reacted templates to create int ***chiral_atoms; // pre-react chiral atoms. 1) flag 2) orientation 3-4) ordered atom types int **nxspecial,**onemol_nxspecial,**twomol_nxspecial; // full number of 1-4 neighbors @@ -153,6 +154,7 @@ class FixBondReact : public Fix { void Equivalences(char *, int); void CustomEdges(char *, int); void DeleteAtoms(char *, int); + void CreateAtoms(char *,int); void ChiralCenters(char *, int); void Constraints(char *, int); void readID(char *, int, int, int); From dbd7b1e001390a82d699712ea09ac2fad3601caf Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Sat, 19 Sep 2020 10:02:45 -0400 Subject: [PATCH 03/39] bond/react: manual rebase header --- src/USER-REACTION/fix_bond_react.h | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.h b/src/USER-REACTION/fix_bond_react.h index 4ee767e815..118770864f 100644 --- a/src/USER-REACTION/fix_bond_react.h +++ b/src/USER-REACTION/fix_bond_react.h @@ -64,7 +64,7 @@ class FixBondReact : public Fix { int reset_mol_ids_flag; int custom_exclude_flag; int *stabilize_steps_flag; - int *update_edges_flag; + int *custom_charges_fragid; int nconstraints; int narrhenius; double **constraints; @@ -80,10 +80,10 @@ class FixBondReact : public Fix { int max_natoms; // max natoms in a molecule template tagint *partner,*finalpartner; double **distsq,*probability; - int *nattempt; - int maxattempt; - int allnattempt; - tagint ***attempt; + int *ncreate; + int maxcreate; + int allncreate; + tagint ***created; class Molecule *onemol; // pre-reacted molecule template class Molecule *twomol; // post-reacted molecule template @@ -113,7 +113,7 @@ class FixBondReact : public Fix { int *ibonding,*jbonding; int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors - int nedge,nequivalent,ncustom,ndelete,ncreate,nchiral,nconstr; // # edge, equivalent, custom atoms in mapping file + int nedge,nequivalent,ndelete,ncreate,nchiral,nconstr; // # edge, equivalent, custom atoms in mapping file int attempted_rxn; // there was an attempt! int *local_rxn_count; int *ghostly_rxn_count; @@ -127,7 +127,7 @@ class FixBondReact : public Fix { int ***equivalences; // relation between pre- and post-reacted templates int ***reverse_equiv; // re-ordered equivalences int **landlocked_atoms; // all atoms at least three bonds away from edge atoms - int **custom_edges; // atoms in molecule templates with incorrect valences + int **custom_charges; // atoms whose charge should be updated int **delete_atoms; // atoms in pre-reacted templates to delete int **create_atoms; // atoms in post-reacted templates to create int ***chiral_atoms; // pre-react chiral atoms. 1) flag 2) orientation 3-4) ordered atom types @@ -152,9 +152,9 @@ class FixBondReact : public Fix { void read(int); void EdgeIDs(char *, int); void Equivalences(char *, int); - void CustomEdges(char *, int); void DeleteAtoms(char *, int); void CreateAtoms(char *,int); + void CustomCharges(int, int); void ChiralCenters(char *, int); void Constraints(char *, int); void readID(char *, int, int, int); @@ -183,6 +183,7 @@ class FixBondReact : public Fix { void glove_ghostcheck(); void ghost_glovecast(); void update_everything(); + void insert_atoms(int, tagint **, int); void unlimit_bond(); void limit_bond(int); void dedup_mega_gloves(int); //dedup global mega_glove From 74e3a1fe8c6d9a848ca1965c2f30983ea3c42ebe Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Sat, 19 Sep 2020 10:41:50 -0400 Subject: [PATCH 04/39] manual rebase take 2 --- src/USER-REACTION/fix_bond_react.cpp | 224 +++++++++++++-------------- src/USER-REACTION/fix_bond_react.h | 10 +- 2 files changed, 111 insertions(+), 123 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index fd1448e859..995c3a53da 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -16,36 +16,37 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) ------------------------------------------------------------------------- */ #include "fix_bond_react.h" -#include -#include -#include -#include -#include "update.h" -#include "modify.h" -#include "respa.h" + #include "atom.h" #include "atom_vec.h" -#include "force.h" -#include "pair.h" +#include "citeme.h" #include "comm.h" #include "domain.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "random_mars.h" -#include "reset_mol_ids.h" -#include "molecule.h" +#include "error.h" +#include "force.h" #include "group.h" -#include "citeme.h" +#include "input.h" #include "math_const.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "input.h" +#include "modify.h" +#include "molecule.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "random_mars.h" +#include "reset_mol_ids.h" +#include "respa.h" +#include "update.h" #include "variable.h" -#include "fmt/format.h" + #include "superpose3d.h" +#include +#include +#include + #include using namespace LAMMPS_NS; @@ -84,6 +85,9 @@ enum{DISTANCE,ANGLE,DIHEDRAL,ARRHENIUS,RMSD}; // keyword values that accept variables as input enum{NEVERY,RMIN,RMAX,PROB}; +// flag for one-proc vs shared reaction sites +enum{LOCAL,GLOBAL}; + /* ---------------------------------------------------------------------- */ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : @@ -91,10 +95,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : { if (lmp->citeme) lmp->citeme->add(cite_fix_bond_react); - fix1 = NULL; - fix2 = NULL; - fix3 = NULL; - reset_mol_ids = NULL; + fix1 = nullptr; + fix2 = nullptr; + fix3 = nullptr; + reset_mol_ids = nullptr; if (narg < 8) error->all(FLERR,"Illegal fix bond/react command: " "too few arguments"); @@ -115,12 +119,12 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : narrhenius = 0; status = PROCEED; - nxspecial = NULL; - onemol_nxspecial = NULL; - twomol_nxspecial = NULL; - xspecial = NULL; - onemol_xspecial = NULL; - twomol_xspecial = NULL; + nxspecial = nullptr; + onemol_nxspecial = nullptr; + twomol_nxspecial = nullptr; + xspecial = nullptr; + onemol_xspecial = nullptr; + twomol_xspecial = nullptr; // these group names are reserved for use exclusively by bond/react master_group = (char *) "bond_react_MASTER_group"; @@ -200,7 +204,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : memory->create(seed,nreacts,"bond/react:seed"); memory->create(limit_duration,nreacts,"bond/react:limit_duration"); memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag"); - memory->create(update_edges_flag,nreacts,"bond/react:update_edges_flag"); + memory->create(custom_charges_fragid,nreacts,"bond/react:custom_charges_fragid"); memory->create(constraints,1,MAXCONARGS,"bond/react:constraints"); memory->create(var_flag,NUMVARVALS,nreacts,"bond/react:var_flag"); memory->create(var_id,NUMVARVALS,nreacts,"bond/react:var_id"); @@ -220,7 +224,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : seed[i] = 12345; max_rxn[i] = INT_MAX; stabilize_steps_flag[i] = 0; - update_edges_flag[i] = 0; + custom_charges_fragid[i] = -1; // set default limit duration to 60 timesteps limit_duration[i] = 60; reaction_count[i] = 0; @@ -366,13 +370,15 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : limit_duration[rxn] = utils::numeric(FLERR,arg[iarg+1],false,lmp); stabilize_steps_flag[rxn] = 1; iarg += 2; - } else if (strcmp(arg[iarg],"update_edges") == 0) { + } else if (strcmp(arg[iarg],"custom_charges") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: " - "'update_edges' has too few arguments"); - if (strcmp(arg[iarg+1],"none") == 0) update_edges_flag[rxn] = 0; - else if (strcmp(arg[iarg+1],"charges") == 0) update_edges_flag[rxn] = 1; - else if (strcmp(arg[iarg+1],"custom") == 0) update_edges_flag[rxn] = 2; - else error->all(FLERR,"Illegal value for 'update_edges' keyword'"); + "'custom_charges' has too few arguments"); + if (strcmp(arg[iarg+1],"no") == 0) custom_charges_fragid[rxn] = -1; //default + else { + custom_charges_fragid[rxn] = atom->molecules[unreacted_mol[rxn]]->findfragment(arg[iarg+1]); + if (custom_charges_fragid[rxn] < 0) error->one(FLERR,"Bond/react: Molecule fragment for " + "'custom_charges' keyword does not exist"); + } iarg += 2; } else error->all(FLERR,"Illegal fix bond/react command: unknown keyword"); } @@ -388,7 +394,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : memory->create(reverse_equiv,max_natoms,2,nreacts,"bond/react:reverse_equiv"); memory->create(edge,max_natoms,nreacts,"bond/react:edge"); memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms"); - memory->create(custom_edges,max_natoms,nreacts,"bond/react:custom_edges"); + memory->create(custom_charges,max_natoms,nreacts,"bond/react:custom_charges"); memory->create(delete_atoms,max_natoms,nreacts,"bond/react:delete_atoms"); memory->create(create_atoms,max_natoms,nreacts,"bond/react:create_atoms"); memory->create(chiral_atoms,max_natoms,6,nreacts,"bond/react:chiral_atoms"); @@ -396,13 +402,17 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : for (int j = 0; j < nreacts; j++) for (int i = 0; i < max_natoms; i++) { edge[i][j] = 0; - if (update_edges_flag[j] == 1) custom_edges[i][j] = 1; - else custom_edges[i][j] = 0; + custom_charges[i][j] = 1; // update all partial charges by default delete_atoms[i][j] = 0; create_atoms[i][j] = 0; for (int k = 0; k < 6; k++) { chiral_atoms[i][k][j] = 0; } + // default equivalences to their own mol index + // all but created atoms will be updated + for (int m = 0; m < 2; m++) { + equivalences[i][m][j] = i+1; + } } // read all map files afterward @@ -422,6 +432,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : iatomtype[i] = onemol->type[ibonding[i]-1]; jatomtype[i] = onemol->type[jbonding[i]-1]; find_landlocked_atoms(i); + if (custom_charges_fragid[i] >= 0) CustomCharges(custom_charges_fragid[i],i); } // initialize Marsaglia RNG with processor-unique seed (Arrhenius prob) @@ -439,7 +450,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : } delete [] files; - if (atom->molecular != 1) + if (atom->molecular != Atom::MOLECULAR) error->all(FLERR,"Bond/react: Cannot use fix bond/react with non-molecular systems"); // check if bonding atoms are 1-2, 1-3, or 1-4 bonded neighbors @@ -475,16 +486,16 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : // allocate arrays local to this fix nmax = 0; - partner = finalpartner = NULL; - distsq = NULL; - probability = NULL; + partner = finalpartner = nullptr; + distsq = nullptr; + probability = nullptr; maxattempt = 0; - attempt = NULL; - nattempt = NULL; + attempt = nullptr; + nattempt = nullptr; allnattempt = 0; local_num_mega = 0; ghostly_num_mega = 0; - restore = NULL; + restore = nullptr; // zero out stats global_megasize = 0; @@ -492,17 +503,17 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : glove_counter = 0; guess_branch = new int[MAXGUESS](); pioneer_count = new int[max_natoms]; - local_mega_glove = NULL; - ghostly_mega_glove = NULL; - global_mega_glove = NULL; + local_mega_glove = nullptr; + ghostly_mega_glove = nullptr; + global_mega_glove = nullptr; // these are merely loop indices that became important pion = neigh = trace = 0; - id_fix1 = NULL; - id_fix2 = NULL; - id_fix3 = NULL; - statted_id = NULL; + id_fix1 = nullptr; + id_fix2 = nullptr; + id_fix3 = nullptr; + statted_id = nullptr; custom_exclude_flag = 0; // used to store restart info @@ -531,7 +542,7 @@ FixBondReact::~FixBondReact() memory->destroy(equivalences); memory->destroy(reverse_equiv); memory->destroy(landlocked_atoms); - memory->destroy(custom_edges); + memory->destroy(custom_charges); memory->destroy(delete_atoms); memory->destroy(create_atoms); memory->destroy(chiral_atoms); @@ -549,7 +560,7 @@ FixBondReact::~FixBondReact() memory->destroy(var_flag); memory->destroy(var_id); memory->destroy(stabilize_steps_flag); - memory->destroy(update_edges_flag); + memory->destroy(custom_charges_fragid); memory->destroy(iatomtype); memory->destroy(jatomtype); @@ -712,7 +723,7 @@ void FixBondReact::post_constructor() int unused; char * idprop; idprop = (char *) fix->extract("property",unused); - if (idprop == NULL) + if (idprop == nullptr) error->all(FLERR,"Exclude group must be a per-atom property group"); len = strlen(idprop) + 1; @@ -754,7 +765,7 @@ void FixBondReact::init() // check cutoff for iatomtype,jatomtype for (int i = 0; i < nreacts; i++) { - if (force->pair == NULL || cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]]) + if (force->pair == nullptr || cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]]) error->all(FLERR,"Bond/react: Fix bond/react cutoff is longer than pairwise cutoff"); } @@ -1315,7 +1326,7 @@ void FixBondReact::superimpose_algorithm() global_megasize = 0; ghost_glovecast(); // consolidate all mega_gloves to all processors - dedup_mega_gloves(0); // make sure atoms aren't added to more than one reaction + dedup_mega_gloves(LOCAL); // make sure atoms aren't added to more than one reaction MPI_Allreduce(&local_rxn_count[0],&reaction_count[0],nreacts,MPI_INT,MPI_SUM,world); @@ -1367,8 +1378,8 @@ void FixBondReact::superimpose_algorithm() next_reneighbor = update->ntimestep; // call limit_bond in 'global_mega_glove mode.' oh, and local mode - limit_bond(0); // add reacting atoms to nve/limit - limit_bond(1); + limit_bond(LOCAL); // add reacting atoms to nve/limit + limit_bond(GLOBAL); update_everything(); // change topology } @@ -2208,30 +2219,30 @@ allows for same site undergoing different pathways, in parallel void FixBondReact::dedup_mega_gloves(int dedup_mode) { - // dedup_mode == 0 for local_dedup - // dedup_mode == 1 for global_mega_glove + // dedup_mode == LOCAL for local_dedup + // dedup_mode == GLOBAL for global_mega_glove for (int i = 0; i < nreacts; i++) { - if (dedup_mode == 0) local_rxn_count[i] = 0; - if (dedup_mode == 1) ghostly_rxn_count[i] = 0; + if (dedup_mode == LOCAL) local_rxn_count[i] = 0; + if (dedup_mode == GLOBAL) ghostly_rxn_count[i] = 0; } int dedup_size = 0; - if (dedup_mode == 0) { + if (dedup_mode == LOCAL) { dedup_size = local_num_mega; - } else if (dedup_mode == 1) { + } else if (dedup_mode == GLOBAL) { dedup_size = global_megasize; } tagint **dedup_glove; memory->create(dedup_glove,max_natoms+1,dedup_size,"bond/react:dedup_glove"); - if (dedup_mode == 0) { + if (dedup_mode == LOCAL) { for (int i = 0; i < dedup_size; i++) { for (int j = 0; j < max_natoms+1; j++) { dedup_glove[j][i] = local_mega_glove[j][i]; } } - } else if (dedup_mode == 1) { + } else if (dedup_mode == GLOBAL) { for (int i = 0; i < dedup_size; i++) { for (int j = 0; j < max_natoms+1; j++) { dedup_glove[j][i] = global_mega_glove[j][i]; @@ -2311,7 +2322,7 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode) // we must update local_mega_glove and local_megasize // we can simply overwrite local_mega_glove column by column - if (dedup_mode == 0) { + if (dedup_mode == LOCAL) { int new_local_megasize = 0; for (int i = 0; i < local_num_mega; i++) { if (dedup_mask[i] == 0) { @@ -2328,7 +2339,7 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode) // we must update global_mega_glove and global_megasize // we can simply overwrite global_mega_glove column by column - if (dedup_mode == 1) { + if (dedup_mode == GLOBAL) { int new_global_megasize = 0; for (int i = 0; i < global_megasize; i++) { if (dedup_mask[i] == 0) { @@ -2365,7 +2376,7 @@ void FixBondReact::limit_bond(int limit_bond_mode) int nlocal = atom->nlocal; int temp_limit_num = 0; tagint *temp_limit_glove; - if (limit_bond_mode == 0) { + if (limit_bond_mode == LOCAL) { int max_temp = local_num_mega * (max_natoms + 1); temp_limit_glove = new tagint[max_temp]; for (int j = 0; j < local_num_mega; j++) { @@ -2376,7 +2387,7 @@ void FixBondReact::limit_bond(int limit_bond_mode) } } - } else if (limit_bond_mode == 1) { + } else if (limit_bond_mode == GLOBAL) { int max_temp = global_megasize * (max_natoms + 1); temp_limit_glove = new tagint[max_temp]; for (int j = 0; j < global_megasize; j++) { @@ -2564,7 +2575,7 @@ void FixBondReact::ghost_glovecast() column, 0, world); } - if (me == 0) dedup_mega_gloves(1); // global_mega_glove mode + if (me == 0) dedup_mega_gloves(GLOBAL); // global_mega_glove mode MPI_Bcast(&global_megasize,1,MPI_INT,0,world); MPI_Bcast(&(global_mega_glove[0][0]), global_megasize, column, 0, world); @@ -2659,11 +2670,11 @@ void FixBondReact::update_everything() twomol = atom->molecules[reacted_mol[rxnID]]; for (int j = 0; j < twomol->natoms; j++) { int jj = equivalences[j][1][rxnID]-1; - if ((landlocked_atoms[j][rxnID] == 1 || custom_edges[jj][rxnID] == 1) && - atom->map(update_mega_glove[jj+1][i]) >= 0 && + if (atom->map(update_mega_glove[jj+1][i]) >= 0 && atom->map(update_mega_glove[jj+1][i]) < nlocal) { - type[atom->map(update_mega_glove[jj+1][i])] = twomol->type[j]; - if (twomol->qflag && atom->q_flag) { + if (landlocked_atoms[j][rxnID] == 1) + type[atom->map(update_mega_glove[jj+1][i])] = twomol->type[j]; + if (twomol->qflag && atom->q_flag && custom_charges[jj][rxnID] == 1) { double *q = atom->q; q[atom->map(update_mega_glove[jj+1][i])] = twomol->q[j]; } @@ -3150,7 +3161,7 @@ void FixBondReact::read(int myrxn) // skip 1st line of file eof = fgets(line,MAXLINE,fp); - if (eof == NULL) error->one(FLERR,"Bond/react: Unexpected end of superimpose file"); + if (eof == nullptr) error->one(FLERR,"Bond/react: Unexpected end of superimpose file"); // read header lines // skip blank lines or lines that start with "#" @@ -3174,7 +3185,6 @@ void FixBondReact::read(int myrxn) error->one(FLERR,"Bond/react: Number of equivalences in map file must " "equal number of atoms in reaction templates"); } - else if (strstr(line,"customIDs")) sscanf(line,"%d",&ncustom); else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete); else if (strstr(line,"createIDs")) sscanf(line,"%d",&ncreate); else if (strstr(line,"chiralIDs")) sscanf(line,"%d",&nchiral); @@ -3191,7 +3201,7 @@ void FixBondReact::read(int myrxn) // loop over sections of superimpose file - int equivflag = 0, bondflag = 0, customedgesflag = 0; + int equivflag = 0, bondflag = 0; while (strlen(keyword)) { if (strcmp(keyword,"BondingIDs") == 0) { bondflag = 1; @@ -3208,9 +3218,6 @@ void FixBondReact::read(int myrxn) } else if (strcmp(keyword,"Equivalences") == 0) { equivflag = 1; Equivalences(line, myrxn); - } else if (strcmp(keyword,"Custom Edges") == 0) { - customedgesflag = 1; - CustomEdges(line, myrxn); } else if (strcmp(keyword,"DeleteIDs") == 0) { DeleteAtoms(line, myrxn); } else if (strcmp(keyword,"CreateIDs") == 0) { @@ -3228,12 +3235,6 @@ void FixBondReact::read(int myrxn) // error check if (bondflag == 0 || equivflag == 0) error->all(FLERR,"Bond/react: Map file missing BondingIDs or Equivalences section\n"); - - if (update_edges_flag[myrxn] == 2 && customedgesflag == 0) - error->all(FLERR,"Bond/react: Map file must have a Custom Edges section when using 'update_edges custom'\n"); - - if (update_edges_flag[myrxn] != 2 && customedgesflag == 1) - error->all(FLERR,"Bond/react: Specify 'update_edges custom' to include Custom Edges section in map file\n"); } void FixBondReact::EdgeIDs(char *line, int myrxn) @@ -3268,28 +3269,6 @@ void FixBondReact::Equivalences(char *line, int myrxn) } } -void FixBondReact::CustomEdges(char *line, int myrxn) -{ - // 0 for 'none', 1 for 'charges' - - int tmp; - int n = MAX(strlen("none"),strlen("charges")) + 1; - char *edgemode = new char[n]; - for (int i = 0; i < ncustom; i++) { - readline(line); - sscanf(line,"%d %s",&tmp,edgemode); - if (tmp > onemol->natoms) - error->one(FLERR,"Bond/react: Invalid template atom ID in map file"); - if (strcmp(edgemode,"none") == 0) - custom_edges[tmp-1][myrxn] = 0; - else if (strcmp(edgemode,"charges") == 0) - custom_edges[tmp-1][myrxn] = 1; - else - error->one(FLERR,"Bond/react: Illegal value in 'Custom Edges' section of map file"); - } - delete [] edgemode; -} - void FixBondReact::DeleteAtoms(char *line, int myrxn) { int tmp; @@ -3312,6 +3291,15 @@ void FixBondReact::CreateAtoms(char *line, int myrxn) } } +void FixBondReact::CustomCharges(int ifragment, int myrxn) +{ + for (int i = 0; i < onemol->natoms; i++) + if (onemol->fragmentmask[ifragment][i]) + custom_charges[i][myrxn] = 1; + else + custom_charges[i][myrxn] = 0; +} + void FixBondReact::ChiralCenters(char *line, int myrxn) { int tmp; @@ -3435,7 +3423,7 @@ void FixBondReact::readID(char *strarg, int iconstr, int mode, int myID) void FixBondReact::open(char *file) { fp = fopen(file,"r"); - if (fp == NULL) { + if (fp == nullptr) { char str[128]; snprintf(str,128,"Bond/react: Cannot open map file %s",file); error->one(FLERR,str); @@ -3446,7 +3434,7 @@ void FixBondReact::readline(char *line) { int n; if (me == 0) { - if (fgets(line,MAXLINE,fp) == NULL) n = 0; + if (fgets(line,MAXLINE,fp) == nullptr) n = 0; else n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); @@ -3463,11 +3451,11 @@ void FixBondReact::parse_keyword(int flag, char *line, char *keyword) int eof = 0; if (me == 0) { - if (fgets(line,MAXLINE,fp) == NULL) eof = 1; + if (fgets(line,MAXLINE,fp) == nullptr) eof = 1; while (eof == 0 && strspn(line," \t\n\r") == strlen(line)) { - if (fgets(line,MAXLINE,fp) == NULL) eof = 1; + if (fgets(line,MAXLINE,fp) == nullptr) eof = 1; } - if (fgets(keyword,MAXLINE,fp) == NULL) eof = 1; + if (fgets(keyword,MAXLINE,fp) == nullptr) eof = 1; } // if eof, set keyword empty and return @@ -3509,7 +3497,7 @@ int FixBondReact::parse(char *line, char **words, int max) int nwords = 0; words[nwords++] = strtok(line," \t\n\r\f"); - while ((ptr = strtok(NULL," \t\n\r\f"))) { + while ((ptr = strtok(nullptr," \t\n\r\f"))) { if (nwords < max) words[nwords] = ptr; nwords++; } diff --git a/src/USER-REACTION/fix_bond_react.h b/src/USER-REACTION/fix_bond_react.h index 118770864f..2696d84768 100644 --- a/src/USER-REACTION/fix_bond_react.h +++ b/src/USER-REACTION/fix_bond_react.h @@ -80,10 +80,10 @@ class FixBondReact : public Fix { int max_natoms; // max natoms in a molecule template tagint *partner,*finalpartner; double **distsq,*probability; - int *ncreate; - int maxcreate; - int allncreate; - tagint ***created; + int *nattempt; + int maxattempt; + int allnattempt; + tagint ***attempt; class Molecule *onemol; // pre-reacted molecule template class Molecule *twomol; // post-reacted molecule template @@ -113,7 +113,7 @@ class FixBondReact : public Fix { int *ibonding,*jbonding; int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors - int nedge,nequivalent,ndelete,ncreate,nchiral,nconstr; // # edge, equivalent, custom atoms in mapping file + int nedge,nequivalent,ndelete,ncreate,nchiral,nconstr; // # edge, equivalent atoms in mapping file int attempted_rxn; // there was an attempt! int *local_rxn_count; int *ghostly_rxn_count; From 0236cabce99bc31b68b4fd2787c0feb2c810cb8c Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Mon, 21 Sep 2020 10:29:42 -0400 Subject: [PATCH 05/39] bond/react:add-modify-create-keyword --- src/USER-REACTION/fix_bond_react.cpp | 22 +++++++++++++++++++--- src/USER-REACTION/fix_bond_react.h | 1 + 2 files changed, 20 insertions(+), 3 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 995c3a53da..93cf55000a 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -205,6 +205,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : memory->create(limit_duration,nreacts,"bond/react:limit_duration"); memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag"); memory->create(custom_charges_fragid,nreacts,"bond/react:custom_charges_fragid"); + memory->create(modify_create_fragid,nreacts,"bond/react:modify_create_fragid"); memory->create(constraints,1,MAXCONARGS,"bond/react:constraints"); memory->create(var_flag,NUMVARVALS,nreacts,"bond/react:var_flag"); memory->create(var_id,NUMVARVALS,nreacts,"bond/react:var_id"); @@ -225,6 +226,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : max_rxn[i] = INT_MAX; stabilize_steps_flag[i] = 0; custom_charges_fragid[i] = -1; + modify_create_fragid[i] = -1; // set default limit duration to 60 timesteps limit_duration[i] = 60; reaction_count[i] = 0; @@ -380,6 +382,16 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : "'custom_charges' keyword does not exist"); } iarg += 2; + } else if (strcmp(arg[iarg],"modify_create") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: " + "'modify_create' has too few arguments"); + if (strcmp(arg[iarg+1],"no") == 0) modify_create_fragid[rxn] = -1; //default + else { + modify_create_fragid[rxn] = atom->molecules[unreacted_mol[rxn]]->findfragment(arg[iarg+1]); + if (modify_create_fragid[rxn] < 0) error->one(FLERR,"Bond/react: Molecule fragment for " + "'modify_create' keyword does not exist"); + } + iarg += 2; } else error->all(FLERR,"Illegal fix bond/react command: unknown keyword"); } } @@ -561,6 +573,7 @@ FixBondReact::~FixBondReact() memory->destroy(var_id); memory->destroy(stabilize_steps_flag); memory->destroy(custom_charges_fragid); + memory->destroy(modify_create_fragid); memory->destroy(iatomtype); memory->destroy(jatomtype); @@ -2605,8 +2618,7 @@ void FixBondReact::update_everything() // used when deleting atoms int ndel,ndelone; - int *mark = new int[nlocal]; - for (int i = 0; i < nlocal; i++) mark[i] = 0; + int *mark; tagint *tag = atom->tag; AtomVec *avec = atom->avec; @@ -2653,6 +2665,8 @@ void FixBondReact::update_everything() delete [] iskip; // mark to-delete atoms + mark = new int[nlocal]; + for (int i = 0; i < nlocal; i++) mark[i] = 0; for (int i = 0; i < update_num_mega; i++) { rxnID = update_mega_glove[0][i]; onemol = atom->molecules[unreacted_mol[rxnID]]; @@ -3150,6 +3164,8 @@ void FixBondReact::update_everything() atom->nimpropers += Tdelta_imprp; } + + /* ---------------------------------------------------------------------- read superimpose file ------------------------------------------------------------------------- */ @@ -3258,7 +3274,7 @@ void FixBondReact::Equivalences(char *line, int myrxn) for (int i = 0; i < nequivalent; i++) { readline(line); sscanf(line,"%d %d",&tmp1,&tmp2); - if (tmp1 > onemol->natoms || tmp2 > onemol->natoms) + if (tmp1 > onemol->natoms || tmp2 > twomol->natoms) error->one(FLERR,"Bond/react: Invalid template atom ID in map file"); //equivalences is-> clmn 1: post-reacted, clmn 2: pre-reacted equivalences[tmp2-1][0][myrxn] = tmp2; diff --git a/src/USER-REACTION/fix_bond_react.h b/src/USER-REACTION/fix_bond_react.h index 2696d84768..506a98c4ec 100644 --- a/src/USER-REACTION/fix_bond_react.h +++ b/src/USER-REACTION/fix_bond_react.h @@ -65,6 +65,7 @@ class FixBondReact : public Fix { int custom_exclude_flag; int *stabilize_steps_flag; int *custom_charges_fragid; + int *modify_create_fragid; int nconstraints; int narrhenius; double **constraints; From ede28cc1bfae3cde696243c08d557afdfd22878d Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Mon, 21 Sep 2020 12:01:40 -0400 Subject: [PATCH 06/39] bond/react:modify-create-correction --- src/USER-REACTION/fix_bond_react.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 93cf55000a..194f548632 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -387,7 +387,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : "'modify_create' has too few arguments"); if (strcmp(arg[iarg+1],"no") == 0) modify_create_fragid[rxn] = -1; //default else { - modify_create_fragid[rxn] = atom->molecules[unreacted_mol[rxn]]->findfragment(arg[iarg+1]); + modify_create_fragid[rxn] = atom->molecules[reacted_mol[rxn]]->findfragment(arg[iarg+1]); if (modify_create_fragid[rxn] < 0) error->one(FLERR,"Bond/react: Molecule fragment for " "'modify_create' keyword does not exist"); } From 0b903fa7c2722a615cb90aeba9ca251b89bab7c9 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Mon, 21 Sep 2020 14:53:30 -0400 Subject: [PATCH 07/39] bond/react: create-atoms-draft-docs --- doc/src/fix_bond_react.rst | 81 +++++++++++++++++++++++--------------- 1 file changed, 50 insertions(+), 31 deletions(-) diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index 159e39d075..587ed29980 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -55,6 +55,9 @@ Syntax *custom_charges* value = *no* or *fragmentID* no = update all atomic charges (default) fragmentID = ID of molecule fragment whose charges are updated + *modify_create* value = *no* or *fragmentID* + no = use all eligible atoms for create-atoms fit (default) + fragmentID = ID of molecule fragment used for create-atoms fit Examples """""""" @@ -85,7 +88,9 @@ documentation. Topology changes are defined in pre- and post-reaction molecule templates and can include creation and deletion of bonds, angles, dihedrals, impropers, bond types, angle types, dihedral types, atom types, or atomic charges. In addition, reaction by-products or -other molecules can be identified and deleted. +other molecules can be identified and deleted. Finally, atoms can be +created and inserted at specific positions relative to the reaction +site. Fix bond/react does not use quantum mechanical (eg. fix qmmm) or pairwise bond-order potential (eg. Tersoff or AIREBO) methods to @@ -249,14 +254,14 @@ command page. The post-reacted molecule template contains a sample of the reaction site and its surrounding topology after the reaction has occurred. It -must contain the same number of atoms as the pre-reacted template. A -one-to-one correspondence between the atom IDs in the pre- and -post-reacted templates is specified in the map file as described -below. Note that during a reaction, an atom, bond, etc. type may -change to one that was previously not present in the simulation. These -new types must also be defined during the setup of a given simulation. -A discussion of correctly handling this is also provided on the -:doc:`molecule ` command page. +must contain the same number of atoms as the pre-reacted template +(unless there are created atoms). A one-to-one correspondence between +the atom IDs in the pre- and post-reacted templates is specified in +the map file as described below. Note that during a reaction, an atom, +bond, etc. type may change to one that was previously not present in +the simulation. These new types must also be defined during the setup +of a given simulation. A discussion of correctly handling this is also +provided on the :doc:`molecule ` command page. .. note:: @@ -270,7 +275,7 @@ A discussion of correctly handling this is also provided on the The map file is a text document with the following format: A map file has a header and a body. The header of map file the -contains one mandatory keyword and four optional keywords. The +contains one mandatory keyword and five optional keywords. The mandatory keyword is 'equivalences': .. parsed-literal:: @@ -283,11 +288,12 @@ The optional keywords are 'edgeIDs', 'deleteIDs', 'chiralIDs' and .. parsed-literal:: N *edgeIDs* = # of edge atoms N in the pre-reacted molecule template - N *deleteIDs* = # of atoms N that are specified for deletion - N *chiralIDs* = # of specified chiral centers N - N *constraints* = # of specified reaction constraints N + N *deleteIDs* = # of atoms N that are deleted + N *createIDs* = # of atoms N that are created + N *chiralIDs* = # of chiral centers N + N *constraints* = # of reaction constraints N -The body of the map file contains two mandatory sections and four +The body of the map file contains two mandatory sections and five optional sections. The first mandatory section begins with the keyword 'BondingIDs' and lists the atom IDs of the bonding atom pair in the pre-reacted molecule template. The second mandatory section begins @@ -299,13 +305,15 @@ molecule template. The first optional section begins with the keyword 'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted molecule template. The second optional section begins with the keyword 'DeleteIDs' and lists the atom IDs of pre-reaction template atoms to -delete. The third optional section begins with the keyword 'ChiralIDs' -lists the atom IDs of chiral atoms whose handedness should be -enforced. The fourth optional section begins with the keyword -'Constraints' and lists additional criteria that must be satisfied in -order for the reaction to occur. Currently, there are five types of -constraints available, as discussed below: 'distance', 'angle', -'dihedral', 'arrhenius', and 'rmsd'. +delete. The third optional section begins with the keyword 'CreateIDs' +and lists the atom IDs of the post-reaction template atoms to create. +The fourth optional section begins with the keyword 'ChiralIDs' lists +the atom IDs of chiral atoms whose handedness should be enforced. The +fifth optional section begins with the keyword 'Constraints' and lists +additional criteria that must be satisfied in order for the reaction +to occur. Currently, there are five types of constraints available, as +discussed below: 'distance', 'angle', 'dihedral', 'arrhenius', and +'rmsd'. A sample map file is given below: @@ -340,6 +348,26 @@ A sample map file is given below: ---------- +A user-specified set of atoms can be deleted by listing their +pre-reaction template IDs in the DeleteIDs section. A deleted atom +must still be included in the post-reaction molecule template, in +which it cannot be bonded to an atom that is not deleted. In addition +to deleting unwanted reaction by-products, this feature can be used to +remove specific topologies, such as small rings, that may be otherwise +indistinguishable. + +Atoms can be created by listing their post-reaction template IDs in +the CreateIDs section. A created atom should not be included in the +pre-reaction template. The inserted positions of created atoms are +determined by the coordinates of the post-reaction template, after +optimal translation and rotation of the post-reaction template to the +reaction site (using a fit with atoms that are neither created nor +deleted). Or, the *modify_create* keyword can be used to specify which +post-reaction atoms are used for this fit. The *fragmentID* value must +be the name of a molecule fragment defined in the post-reaction +:doc:`molecule ` template, and only atoms in this fragment +are used for the fit. + The handedness of atoms that are chiral centers can be enforced by listing their IDs in the ChiralIDs section. A chiral atom must be bonded to four atoms with mutually different atom types. This feature @@ -490,15 +518,6 @@ only the atomic charges of atoms in the molecule fragment are updated. A few other considerations: -Many reactions result in one or more atoms that are considered -unwanted by-products. Therefore, bond/react provides the option to -delete a user-specified set of atoms. These pre-reaction atoms are -identified in the map file. A deleted atom must still be included in -the post-reaction molecule template, in which it cannot be bonded to -an atom that is not deleted. In addition to deleting unwanted reaction -by-products, this feature can be used to remove specific topologies, -such as small rings, that may be otherwise indistinguishable. - Optionally, you can enforce additional behaviors on reacting atoms. For example, it may be beneficial to force reacting atoms to remain at a certain temperature. For this, you can use the internally-created @@ -572,7 +591,7 @@ Default """"""" The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, -reset_mol_ids = yes, custom_charges = no +reset_mol_ids = yes, custom_charges = no, modify_create = no ---------- From 61c51847c2ce363bfceecc8525f2fab48105fdfd Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Fri, 2 Oct 2020 20:53:27 -0400 Subject: [PATCH 08/39] bond/react: basic create atoms feature --- src/USER-REACTION/fix_bond_react.cpp | 295 +++++++++++++++++++++++++-- src/USER-REACTION/fix_bond_react.h | 3 +- 2 files changed, 276 insertions(+), 22 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 194f548632..c824e2ae86 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -205,6 +205,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : memory->create(limit_duration,nreacts,"bond/react:limit_duration"); memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag"); memory->create(custom_charges_fragid,nreacts,"bond/react:custom_charges_fragid"); + memory->create(create_atoms_flag,nreacts,"bond/react:create_atoms_flag"); memory->create(modify_create_fragid,nreacts,"bond/react:modify_create_fragid"); memory->create(constraints,1,MAXCONARGS,"bond/react:constraints"); memory->create(var_flag,NUMVARVALS,nreacts,"bond/react:var_flag"); @@ -226,6 +227,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : max_rxn[i] = INT_MAX; stabilize_steps_flag[i] = 0; custom_charges_fragid[i] = -1; + create_atoms_flag[i] = 0; modify_create_fragid[i] = -1; // set default limit duration to 60 timesteps limit_duration[i] = 60; @@ -573,6 +575,7 @@ FixBondReact::~FixBondReact() memory->destroy(var_id); memory->destroy(stabilize_steps_flag); memory->destroy(custom_charges_fragid); + memory->destroy(create_atoms_flag); memory->destroy(modify_create_fragid); memory->destroy(iatomtype); @@ -1387,6 +1390,13 @@ void FixBondReact::superimpose_algorithm() } } + // abort here, for processes that have no reactions + // only MPI in get_everything is for create_atoms, which are always in global_megasize + if (local_num_mega == 0 && global_megasize == 0) { + unlimit_bond(); + return; + } + // this updates topology next step next_reneighbor = update->ntimestep; @@ -2496,11 +2506,15 @@ void FixBondReact::glove_ghostcheck() int ghostly = 0; #if !defined(MPI_STUBS) if (comm->style == 0) { - for (int i = 0; i < onemol->natoms; i++) { - int ilocal = atom->map(glove[i][1]); - if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) { - ghostly = 1; - break; + if (create_atoms_flag[rxnID] == 1) { + ghostly = 1; + } else { + for (int i = 0; i < onemol->natoms; i++) { + int ilocal = atom->map(glove[i][1]); + if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) { + ghostly = 1; + break; + } } } } else { @@ -2663,6 +2677,22 @@ void FixBondReact::update_everything() } } delete [] iskip; + if (update_num_mega == 0) continue; + + // we can insert atoms here, now that reactions are finalized + // can't do it any earlier, due to skipped reactions (max_rxn) + // reactions that create atoms are always treated as 'global' + if (pass == 1) { + for (int i = 0; i < update_num_mega; i++) { + rxnID = update_mega_glove[0][i]; + if (create_atoms_flag[rxnID] == 1) { + onemol = atom->molecules[unreacted_mol[rxnID]]; + twomol = atom->molecules[reacted_mol[rxnID]]; + insert_atoms(update_mega_glove,i); + nlocal = atom->nlocal; + } + } + } // mark to-delete atoms mark = new int[nlocal]; @@ -2698,22 +2728,24 @@ void FixBondReact::update_everything() //maybe add check that all 1-3 neighbors of a local atoms are at least ghosts -> unneeded --jg //okay, here goes: - for (int i = 0; i < update_num_mega; i++) { - rxnID = update_mega_glove[0][i]; - twomol = atom->molecules[reacted_mol[rxnID]]; - for (int j = 0; j < twomol->natoms; j++) { - int jj = equivalences[j][1][rxnID]-1; - if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { - if (landlocked_atoms[j][rxnID] == 1) { - for (int k = 0; k < nspecial[atom->map(update_mega_glove[jj+1][i])][2]; k++) { - if (atom->map(special[atom->map(update_mega_glove[jj+1][i])][k]) < 0) { - error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away - most likely too many processors"); - } - } - } - } - } - } + //for (int i = 0; i < update_num_mega; i++) { + // rxnID = update_mega_glove[0][i]; + // twomol = atom->molecules[reacted_mol[rxnID]]; + // for (int j = 0; j < twomol->natoms; j++) { + // int jj = equivalences[j][1][rxnID]-1; + // int jlocal = atom->map(update_mega_glove[jj+1][i]); + // if (jlocal < nlocal && jlocal >= 0) { + // if (landlocked_atoms[j][rxnID] == 1) { + // for (int k = 0; k < nspecial[jlocal][2]; k++) { + // if (atom->map(special[jlocal][k]) < 0 && create_atoms[j][rxnID] == 0) { + // //error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away - most likely too many processors"); + // printf("local is %d other is %d on %d\n", update_mega_glove[jj+1][i],special[jlocal][k],me); + // } + // } + // } + // } + // } + //} int insert_num; // very nice and easy to completely overwrite special bond info for landlocked atoms @@ -3164,7 +3196,227 @@ void FixBondReact::update_everything() atom->nimpropers += Tdelta_imprp; } +/* ---------------------------------------------------------------------- +insert created atoms +------------------------------------------------------------------------- */ +void FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) +{ + // inserting atoms based off fix_deposit->pre_exchange + int flag; + imageint imageflag; + double coord[3],lamda[3],rotmat[3][3],vnew[3]; + double *newcoord; + + // clear ghost count and any ghost bonus data internal to AtomVec + // same logic as beginning of Comm::exchange() + // do it now b/c inserting atoms will overwrite ghost atoms + atom->nghost = 0; + atom->avec->clear_bonus(); + + double *sublo,*subhi; + if (domain->triclinic == 0) { + sublo = domain->sublo; + subhi = domain->subhi; + } else { + sublo = domain->sublo_lamda; + subhi = domain->subhi_lamda; + } + + // find current max atom and molecule IDs + tagint *tag = atom->tag; + double **x = atom->x; + tagint *molecule = atom->molecule; + int nlocal = atom->nlocal; + + tagint maxtag_all,maxmol_all; + tagint max = 0; + for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]); + MPI_Allreduce(&max,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world); + + max = 0; + for (int i = 0; i < nlocal; i++) max = MAX(max,molecule[i]); + MPI_Allreduce(&max,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world); + + int dimension = domain->dimension; + + // only proc that owns reacting atom (use ibonding), + // fits post-reaction template to reaction site, for creating atoms + int n2superpose = 0; + for (int j = 0; j < twomol->natoms; j++) { + if (modify_create_fragid[rxnID] >= 0) + if (!twomol->fragmentmask[modify_create_fragid[rxnID]][j]) continue; + if (!create_atoms[j][rxnID] && !delete_atoms[equivalences[j][1][rxnID]][rxnID]) + n2superpose++; + } + + int ifit = atom->map(my_mega_glove[ibonding[rxnID]+1][iupdate]); // use this local ID to find fitting proc + Superpose3D superposer(n2superpose); + if (ifit >= 0 && ifit < atom->nlocal) { + double **xfrozen; // coordinates for the "frozen" target molecule + double **xmobile; // coordinates for the "mobile" molecule + memory->create(xfrozen,n2superpose,3,"bond/react:xfrozen"); + memory->create(xmobile,n2superpose,3,"bond/react:xmobile"); + tagint iatom; + tagint iref = -1; // choose first atom as reference + int fit_incr = 0; + for (int j = 0; j < twomol->natoms; j++) { + if (modify_create_fragid[rxnID] >= 0) + if (!twomol->fragmentmask[modify_create_fragid[rxnID]][j]) continue; + int ipre = equivalences[j][1][rxnID]-1; // equiv pre-reaction template index + if (!create_atoms[j][rxnID] && !delete_atoms[ipre][rxnID]) { + if (atom->map(my_mega_glove[ipre+1][iupdate]) < 0) { + printf("WARNING: eligible atoms skipped for created-atoms fit on %d\n",me); + continue; + } + iatom = atom->map(my_mega_glove[ipre+1][iupdate]); + if (iref == -1) iref = iatom; + iatom = domain->closest_image(iref,iatom); + for (int k = 0; k < 3; k++) { + xfrozen[fit_incr][k] = x[iatom][k]; + xmobile[fit_incr][k] = twomol->x[j][k]; + } + fit_incr++; + } + } + double rmsd = superposer.Superpose(xfrozen, xmobile); + for (int i = 0; i < 3; i++) + for (int j = 0; j < 3; j++) + rotmat[i][j] = superposer.R[i][j]; + memory->destroy(xfrozen); + memory->destroy(xmobile); + } + + // choose random velocity for new particle + // used for every atom in molecule + //currently insert with zero velocities + //vnew[0] = vxlo + random->uniform() * (vxhi-vxlo); + //vnew[1] = vylo + random->uniform() * (vyhi-vylo); + //vnew[2] = vzlo + random->uniform() * (vzhi-vzlo); + + // check if new atoms are in my sub-box or above it if I am highest proc + // if so, add atom to my list via create_atom() + // initialize additional info about the atoms + // set group mask to "all" plus fix group + int preID; // new equivalences index + int root = 0; + int add_count = 0; + for (int m = 0; m < twomol->natoms; m++) { + if (create_atoms[m][rxnID] == 1) { + // increase atom count + add_count++; + preID = onemol->natoms+add_count; + + // apply optimal rotation/translation for created atom coords + // also map coords back into simulation box + root = 0; + if (ifit >= 0 && ifit < atom->nlocal) { + root = me; + MathExtra::matvec(rotmat,twomol->x[m],coord); + for (int i = 0; i < 3; i++) coord[i] += superposer.T[i]; + imageflag = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + domain->remap(coord,imageflag); + } + MPI_Allreduce(MPI_IN_PLACE,&root,1,MPI_INT,MPI_SUM,world); + MPI_Bcast(coord,3,MPI_DOUBLE,root,world); + + if (domain->triclinic) { + domain->x2lamda(coord,lamda); + newcoord = lamda; + } else newcoord = coord; + + flag = 0; + if (newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] && + newcoord[1] >= sublo[1] && newcoord[1] < subhi[1] && + newcoord[2] >= sublo[2] && newcoord[2] < subhi[2]) flag = 1; + else if (dimension == 3 && newcoord[2] >= domain->boxhi[2]) { + if (comm->layout != Comm::LAYOUT_TILED) { + if (comm->myloc[2] == comm->procgrid[2]-1 && + newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] && + newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1; + } else { + if (comm->mysplit[2][1] == 1.0 && + newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] && + newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1; + } + } else if (dimension == 2 && newcoord[1] >= domain->boxhi[1]) { + if (comm->layout != Comm::LAYOUT_TILED) { + if (comm->myloc[1] == comm->procgrid[1]-1 && + newcoord[0] >= sublo[0] && newcoord[0] < subhi[0]) flag = 1; + } else { + if (comm->mysplit[1][1] == 1.0 && + newcoord[0] >= sublo[0] && newcoord[0] < subhi[0]) flag = 1; + } + } + root = 0; + if (flag) { + root = me; + + atom->avec->create_atom(twomol->type[m],coord); + int n = atom->nlocal - 1; + atom->tag[n] = maxtag_all + add_count; + + // locally update mega_glove + my_mega_glove[preID][iupdate] = atom->tag[n]; + + if (atom->molecule_flag) atom->molecule[n] = maxmol_all+1; + if (atom->molecular == 2) { + atom->molindex[n] = 0; + atom->molatom[n] = m; + } + + atom->mask[n] = 1 | groupbit; + atom->image[n] = imageflag; + atom->v[n][0] = 0.01;//vnew[0]; + atom->v[n][1] = 0.01;//vnew[1]; + atom->v[n][2] = 0.01;//vnew[2]; + modify->create_attribute(n); + + // initialize group statuses + // why aren't these more global... + int flag; + int index1 = atom->find_custom("limit_tags",flag); + int *i_limit_tags = atom->ivector[index1]; + + int *i_statted_tags; + if (stabilization_flag == 1) { + int index2 = atom->find_custom(statted_id,flag); + i_statted_tags = atom->ivector[index2]; + } + + int index3 = atom->find_custom("react_tags",flag); + int *i_react_tags = atom->ivector[index3]; + + i_limit_tags[n] = update->ntimestep + 1; + if (stabilization_flag == 1) i_statted_tags[n] = 0; + i_react_tags[n] = rxnID; + } + // globally update mega_glove and equivalences + MPI_Allreduce(MPI_IN_PLACE,&root,1,MPI_INT,MPI_SUM,world); + MPI_Bcast(&my_mega_glove[preID][iupdate],1,MPI_LMP_TAGINT,root,world); + equivalences[m][0][rxnID] = m+1; + equivalences[m][1][rxnID] = preID; + reverse_equiv[preID-1][0][rxnID] = preID; + reverse_equiv[preID-1][1][rxnID] = m+1; + } + } + + // reset global natoms + // if global map exists, reset it now instead of waiting for comm + // since other pre-exchange fixes may use it + // invoke map_init() b/c atom count has grown + atom->natoms += add_count; + if (atom->natoms < 0) + error->all(FLERR,"Too many total atoms"); + maxtag_all += add_count; + if (maxtag_all >= MAXTAGINT) + error->all(FLERR,"New atom IDs exceed maximum allowed ID"); + if (atom->map_style != Atom::MAP_NONE) { + atom->map_init(); + atom->map_set(); + } +} /* ---------------------------------------------------------------------- read superimpose file @@ -3299,6 +3551,7 @@ void FixBondReact::DeleteAtoms(char *line, int myrxn) void FixBondReact::CreateAtoms(char *line, int myrxn) { + create_atoms_flag[myrxn] = 1; int tmp; for (int i = 0; i < ncreate; i++) { readline(line); diff --git a/src/USER-REACTION/fix_bond_react.h b/src/USER-REACTION/fix_bond_react.h index 506a98c4ec..e33d14f7d6 100644 --- a/src/USER-REACTION/fix_bond_react.h +++ b/src/USER-REACTION/fix_bond_react.h @@ -65,6 +65,7 @@ class FixBondReact : public Fix { int custom_exclude_flag; int *stabilize_steps_flag; int *custom_charges_fragid; + int *create_atoms_flag; int *modify_create_fragid; int nconstraints; int narrhenius; @@ -184,7 +185,7 @@ class FixBondReact : public Fix { void glove_ghostcheck(); void ghost_glovecast(); void update_everything(); - void insert_atoms(int, tagint **, int); + void insert_atoms(tagint **, int); void unlimit_bond(); void limit_bond(int); void dedup_mega_gloves(int); //dedup global mega_glove From ccb7a6ee11182c8727fa4d28ba3f22bf68367864 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Mon, 5 Oct 2020 23:16:46 -0400 Subject: [PATCH 09/39] remove unnecessary check because it breaks create_atoms feature --- src/USER-REACTION/fix_bond_react.cpp | 21 --------------------- 1 file changed, 21 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index c824e2ae86..db629d8bee 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -2726,27 +2726,6 @@ void FixBondReact::update_everything() } } - //maybe add check that all 1-3 neighbors of a local atoms are at least ghosts -> unneeded --jg - //okay, here goes: - //for (int i = 0; i < update_num_mega; i++) { - // rxnID = update_mega_glove[0][i]; - // twomol = atom->molecules[reacted_mol[rxnID]]; - // for (int j = 0; j < twomol->natoms; j++) { - // int jj = equivalences[j][1][rxnID]-1; - // int jlocal = atom->map(update_mega_glove[jj+1][i]); - // if (jlocal < nlocal && jlocal >= 0) { - // if (landlocked_atoms[j][rxnID] == 1) { - // for (int k = 0; k < nspecial[jlocal][2]; k++) { - // if (atom->map(special[jlocal][k]) < 0 && create_atoms[j][rxnID] == 0) { - // //error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away - most likely too many processors"); - // printf("local is %d other is %d on %d\n", update_mega_glove[jj+1][i],special[jlocal][k],me); - // } - // } - // } - // } - // } - //} - int insert_num; // very nice and easy to completely overwrite special bond info for landlocked atoms for (int i = 0; i < update_num_mega; i++) { From d5c6007797cf76bc3643c78880ae0daf3098fb49 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Sun, 25 Oct 2020 17:19:03 -0400 Subject: [PATCH 10/39] bond/react: revert some overzealous optimization could cause hang --- src/USER-REACTION/fix_bond_react.cpp | 8 -------- 1 file changed, 8 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index f2fb3d4f92..1b0c4a9be7 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -1390,13 +1390,6 @@ void FixBondReact::superimpose_algorithm() } } - // abort here, for processes that have no reactions - // only MPI in get_everything is for create_atoms, which are always in global_megasize - if (local_num_mega == 0 && global_megasize == 0) { - unlimit_bond(); - return; - } - // this updates topology next step next_reneighbor = update->ntimestep; @@ -2687,7 +2680,6 @@ void FixBondReact::update_everything() } } delete [] iskip; - if (update_num_mega == 0) continue; // we can insert atoms here, now that reactions are finalized // can't do it any earlier, due to skipped reactions (max_rxn) From b8d2b65d8dd77ad01c0fd4cc3ad36b99d9af7af3 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Sun, 25 Oct 2020 18:56:00 -0400 Subject: [PATCH 11/39] bond/react: generalize get_temperature --- src/USER-REACTION/fix_bond_react.cpp | 8 ++++---- src/USER-REACTION/fix_bond_react.h | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 1b0c4a9be7..8b6c1317af 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -1886,7 +1886,7 @@ int FixBondReact::check_constraints() } if (ANDgate != 1) return 0; } else if (constraints[i][1] == ARRHENIUS) { - t = get_temperature(); + t = get_temperature(glove,0,1); prrhob = constraints[i][3]*pow(t,constraints[i][4])* exp(-constraints[i][5]/(force->boltz*t)); if (prrhob < rrhandom[(int) constraints[i][2]]->uniform()) return 0; @@ -2007,7 +2007,7 @@ void FixBondReact::get_IDcoords(int mode, int myID, double *center) compute local temperature: average over all atoms in reaction template ------------------------------------------------------------------------- */ -double FixBondReact::get_temperature() +double FixBondReact::get_temperature(tagint **myglove, int row_offset, int col) { int i,ilocal; double adof = domain->dimension; @@ -2021,13 +2021,13 @@ double FixBondReact::get_temperature() if (rmass) { for (i = 0; i < onemol->natoms; i++) { - ilocal = atom->map(glove[i][1]); + ilocal = atom->map(myglove[i+row_offset][col]); t += (v[ilocal][0]*v[ilocal][0] + v[ilocal][1]*v[ilocal][1] + v[ilocal][2]*v[ilocal][2]) * rmass[ilocal]; } } else { for (i = 0; i < onemol->natoms; i++) { - ilocal = atom->map(glove[i][1]); + ilocal = atom->map(myglove[i+row_offset][col]); t += (v[ilocal][0]*v[ilocal][0] + v[ilocal][1]*v[ilocal][1] + v[ilocal][2]*v[ilocal][2]) * mass[type[ilocal]]; } diff --git a/src/USER-REACTION/fix_bond_react.h b/src/USER-REACTION/fix_bond_react.h index e33d14f7d6..d8ff4154e3 100644 --- a/src/USER-REACTION/fix_bond_react.h +++ b/src/USER-REACTION/fix_bond_react.h @@ -169,7 +169,7 @@ class FixBondReact : public Fix { void ring_check(); int check_constraints(); void get_IDcoords(int, int, double *); - double get_temperature(); + double get_temperature(tagint **, int, int); int get_chirality(double[12]); // get handedness given an ordered set of coordinates void open(char *); From 4b111d7c43752ca2abc53828c263749b40c0e4e5 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Sun, 25 Oct 2020 20:57:46 -0400 Subject: [PATCH 12/39] bond/react:better initial vels for created atoms --- src/USER-REACTION/fix_bond_react.cpp | 34 +++++++++++++++++++--------- src/USER-REACTION/fix_bond_react.h | 0 2 files changed, 23 insertions(+), 11 deletions(-) mode change 100644 => 100755 src/USER-REACTION/fix_bond_react.cpp mode change 100644 => 100755 src/USER-REACTION/fix_bond_react.h diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp old mode 100644 new mode 100755 index 8b6c1317af..3a5f91177b --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -3188,6 +3188,8 @@ void FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) imageint imageflag; double coord[3],lamda[3],rotmat[3][3],vnew[3]; double *newcoord; + double **v = atom->v; + double t; // clear ghost count and any ghost bonus data internal to AtomVec // same logic as beginning of Comm::exchange() @@ -3233,7 +3235,13 @@ void FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) int ifit = atom->map(my_mega_glove[ibonding[rxnID]+1][iupdate]); // use this local ID to find fitting proc Superpose3D superposer(n2superpose); + int root = 0; if (ifit >= 0 && ifit < atom->nlocal) { + root = me; + + // get 'temperatere' averaged over site, used for created atoms' vels + t = get_temperature(my_mega_glove,1,iupdate); + double **xfrozen; // coordinates for the "frozen" target molecule double **xmobile; // coordinates for the "mobile" molecule memory->create(xfrozen,n2superpose,3,"bond/react:xfrozen"); @@ -3267,20 +3275,15 @@ void FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) memory->destroy(xfrozen); memory->destroy(xmobile); } - - // choose random velocity for new particle - // used for every atom in molecule - //currently insert with zero velocities - //vnew[0] = vxlo + random->uniform() * (vxhi-vxlo); - //vnew[1] = vylo + random->uniform() * (vyhi-vylo); - //vnew[2] = vzlo + random->uniform() * (vzhi-vzlo); + MPI_Allreduce(MPI_IN_PLACE,&root,1,MPI_INT,MPI_SUM,world); + MPI_Bcast(&t,1,MPI_DOUBLE,root,world); // check if new atoms are in my sub-box or above it if I am highest proc // if so, add atom to my list via create_atom() // initialize additional info about the atoms // set group mask to "all" plus fix group int preID; // new equivalences index - int root = 0; + root = 0; int add_count = 0; for (int m = 0; m < twomol->natoms; m++) { if (create_atoms[m][rxnID] == 1) { @@ -3349,9 +3352,18 @@ void FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) atom->mask[n] = 1 | groupbit; atom->image[n] = imageflag; - atom->v[n][0] = 0.01;//vnew[0]; - atom->v[n][1] = 0.01;//vnew[1]; - atom->v[n][2] = 0.01;//vnew[2]; + + // guess a somewhat reasonable initial velocity based on reaction site + // further control is possible using bond_react_MASTER_group + // compute |velocity| corresponding to a given temperature t, using specific atom's mass + double vtnorm = sqrt(t / (force->mvv2e / (dimension * force->boltz)) / atom->mass[twomol->type[m]]); + v[n][0] = random[rxnID]->uniform(); + v[n][1] = random[rxnID]->uniform(); + v[n][2] = random[rxnID]->uniform(); + double vnorm = sqrt(v[n][0]*v[n][0] + v[n][1]*v[n][1] + v[n][2]*v[n][2]); + v[n][0] = v[n][0]/vnorm*vtnorm; + v[n][1] = v[n][1]/vnorm*vtnorm; + v[n][2] = v[n][2]/vnorm*vtnorm; modify->create_attribute(n); // initialize group statuses diff --git a/src/USER-REACTION/fix_bond_react.h b/src/USER-REACTION/fix_bond_react.h old mode 100644 new mode 100755 From 254963cddd7515441dbca7f93eef81437dbf9ed5 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Sun, 25 Oct 2020 21:16:04 -0400 Subject: [PATCH 13/39] Update fix_bond_react.rst --- doc/src/fix_bond_react.rst | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) mode change 100644 => 100755 doc/src/fix_bond_react.rst diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst old mode 100644 new mode 100755 index 587ed29980..cd40828e7d --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -366,7 +366,9 @@ deleted). Or, the *modify_create* keyword can be used to specify which post-reaction atoms are used for this fit. The *fragmentID* value must be the name of a molecule fragment defined in the post-reaction :doc:`molecule ` template, and only atoms in this fragment -are used for the fit. +are used for the fit. The velocity of each created atom is initialized +in a random direction with a magnitude calculated from the +instantaneous temperature of the reaction site. The handedness of atoms that are chiral centers can be enforced by listing their IDs in the ChiralIDs section. A chiral atom must be From 4435ed4870666822cfe9c3766e431edb0589d4c5 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 29 Oct 2020 23:08:10 -0400 Subject: [PATCH 14/39] bond/react:example for create_atoms feature builds a polysytrene 50-mer in vacuum --- .../8procs_out.lammps | 4137 +++++++++++++++++ .../chain_plus_styrene_map_create_atoms | 66 + .../chain_plus_styrene_reacted.data_template | 456 ++ ...yrene_unreacted_create_atoms.data_template | 294 ++ .../infromdata.class2 | 49 + .../polystyrene_create_atoms/trimer.data | 797 ++++ 6 files changed, 5799 insertions(+) create mode 100644 examples/USER/reaction/polystyrene_create_atoms/8procs_out.lammps create mode 100644 examples/USER/reaction/polystyrene_create_atoms/chain_plus_styrene_map_create_atoms create mode 100755 examples/USER/reaction/polystyrene_create_atoms/chain_plus_styrene_reacted.data_template create mode 100644 examples/USER/reaction/polystyrene_create_atoms/chain_plus_styrene_unreacted_create_atoms.data_template create mode 100755 examples/USER/reaction/polystyrene_create_atoms/infromdata.class2 create mode 100644 examples/USER/reaction/polystyrene_create_atoms/trimer.data diff --git a/examples/USER/reaction/polystyrene_create_atoms/8procs_out.lammps b/examples/USER/reaction/polystyrene_create_atoms/8procs_out.lammps new file mode 100644 index 0000000000..953a32394a --- /dev/null +++ b/examples/USER/reaction/polystyrene_create_atoms/8procs_out.lammps @@ -0,0 +1,4137 @@ +LAMMPS (22 Oct 2020) +Reading data file ... + orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 48 atoms + reading velocities ... + 48 velocities + scanning bonds ... + 8 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 33 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 50 bonds + reading angles ... + 84 angles + reading dihedrals ... + 127 dihedrals + reading impropers ... + 36 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0.0 0.0 0.0 + special bond factors coul: 0.0 0.0 0.0 + 4 = max # of 1-2 neighbors + 8 = max # of 1-3 neighbors + 17 = max # of 1-4 neighbors + 46 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.022 seconds +Read molecule template mol3: + 1 molecules + 30 atoms with max type 6 + 31 bonds with max type 10 + 51 angles with max type 16 + 73 dihedrals with max type 19 + 21 impropers with max type 7 +Read molecule template mol4: + 1 molecules + 46 atoms with max type 6 + 48 bonds with max type 13 + 81 angles with max type 22 + 121 dihedrals with max type 36 + 35 impropers with max type 9 +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined +PPPM initialization ... +WARNING: System is not charge neutral, net charge = -0.0006 (../kspace.cpp:313) + using 12-bit tables for long-range coulomb (../kspace.cpp:328) + G vector (1/distance) = 0.20144813 + grid = 45 45 45 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00053712952 + estimated relative force accuracy = 1.6175496e-06 + using double precision KISS FFT + 3d grid and FFT values/proc = 21952 12167 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 39 39 39 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1.0 +WARNING: Inconsistent image flags (../domain.cpp:812) +Per MPI rank memory allocation (min/avg/max) = 37.97 | 38.12 | 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3.7897264 0.0011457984 50 + 8000 9337.5805 4.2404387 0.0011457984 50 +Loop time of 107.636 on 8 procs for 8000 steps with 848 atoms + +Performance: 6.422 ns/day, 3.737 hours/ns, 74.325 timesteps/s +93.6% CPU use with 8 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0071581 | 0.99286 | 4.3913 | 151.9 | 0.92 +Bond | 0.023263 | 2.2103 | 10.081 | 229.9 | 2.05 +Kspace | 28.814 | 39.764 | 42.853 | 76.0 | 36.94 +Neigh | 6.4084 | 6.4395 | 6.4689 | 1.0 | 5.98 +Comm | 0.19227 | 0.25072 | 0.36267 | 12.4 | 0.23 +Output | 56.437 | 56.509 | 56.849 | 1.7 | 52.50 +Modify | 0.78657 | 1.4521 | 1.6493 | 23.1 | 1.35 +Other | | 0.0172 | | | 0.02 + +Nlocal: 106.000 ave 407 max 0 min +Histogram: 5 0 0 0 1 0 1 0 0 1 +Nghost: 71.1250 ave 338 max 0 min +Histogram: 5 0 1 0 1 0 0 0 0 1 +Neighs: 7377.88 ave 29891 max 0 min +Histogram: 5 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 59023 +Ave neighs/atom = 69.602594 +Ave special neighs/atom = 11.443396 +Neighbor list builds = 8000 +Dangerous builds = 0 +System init for write_data ... +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:328) + G vector (1/distance) = 0.20144813 + grid = 45 45 45 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0022576485 + estimated relative force accuracy = 6.7988414e-06 + using double precision KISS FFT + 3d grid and FFT values/proc = 21952 12167 +System init for write_data ... +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:328) + G vector (1/distance) = 0.20144813 + grid = 45 45 45 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0022576485 + estimated relative force accuracy = 6.7988414e-06 + using double precision KISS FFT + 3d grid and FFT values/proc = 21952 12167 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:48 diff --git a/examples/USER/reaction/polystyrene_create_atoms/chain_plus_styrene_map_create_atoms b/examples/USER/reaction/polystyrene_create_atoms/chain_plus_styrene_map_create_atoms new file mode 100644 index 0000000000..a90f1528bb --- /dev/null +++ b/examples/USER/reaction/polystyrene_create_atoms/chain_plus_styrene_map_create_atoms @@ -0,0 +1,66 @@ +this is a map file + +1 edgeIDs +30 equivalences +16 createIDs + +EdgeIDs + +30 + +BondingIDs + +4 +13 + +CreateIDs + +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 + +Equivalences + +1 45 +2 46 +3 44 +4 43 +5 42 +6 41 +7 40 +8 39 +9 38 +10 37 +11 36 +12 35 +13 34 +14 33 +15 32 +16 31 +17 17 +18 18 +19 19 +20 20 +21 21 +22 22 +23 23 +24 24 +25 25 +26 26 +27 27 +28 28 +29 29 +30 30 diff --git a/examples/USER/reaction/polystyrene_create_atoms/chain_plus_styrene_reacted.data_template b/examples/USER/reaction/polystyrene_create_atoms/chain_plus_styrene_reacted.data_template new file mode 100755 index 0000000000..83f04899b1 --- /dev/null +++ b/examples/USER/reaction/polystyrene_create_atoms/chain_plus_styrene_reacted.data_template @@ -0,0 +1,456 @@ +LAMMPS data file. msi2lmp v3.9.8 / 06 Oct 2016 / CGCMM for chain_plus_styrene_reacted + +46 atoms +48 bonds +81 angles +121 dihedrals +35 impropers +1 fragments + +Fragments + +create_fit 34 44 + +Types + +1 1 +2 2 +3 1 +4 5 +5 1 +6 2 +7 1 +8 2 +9 1 +10 2 +11 1 +12 2 +13 2 +14 6 +15 2 +16 2 +17 1 +18 2 +19 1 +20 5 +21 1 +22 2 +23 1 +24 2 +25 1 +26 2 +27 1 +28 2 +29 2 +30 6 +31 1 +32 2 +33 1 +34 5 +35 1 +36 2 +37 1 +38 2 +39 1 +40 2 +41 1 +42 2 +43 2 +44 6 +45 2 +46 2 + +Charges + +1 -0.129000 +2 0.123700 +3 0.026600 +4 -0.018200 +5 -0.129000 +6 0.123700 +7 -0.173400 +8 0.140300 +9 -0.113400 +10 0.128800 +11 -0.173400 +12 0.140300 +13 0.051600 +14 -0.069600 +15 0.035400 +16 0.035400 +17 -0.129000 +18 0.123700 +19 0.026600 +20 -0.018200 +21 -0.129000 +22 0.123700 +23 -0.173400 +24 0.140300 +25 -0.113400 +26 0.128800 +27 -0.173400 +28 0.140300 +29 0.051600 +30 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20 3 +45 12 21 19 20 29 +46 13 21 19 20 30 +47 13 21 19 20 3 +48 2 17 19 21 22 +49 4 17 19 21 23 +50 17 19 20 3 13 +51 14 19 20 3 2 +52 14 19 20 3 1 +53 18 29 20 3 13 +54 15 29 20 3 2 +55 15 29 20 3 1 +56 19 30 20 3 13 +57 16 30 20 3 2 +58 16 30 20 3 1 +59 10 22 21 19 20 +60 11 23 21 19 20 +61 2 19 21 23 24 +62 4 19 21 23 25 +63 5 22 21 23 24 +64 2 25 23 21 22 +65 2 21 23 25 26 +66 4 21 23 25 27 +67 5 24 23 25 26 +68 2 27 25 23 24 +69 4 23 25 27 17 +70 2 23 25 27 28 +71 5 26 25 27 28 +72 2 25 27 17 18 +73 2 17 27 25 26 + +Impropers + +1 1 2 3 13 20 +2 1 1 3 13 20 +3 1 2 3 1 20 +4 1 2 3 1 13 +5 1 16 6 8 5 +6 1 10 8 6 7 +7 1 12 10 8 9 +8 1 14 12 10 11 +9 7 14 13 4 3 +10 5 16 14 12 13 +11 1 14 16 6 15 +12 1 19 17 27 18 +13 5 17 19 21 20 +14 1 19 20 29 30 +15 1 19 20 29 3 +16 1 19 20 30 3 +17 1 29 20 30 3 +18 1 19 21 23 22 +19 1 21 23 25 24 +20 1 23 25 27 26 +21 1 17 27 25 28 diff --git a/examples/USER/reaction/polystyrene_create_atoms/infromdata.class2 b/examples/USER/reaction/polystyrene_create_atoms/infromdata.class2 new file mode 100755 index 0000000000..3affb24904 --- /dev/null +++ b/examples/USER/reaction/polystyrene_create_atoms/infromdata.class2 @@ -0,0 +1,49 @@ +# Jake practice run + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +variable T equal 530 + +read_data trimer.data & + extra/bond/per/atom 5 & + extra/angle/per/atom 15 & + extra/dihedral/per/atom 15 & + extra/improper/per/atom 25 & + extra/special/per/atom 25 + +molecule mol3 chain_plus_styrene_unreacted_create_atoms.data_template +molecule mol4 chain_plus_styrene_reacted.data_template + +fix rxn1 all bond/react stabilization yes statted_grp .03 & + react rxn2 all 1 0 3.0 mol3 mol4 chain_plus_styrene_map_create_atoms & + modify_create create_fit stabilize_steps 100 max_rxn 50 + +fix 1 statted_grp_REACT nvt temp $T $T 100 #iso 1 1 1000 + +fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1 + +thermo_style custom step temp press density f_rxn1[1] + +#restart 1 restart1 restart2 + +thermo 2 + +run 8000 + +write_data restart_longrun.data nofix diff --git a/examples/USER/reaction/polystyrene_create_atoms/trimer.data b/examples/USER/reaction/polystyrene_create_atoms/trimer.data new file mode 100644 index 0000000000..5a40205e16 --- /dev/null +++ b/examples/USER/reaction/polystyrene_create_atoms/trimer.data @@ -0,0 +1,797 @@ +LAMMPS data file via write_data, version 15 May 2019, timestep = 500 + +48 atoms +7 atom types +50 bonds +13 bond types +84 angles +22 angle types +127 dihedrals +36 dihedral types +36 impropers +9 improper types + +50 250 xlo xhi +50 250 ylo yhi +50 250 zlo zhi + +Masses + +1 12.0112 +2 1.00797 +3 12.0112 +4 12.0112 +5 12.0112 +6 12.0112 +7 12.0112 + +Pair Coeffs # lj/class2/coul/long + +1 0.064 4.01 +2 0.02 2.7 +3 0.064 4.01 +4 0.064 3.9 +5 0.054 4.01 +6 0.054 4.01 +7 0.054 4.01 + +Bond Coeffs # class2 + +1 1.0982 372.825 -803.453 894.317 +2 1.417 470.836 -627.618 1327.63 +3 1.501 321.902 -521.821 572.163 +4 1.0883 365.768 -725.54 781.662 +5 1.34 543.99 -1238.2 1644.03 +6 1.0883 365.768 -725.54 781.662 +7 1.501 321.902 -521.821 572.163 +8 1.101 345 -691.89 844.6 +9 1.53 299.67 -501.77 679.81 +10 1.101 345 -691.89 844.6 +11 1.501 321.902 -521.821 572.163 +12 1.101 345 -691.89 844.6 +13 1.53 299.67 -501.77 679.81 + +Angle Coeffs # class2 + +1 117.94 35.1558 -12.4682 0 +2 118.9 61.0226 -34.9931 0 +3 120.05 44.7148 -22.7352 0 +4 111 44.3234 -9.4454 0 +5 108.4 43.9594 -8.3924 -9.3379 +6 124.88 35.2766 -17.774 -1.6215 +7 124.88 35.2766 -17.774 -1.6215 +8 115.49 29.6363 -12.4853 -6.2218 +9 120.05 44.7148 -22.7352 0 +10 111 44.3234 -9.4454 0 +11 108.4 43.9594 -8.3924 -9.3379 +12 110.77 41.453 -10.604 5.129 +13 112.67 39.516 -7.443 -9.5583 +14 110.77 41.453 -10.604 5.129 +15 107.66 39.641 -12.921 -2.4318 +16 112.67 39.516 -7.443 -9.5583 +17 120.05 44.7148 -22.7352 0 +18 111 44.3234 -9.4454 0 +19 108.4 43.9594 -8.3924 -9.3379 +20 110.77 41.453 -10.604 5.129 +21 110.77 41.453 -10.604 5.129 +22 112.67 39.516 -7.443 -9.5583 + +BondBond Coeffs + +1 1.0795 1.417 1.0982 +2 68.2856 1.417 1.417 +3 12.0676 1.417 1.501 +4 2.9168 1.501 1.0883 +5 0 1.501 1.34 +6 10.1047 1.0883 1.34 +7 10.1047 1.0883 1.34 +8 4.8506 1.0883 1.0883 +9 12.0676 1.417 1.501 +10 2.9168 1.501 1.101 +11 0 1.501 1.53 +12 3.3872 1.101 1.53 +13 0 1.53 1.53 +14 3.3872 1.101 1.53 +15 5.3316 1.101 1.101 +16 0 1.53 1.53 +17 12.0676 1.417 1.501 +18 2.9168 1.501 1.101 +19 0 1.501 1.53 +20 3.3872 1.101 1.53 +21 3.3872 1.101 1.53 +22 0 1.53 1.53 + +BondAngle Coeffs + +1 20.0033 24.2183 1.417 1.0982 +2 28.8708 28.8708 1.417 1.417 +3 31.0771 47.0579 1.417 1.501 +4 26.4608 11.7717 1.501 1.0883 +5 0 0 1.501 1.34 +6 19.0592 23.3588 1.0883 1.34 +7 19.0592 23.3588 1.0883 1.34 +8 17.9795 17.9795 1.0883 1.0883 +9 31.0771 47.0579 1.417 1.501 +10 26.4608 11.7717 1.501 1.101 +11 0 0 1.501 1.53 +12 11.421 20.754 1.101 1.53 +13 8.016 8.016 1.53 1.53 +14 11.421 20.754 1.101 1.53 +15 18.103 18.103 1.101 1.101 +16 8.016 8.016 1.53 1.53 +17 31.0771 47.0579 1.417 1.501 +18 26.4608 11.7717 1.501 1.101 +19 0 0 1.501 1.53 +20 11.421 20.754 1.101 1.53 +21 11.421 20.754 1.101 1.53 +22 8.016 8.016 1.53 1.53 + +Dihedral Coeffs # class2 + +1 0 0 1.559 0 0 0 +2 0 0 3.9661 0 0 0 +3 0 0 4.4072 0 0 0 +4 8.3667 0 1.1932 0 0 0 +5 0 0 1.8769 0 0 0 +6 0 0 0 0 0 0 +7 0 0 0 0 0 0 +8 0 0 0 0 0 0 +9 0 0 4.8974 0 0 0 +10 0 0 1.559 0 0 0 +11 0 0 4.4072 0 0 0 +12 -0.2801 0 -0.0678 0 -0.0122 0 +13 -0.2802 0 -0.0678 0 -0.0122 0 +14 -0.0228 0 0.028 0 -0.1863 0 +15 -0.1432 0 0.0617 0 -0.1083 0 +16 0 0 0.0316 0 -0.1681 0 +17 0 0 0 0 0 0 +18 0 0 0.0316 0 -0.1681 0 +19 0 0 0.0514 0 -0.143 0 +20 0 0 1.559 0 0 0 +21 0 0 4.4072 0 0 0 +22 -0.2801 0 -0.0678 0 -0.0122 0 +23 -0.2802 0 -0.0678 0 -0.0122 0 +24 -0.0228 0 0.028 0 -0.1863 0 +25 0 0 0 0 0 0 +26 -0.1432 0 0.0617 0 -0.1083 0 +27 0 0 0.0316 0 -0.1681 0 +28 0 0 0 0 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35 36 10 +116 4 29 35 36 34 +117 5 47 35 36 10 +118 2 34 36 35 47 +119 2 35 36 34 9 +120 4 35 36 34 33 +121 5 10 36 34 9 +122 2 4 2 6 5 +123 4 6 2 4 15 +124 2 6 2 4 3 +125 5 1 2 4 3 +126 2 2 4 15 14 +127 2 15 4 2 1 + +Impropers + +1 6 45 46 48 28 +2 1 22 18 17 13 +3 1 22 18 13 19 +4 1 17 18 13 19 +5 1 22 18 17 19 +6 1 44 19 18 28 +7 1 23 19 18 28 +8 1 44 19 23 28 +9 1 44 19 23 18 +10 1 22 21 39 38 +11 5 21 22 24 18 +12 1 29 28 27 46 +13 1 29 28 27 19 +14 1 29 28 46 19 +15 1 27 28 46 19 +16 1 22 24 41 20 +17 1 21 39 40 37 +18 1 41 40 39 42 +19 1 24 41 40 43 +20 1 32 33 34 30 +21 1 36 34 33 9 +22 1 7 6 2 5 +23 1 16 7 6 8 +24 9 16 12 26 13 +25 1 25 13 11 12 +26 1 25 13 12 18 +27 1 11 13 12 18 +28 1 25 13 11 18 +29 1 16 15 4 14 +30 8 15 16 7 12 +31 5 32 29 35 28 +32 1 29 32 33 31 +33 1 29 35 36 47 +34 1 35 36 34 10 +35 1 6 2 4 1 +36 1 15 4 2 3 + From 17c14661bc1f0be585f58efe2a5933ef9644bbba Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Mon, 9 Nov 2020 00:18:24 -0500 Subject: [PATCH 15/39] port over some recent bugfixes --- src/USER-REACTION/fix_bond_react.cpp | 31 ++++++++++++++++++++++------ 1 file changed, 25 insertions(+), 6 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 3a5f91177b..9f0d1fd36d 100755 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -485,6 +485,14 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : } } + for (int i = 0; i < nreacts; i++) { + if (closeneigh[i] == -1) { // indicates will search non-bonded neighbors + if (cutsq[i][1] > neighbor->cutneighsq[iatomtype[i]][jatomtype[i]]) { + error->all(FLERR,"Bond/react: Fix bond/react cutoff is longer than pairwise cutoff"); + } + } + } + // initialize Marsaglia RNG with processor-unique seed ('prob' keyword) random = new class RanMars*[nreacts]; @@ -779,12 +787,6 @@ void FixBondReact::init() if (strstr(update->integrate_style,"respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; - // check cutoff for iatomtype,jatomtype - for (int i = 0; i < nreacts; i++) { - if (force->pair == nullptr || cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]]) - error->all(FLERR,"Bond/react: Fix bond/react cutoff is longer than pairwise cutoff"); - } - // need a half neighbor list, built every Nevery steps int irequest = neighbor->request(this,instance_me); neighbor->requests[irequest]->pair = 0; @@ -1747,6 +1749,17 @@ void FixBondReact::ring_check() // ring_check can be made more efficient by re-introducing 'frozen' atoms // 'frozen' atoms have been assigned and also are no longer pioneers + // double check the number of neighbors match for all non-edge atoms + // otherwise, atoms at 'end' of symmetric ring can behave like edge atoms + for (int i = 0; i < onemol->natoms; i++) { + if (edge[i][rxnID] == 0) { + if (onemol_nxspecial[i][0] != nxspecial[atom->map(glove[i][1])][0]) { + status = GUESSFAIL; + return; + } + } + } + for (int i = 0; i < onemol->natoms; i++) { for (int j = 0; j < onemol_nxspecial[i][0]; j++) { int ring_fail = 1; @@ -3175,6 +3188,12 @@ void FixBondReact::update_everything() int Tdelta_imprp; MPI_Allreduce(&delta_imprp,&Tdelta_imprp,1,MPI_INT,MPI_SUM,world); atom->nimpropers += Tdelta_imprp; + + if (ndel && (atom->map_style != Atom::MAP_NONE)) { + atom->nghost = 0; + atom->map_init(); + atom->map_set(); + } } /* ---------------------------------------------------------------------- From fdd7ecd9d9dcb911fcd019f618ec8482b77e9097 Mon Sep 17 00:00:00 2001 From: jrgissing Date: Wed, 11 Nov 2020 14:08:35 -0500 Subject: [PATCH 16/39] bond/react, create_atoms: correctly update molecule IDs --- src/USER-REACTION/fix_bond_react.cpp | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 9f0d1fd36d..1973c54539 100755 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -3363,7 +3363,13 @@ void FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) // locally update mega_glove my_mega_glove[preID][iupdate] = atom->tag[n]; - if (atom->molecule_flag) atom->molecule[n] = maxmol_all+1; + if (atom->molecule_flag) { + if (twomol->moleculeflag) { + atom->molecule[n] = maxmol_all + twomol->molecule[m]; + } else { + atom->molecule[n] = maxmol_all + 1; + } + } if (atom->molecular == 2) { atom->molindex[n] = 0; atom->molatom[n] = m; From b5c2dac6e6a620cc2a6596b94739d7f58f030803 Mon Sep 17 00:00:00 2001 From: jrgissing Date: Wed, 11 Nov 2020 20:55:47 -0500 Subject: [PATCH 17/39] bond/react, create_atoms: fix bug in parallel --- src/USER-REACTION/fix_bond_react.cpp | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 1973c54539..e1e326aa60 100755 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -3254,9 +3254,9 @@ void FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) int ifit = atom->map(my_mega_glove[ibonding[rxnID]+1][iupdate]); // use this local ID to find fitting proc Superpose3D superposer(n2superpose); - int root = 0; + int fitroot = 0; if (ifit >= 0 && ifit < atom->nlocal) { - root = me; + fitroot = me; // get 'temperatere' averaged over site, used for created atoms' vels t = get_temperature(my_mega_glove,1,iupdate); @@ -3294,15 +3294,14 @@ void FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) memory->destroy(xfrozen); memory->destroy(xmobile); } - MPI_Allreduce(MPI_IN_PLACE,&root,1,MPI_INT,MPI_SUM,world); - MPI_Bcast(&t,1,MPI_DOUBLE,root,world); + MPI_Allreduce(MPI_IN_PLACE,&fitroot,1,MPI_INT,MPI_SUM,world); + MPI_Bcast(&t,1,MPI_DOUBLE,fitroot,world); // check if new atoms are in my sub-box or above it if I am highest proc // if so, add atom to my list via create_atom() // initialize additional info about the atoms // set group mask to "all" plus fix group int preID; // new equivalences index - root = 0; int add_count = 0; for (int m = 0; m < twomol->natoms; m++) { if (create_atoms[m][rxnID] == 1) { @@ -3312,17 +3311,14 @@ void FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) // apply optimal rotation/translation for created atom coords // also map coords back into simulation box - root = 0; - if (ifit >= 0 && ifit < atom->nlocal) { - root = me; + if (fitroot == me) { MathExtra::matvec(rotmat,twomol->x[m],coord); for (int i = 0; i < 3; i++) coord[i] += superposer.T[i]; imageflag = ((imageint) IMGMAX << IMG2BITS) | ((imageint) IMGMAX << IMGBITS) | IMGMAX; domain->remap(coord,imageflag); } - MPI_Allreduce(MPI_IN_PLACE,&root,1,MPI_INT,MPI_SUM,world); - MPI_Bcast(coord,3,MPI_DOUBLE,root,world); + MPI_Bcast(coord,3,MPI_DOUBLE,fitroot,world); if (domain->triclinic) { domain->x2lamda(coord,lamda); @@ -3352,7 +3348,8 @@ void FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) newcoord[0] >= sublo[0] && newcoord[0] < subhi[0]) flag = 1; } } - root = 0; + + int root = 0; if (flag) { root = me; From 9d4ed1a2012bc5b5a9e77ba766f63d068f7ced1f Mon Sep 17 00:00:00 2001 From: jrgissing Date: Wed, 11 Nov 2020 21:47:04 -0500 Subject: [PATCH 18/39] bond/react, create_atoms: image flag fix --- src/USER-REACTION/fix_bond_react.cpp | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index e1e326aa60..a6878dbd20 100755 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -3204,11 +3204,12 @@ void FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) { // inserting atoms based off fix_deposit->pre_exchange int flag; - imageint imageflag; double coord[3],lamda[3],rotmat[3][3],vnew[3]; double *newcoord; double **v = atom->v; double t; + imageint imageflag = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX;; // clear ghost count and any ghost bonus data internal to AtomVec // same logic as beginning of Comm::exchange() @@ -3314,8 +3315,6 @@ void FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) if (fitroot == me) { MathExtra::matvec(rotmat,twomol->x[m],coord); for (int i = 0; i < 3; i++) coord[i] += superposer.T[i]; - imageflag = ((imageint) IMGMAX << IMG2BITS) | - ((imageint) IMGMAX << IMGBITS) | IMGMAX; domain->remap(coord,imageflag); } MPI_Bcast(coord,3,MPI_DOUBLE,fitroot,world); From bd19cf73eb66c2650ffa472a4843b6e05b339c2f Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 12 Nov 2020 12:01:59 -0500 Subject: [PATCH 19/39] bond/react, create_atoms: correct image flag fix --- src/USER-REACTION/fix_bond_react.cpp | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index a6878dbd20..366a67c210 100755 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -3204,12 +3204,11 @@ void FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) { // inserting atoms based off fix_deposit->pre_exchange int flag; + imageint imageflag; double coord[3],lamda[3],rotmat[3][3],vnew[3]; double *newcoord; double **v = atom->v; double t; - imageint imageflag = ((imageint) IMGMAX << IMG2BITS) | - ((imageint) IMGMAX << IMGBITS) | IMGMAX;; // clear ghost count and any ghost bonus data internal to AtomVec // same logic as beginning of Comm::exchange() @@ -3315,8 +3314,11 @@ void FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) if (fitroot == me) { MathExtra::matvec(rotmat,twomol->x[m],coord); for (int i = 0; i < 3; i++) coord[i] += superposer.T[i]; + imageflag = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; domain->remap(coord,imageflag); } + MPI_Bcast(&imageflag,1,MPI_LMP_IMAGEINT,fitroot,world); MPI_Bcast(coord,3,MPI_DOUBLE,fitroot,world); if (domain->triclinic) { From fb00fc6646ca4a59d0b4e52450361db6421a2e6c Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 12 Nov 2020 12:21:05 -0500 Subject: [PATCH 20/39] correct image flags in example data file bond/react, create_atoms --- .../polystyrene_create_atoms/trimer.data | 97 +++++++++---------- 1 file changed, 48 insertions(+), 49 deletions(-) diff --git a/examples/USER/reaction/polystyrene_create_atoms/trimer.data b/examples/USER/reaction/polystyrene_create_atoms/trimer.data index 5a40205e16..8bd81f0600 100644 --- a/examples/USER/reaction/polystyrene_create_atoms/trimer.data +++ b/examples/USER/reaction/polystyrene_create_atoms/trimer.data @@ -386,54 +386,54 @@ AngleAngle Coeffs Atoms # full -44 1 2 3.5400000000000001e-02 6.1476397222913839e+01 8.2376490601205234e+01 6.0906939115836181e+01 0 -1 0 -45 1276 2 3.5400000000000001e-02 5.8398688202244472e+01 8.0172948526664996e+01 6.2115536813582672e+01 0 0 1 -46 1276 6 -6.9599999999999995e-02 5.9489073989392523e+01 8.0264057167571636e+01 6.1984002598976552e+01 0 0 1 -48 1276 2 3.5400000000000001e-02 5.9675170230342431e+01 8.0048052449390738e+01 6.0920159395372401e+01 0 0 1 -47 1276 2 1.2370000000000000e-01 5.9297455513100488e+01 8.3187777608476154e+01 5.9645157256520122e+01 0 0 1 -18 1 5 -1.8200000000000001e-02 6.2426251430535707e+01 8.2055473568260709e+01 6.2971661388612958e+01 0 -1 0 -19 1 6 -6.9599999999999995e-02 6.1399255844467369e+01 8.1794665295860213e+01 6.1821819828185660e+01 0 -1 0 -21 1 1 -1.2900000000000000e-01 6.4032918371445831e+01 8.0190179089286701e+01 6.3021564712316334e+01 0 -1 0 -22 1 1 2.6599999999999999e-02 6.3672975135915053e+01 8.1418558650051665e+01 6.2448012627881994e+01 0 -1 0 -23 1 2 3.5400000000000001e-02 6.1545198223694939e+01 8.0836309422842305e+01 6.1349823957467130e+01 0 -1 0 -27 1276 2 5.1600000000000000e-02 5.9809503696580933e+01 8.1831265916389881e+01 6.3253745193271065e+01 0 0 1 -28 1276 5 -1.8200000000000001e-02 5.9900307947967441e+01 8.1677453781363639e+01 6.2190757403657820e+01 0 0 1 -31 1276 2 1.2370000000000000e-01 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6.6569600059599281e+01 7.9514748976494360e+01 6.0810611807135601e+01 +43 1 2 1.4030000000000001e-01 6.5780165393063371e+01 8.1570974991007958e+01 5.9850915261812396e+01 +9 1276 2 1.2880000000000000e-01 5.5651795605743445e+01 8.5074472139235127e+01 6.1094480497979262e+01 +30 1276 2 1.4030000000000001e-01 5.6082982679196888e+01 8.3912863624076010e+01 6.3351889697403472e+01 +33 1276 1 -1.7340000000000000e-01 5.6718133911388506e+01 8.3758479063002000e+01 6.2493293749545209e+01 +34 1276 1 -1.1340000000000000e-01 5.6498352105218459e+01 8.4426576393179090e+01 6.1290147608586011e+01 +6 3822 1 -1.7340000000000000e-01 6.3308103537340351e+01 8.7713509787622499e+01 6.4643082313868433e+01 +7 3822 1 -1.2900000000000000e-01 6.3010291684764312e+01 8.6423650045069493e+01 6.4252844241495922e+01 +8 3822 2 1.2370000000000000e-01 6.2089199187020355e+01 8.6309198636296912e+01 6.3711263099850854e+01 +10 1276 2 1.4030000000000001e-01 5.7266131308654970e+01 8.4599328362003035e+01 5.9281511478144402e+01 +11 3822 2 3.5400000000000001e-02 6.1694306618059791e+01 8.3823470438280594e+01 6.3778953909925114e+01 +12 3822 5 -1.8200000000000001e-02 6.3814926998838651e+01 8.3900077798460728e+01 6.4108991789590448e+01 +13 3822 6 -6.9599999999999995e-02 6.2604540882379787e+01 8.3491998603381077e+01 6.3249610918984622e+01 +14 3822 2 1.2370000000000000e-01 6.5739253131027880e+01 8.4813736128157771e+01 6.5351692111169555e+01 +15 3822 1 -1.2900000000000000e-01 6.5071144269009466e+01 8.5646783550482454e+01 6.5086813218945636e+01 +16 3822 1 2.6599999999999999e-02 6.3957099792282079e+01 8.5375816595044753e+01 6.4385073943729708e+01 +17 1 2 5.1600000000000000e-02 6.2256484483973310e+01 8.1576962161157596e+01 6.3963984654065122e+01 +26 3822 2 5.1600000000000000e-02 6.4196825763126355e+01 8.3291442832977836e+01 6.4907094488854057e+01 +29 1276 1 2.6599999999999999e-02 5.8784742332505303e+01 8.2766055380197670e+01 6.1667239692876961e+01 +32 1276 1 -1.2900000000000000e-01 5.7836199787435064e+01 8.3005060229118428e+01 6.2669788306756018e+01 +35 1276 1 -1.2900000000000000e-01 5.8572661840325132e+01 8.3404075689965083e+01 6.0443288532625175e+01 +36 1276 1 -1.7340000000000000e-01 5.7380616699226330e+01 8.4134680429976896e+01 6.0248710539932475e+01 +25 3822 2 3.5400000000000001e-02 6.2750675036816460e+01 8.3891633300878468e+01 6.2249429178485677e+01 +5 3822 2 1.4030000000000001e-01 6.2626160082050376e+01 8.8416565740835182e+01 6.4093918967496805e+01 +1 3822 2 1.2880000000000000e-01 6.4863557606529355e+01 8.9096029197548390e+01 6.5342927535537825e+01 +2 3822 1 -1.1340000000000000e-01 6.4627442641031166e+01 8.8047381925321190e+01 6.5138073202291650e+01 +3 3822 2 1.4030000000000001e-01 6.6470254992065406e+01 8.6991893750821745e+01 6.5857474890608984e+01 +4 3822 1 -1.7340000000000000e-01 6.5416488888088338e+01 8.6963894801200169e+01 6.5357641085394278e+01 Velocities @@ -794,4 +794,3 @@ Impropers 34 1 35 36 34 10 35 1 6 2 4 1 36 1 15 4 2 3 - From a3ce72c1b2bcfe45d422c7d73e688ff48423cc5f Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 12 Nov 2020 23:07:36 -0500 Subject: [PATCH 21/39] actually correct image flag fix hopefully --- src/USER-REACTION/fix_bond_react.cpp | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 366a67c210..2bc4335b20 100755 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -3314,8 +3314,7 @@ void FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) if (fitroot == me) { MathExtra::matvec(rotmat,twomol->x[m],coord); for (int i = 0; i < 3; i++) coord[i] += superposer.T[i]; - imageflag = ((imageint) IMGMAX << IMG2BITS) | - ((imageint) IMGMAX << IMGBITS) | IMGMAX; + imageflag = atom->image[ifit]; domain->remap(coord,imageflag); } MPI_Bcast(&imageflag,1,MPI_LMP_IMAGEINT,fitroot,world); From bb52af9a0772bdf41e5b795fb62667afab3e757e Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Fri, 13 Nov 2020 00:51:48 -0500 Subject: [PATCH 22/39] revert cutoff check temporary fix for hybrid pair style --- src/USER-REACTION/fix_bond_react.cpp | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 2bc4335b20..200988c44c 100755 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -485,14 +485,6 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : } } - for (int i = 0; i < nreacts; i++) { - if (closeneigh[i] == -1) { // indicates will search non-bonded neighbors - if (cutsq[i][1] > neighbor->cutneighsq[iatomtype[i]][jatomtype[i]]) { - error->all(FLERR,"Bond/react: Fix bond/react cutoff is longer than pairwise cutoff"); - } - } - } - // initialize Marsaglia RNG with processor-unique seed ('prob' keyword) random = new class RanMars*[nreacts]; @@ -787,6 +779,13 @@ void FixBondReact::init() if (strstr(update->integrate_style,"respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; + // check cutoff for iatomtype,jatomtype + for (int i = 0; i < nreacts; i++) { + if (!utils::strmatch(force->pair_style,"^hybrid")) + if (force->pair == nullptr || cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]]) + error->all(FLERR,"Bond/react: Fix bond/react cutoff is longer than pairwise cutoff"); + } + // need a half neighbor list, built every Nevery steps int irequest = neighbor->request(this,instance_me); neighbor->requests[irequest]->pair = 0; From 21e495d5ec486bb7bb0a8e2b028739399c698258 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Tue, 17 Nov 2020 14:47:50 -0500 Subject: [PATCH 23/39] bond/react: update modify_create syntax now, allows for multiple sub-keywords --- src/USER-REACTION/fix_bond_react.cpp | 24 +++++++++++++++++------- 1 file changed, 17 insertions(+), 7 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 200988c44c..d50f876b16 100755 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -385,15 +385,25 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : } iarg += 2; } else if (strcmp(arg[iarg],"modify_create") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: " + if (iarg++ > narg) error->all(FLERR,"Illegal fix bond/react command: " "'modify_create' has too few arguments"); - if (strcmp(arg[iarg+1],"no") == 0) modify_create_fragid[rxn] = -1; //default - else { - modify_create_fragid[rxn] = atom->molecules[reacted_mol[rxn]]->findfragment(arg[iarg+1]); - if (modify_create_fragid[rxn] < 0) error->one(FLERR,"Bond/react: Molecule fragment for " - "'modify_create' keyword does not exist"); + while (iarg < narg && strcmp(arg[iarg],"react") != 0 ) { + if (strcmp(arg[iarg],"fit") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: " + "'modify_create' has too few arguments"); + if (strcmp(arg[iarg+1],"all") == 0) modify_create_fragid[rxn] = -1; //default + else { + modify_create_fragid[rxn] = atom->molecules[reacted_mol[rxn]]->findfragment(arg[iarg+1]); + if (modify_create_fragid[rxn] < 0) error->one(FLERR,"Bond/react: Molecule fragment for " + "'modify_create' keyword does not exist"); + } + iarg += 2; + } else if (strcmp(arg[iarg],"near") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: " + "'modify_create' has too few arguments"); + iarg += 2; + } else break; } - iarg += 2; } else error->all(FLERR,"Illegal fix bond/react command: unknown keyword"); } } From 400812c4f10dbbd0370f8f2ee912e59fd4c3bb59 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Tue, 17 Nov 2020 21:06:47 -0500 Subject: [PATCH 24/39] refactor where/when atoms are insert, set up for near keyword --- src/USER-REACTION/fix_bond_react.cpp | 39 +++++++++++++++------------- src/USER-REACTION/fix_bond_react.h | 3 ++- 2 files changed, 23 insertions(+), 19 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index d50f876b16..af48ec39ec 100755 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -207,6 +207,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : memory->create(custom_charges_fragid,nreacts,"bond/react:custom_charges_fragid"); memory->create(create_atoms_flag,nreacts,"bond/react:create_atoms_flag"); memory->create(modify_create_fragid,nreacts,"bond/react:modify_create_fragid"); + memory->create(nearsq,nreacts,"bond/react:nearsq"); memory->create(constraints,1,MAXCONARGS,"bond/react:constraints"); memory->create(var_flag,NUMVARVALS,nreacts,"bond/react:var_flag"); memory->create(var_id,NUMVARVALS,nreacts,"bond/react:var_id"); @@ -229,6 +230,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : custom_charges_fragid[i] = -1; create_atoms_flag[i] = 0; modify_create_fragid[i] = -1; + nearsq[i] = 0; // set default limit duration to 60 timesteps limit_duration[i] = 60; reaction_count[i] = 0; @@ -401,6 +403,8 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : } else if (strcmp(arg[iarg],"near") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: " "'modify_create' has too few arguments"); + nearsq[rxn] = utils::numeric(FLERR,arg[iarg+1],false,lmp); + nearsq[rxn] *= nearsq[rxn]; iarg += 2; } else break; } @@ -587,6 +591,7 @@ FixBondReact::~FixBondReact() memory->destroy(custom_charges_fragid); memory->destroy(create_atoms_flag); memory->destroy(modify_create_fragid); + memory->destroy(nearsq); memory->destroy(iatomtype); memory->destroy(jatomtype); @@ -2645,9 +2650,8 @@ update molecule IDs, charges, types, special lists and all topology void FixBondReact::update_everything() { + int nlocal; // must be defined after create_atoms int *type = atom->type; - - int nlocal = atom->nlocal; int **nspecial = atom->nspecial; tagint **special = atom->special; @@ -2696,6 +2700,17 @@ void FixBondReact::update_everything() rxnID = global_mega_glove[0][i]; // reactions already shuffled from dedup procedure, so can skip first N if (iskip[rxnID]++ < nghostlyskips[rxnID]) continue; + + // we can insert atoms here, now that reactions are finalized + // can't do it any earlier, due to skipped reactions (max_rxn) + // reactions that create atoms are always treated as 'global' + if (create_atoms_flag[rxnID] == 1) { + onemol = atom->molecules[unreacted_mol[rxnID]]; + twomol = atom->molecules[reacted_mol[rxnID]]; + if (insert_atoms(global_mega_glove,i)) + ; else continue; // create aborted + } + for (int j = 0; j < max_natoms+1; j++) update_mega_glove[j][update_num_mega] = global_mega_glove[j][i]; update_num_mega++; @@ -2703,22 +2718,8 @@ void FixBondReact::update_everything() } delete [] iskip; - // we can insert atoms here, now that reactions are finalized - // can't do it any earlier, due to skipped reactions (max_rxn) - // reactions that create atoms are always treated as 'global' - if (pass == 1) { - for (int i = 0; i < update_num_mega; i++) { - rxnID = update_mega_glove[0][i]; - if (create_atoms_flag[rxnID] == 1) { - onemol = atom->molecules[unreacted_mol[rxnID]]; - twomol = atom->molecules[reacted_mol[rxnID]]; - insert_atoms(update_mega_glove,i); - nlocal = atom->nlocal; - } - } - } - // mark to-delete atoms + nlocal = atom->nlocal; mark = new int[nlocal]; for (int i = 0; i < nlocal; i++) mark[i] = 0; for (int i = 0; i < update_num_mega; i++) { @@ -3209,7 +3210,7 @@ void FixBondReact::update_everything() insert created atoms ------------------------------------------------------------------------- */ -void FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) +int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) { // inserting atoms based off fix_deposit->pre_exchange int flag; @@ -3440,6 +3441,8 @@ void FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) atom->map_init(); atom->map_set(); } + + return 1; } /* ---------------------------------------------------------------------- diff --git a/src/USER-REACTION/fix_bond_react.h b/src/USER-REACTION/fix_bond_react.h index d8ff4154e3..92927b853c 100755 --- a/src/USER-REACTION/fix_bond_react.h +++ b/src/USER-REACTION/fix_bond_react.h @@ -67,6 +67,7 @@ class FixBondReact : public Fix { int *custom_charges_fragid; int *create_atoms_flag; int *modify_create_fragid; + double *nearsq; int nconstraints; int narrhenius; double **constraints; @@ -185,7 +186,7 @@ class FixBondReact : public Fix { void glove_ghostcheck(); void ghost_glovecast(); void update_everything(); - void insert_atoms(tagint **, int); + int insert_atoms(tagint **, int); void unlimit_bond(); void limit_bond(int); void dedup_mega_gloves(int); //dedup global mega_glove From c4bf7766fe52b6a487c458214615aab0ea9697ff Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Tue, 17 Nov 2020 21:37:00 -0500 Subject: [PATCH 25/39] refactor insert_atoms --- src/USER-REACTION/fix_bond_react.cpp | 31 ++++++++++++++++------------ 1 file changed, 18 insertions(+), 13 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index af48ec39ec..2d3fa8b8d8 100755 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -3214,12 +3214,15 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) { // inserting atoms based off fix_deposit->pre_exchange int flag; - imageint imageflag; - double coord[3],lamda[3],rotmat[3][3],vnew[3]; + imageint *imageflags; + double **coords,lamda[3],rotmat[3][3],vnew[3]; double *newcoord; double **v = atom->v; double t; + memory->create(coords,twomol->natoms,3,"bond/react:coords"); + memory->create(imageflags,twomol->natoms,"bond/react:imageflags"); + // clear ghost count and any ghost bonus data internal to AtomVec // same logic as beginning of Comm::exchange() // do it now b/c inserting atoms will overwrite ghost atoms @@ -3322,18 +3325,18 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) // apply optimal rotation/translation for created atom coords // also map coords back into simulation box if (fitroot == me) { - MathExtra::matvec(rotmat,twomol->x[m],coord); - for (int i = 0; i < 3; i++) coord[i] += superposer.T[i]; - imageflag = atom->image[ifit]; - domain->remap(coord,imageflag); + MathExtra::matvec(rotmat,twomol->x[m],coords[m]); + for (int i = 0; i < 3; i++) coords[m][i] += superposer.T[i]; + imageflags[m] = atom->image[ifit]; + domain->remap(coords[m],imageflags[m]); } - MPI_Bcast(&imageflag,1,MPI_LMP_IMAGEINT,fitroot,world); - MPI_Bcast(coord,3,MPI_DOUBLE,fitroot,world); + MPI_Bcast(&imageflags[m],1,MPI_LMP_IMAGEINT,fitroot,world); + MPI_Bcast(coords[m],3,MPI_DOUBLE,fitroot,world); if (domain->triclinic) { - domain->x2lamda(coord,lamda); + domain->x2lamda(coords[m],lamda); newcoord = lamda; - } else newcoord = coord; + } else newcoord = coords[m]; flag = 0; if (newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] && @@ -3363,7 +3366,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) if (flag) { root = me; - atom->avec->create_atom(twomol->type[m],coord); + atom->avec->create_atom(twomol->type[m],coords[m]); int n = atom->nlocal - 1; atom->tag[n] = maxtag_all + add_count; @@ -3383,7 +3386,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) } atom->mask[n] = 1 | groupbit; - atom->image[n] = imageflag; + atom->image[n] = imageflags[m]; // guess a somewhat reasonable initial velocity based on reaction site // further control is possible using bond_react_MASTER_group @@ -3441,7 +3444,9 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) atom->map_init(); atom->map_set(); } - + // atom creation successful + memory->destroy(coords); + memory->destroy(imageflags); return 1; } From 1931cfa56ad2129e85996f25377decad0e463738 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Tue, 17 Nov 2020 22:18:08 -0500 Subject: [PATCH 26/39] add 'near' keyword --- src/USER-REACTION/fix_bond_react.cpp | 62 ++++++++++++++++++++++------ 1 file changed, 49 insertions(+), 13 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 2d3fa8b8d8..dd8883fabc 100755 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -2708,7 +2708,10 @@ void FixBondReact::update_everything() onemol = atom->molecules[unreacted_mol[rxnID]]; twomol = atom->molecules[reacted_mol[rxnID]]; if (insert_atoms(global_mega_glove,i)) - ; else continue; // create aborted + ; else { // create aborted + reaction_count_total[rxnID]--; + continue; + } } for (int j = 0; j < max_natoms+1; j++) @@ -3218,7 +3221,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) double **coords,lamda[3],rotmat[3][3],vnew[3]; double *newcoord; double **v = atom->v; - double t; + double t,delx,dely,delz,rsq; memory->create(coords,twomol->natoms,3,"bond/react:coords"); memory->create(imageflags,twomol->natoms,"bond/react:imageflags"); @@ -3310,6 +3313,50 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) MPI_Allreduce(MPI_IN_PLACE,&fitroot,1,MPI_INT,MPI_SUM,world); MPI_Bcast(&t,1,MPI_DOUBLE,fitroot,world); + // get coordinates and image flags + for (int m = 0; m < twomol->natoms; m++) { + if (create_atoms[m][rxnID] == 1) { + // apply optimal rotation/translation for created atom coords + // also map coords back into simulation box + if (fitroot == me) { + MathExtra::matvec(rotmat,twomol->x[m],coords[m]); + for (int i = 0; i < 3; i++) coords[m][i] += superposer.T[i]; + imageflags[m] = atom->image[ifit]; + domain->remap(coords[m],imageflags[m]); + } + MPI_Bcast(&imageflags[m],1,MPI_LMP_IMAGEINT,fitroot,world); + MPI_Bcast(coords[m],3,MPI_DOUBLE,fitroot,world); + } + } + + // check distance between any existing atom and inserted atom + // if less than near, abort + if (nearsq[rxnID] > 0) { + int abortflag = 0; + for (int m = 0; m < twomol->natoms; m++) { + if (create_atoms[m][rxnID] == 1) { + for (int i = 0; i < nlocal; i++) { + delx = coords[m][0] - x[i][0]; + dely = coords[m][1] - x[i][1]; + delz = coords[m][2] - x[i][2]; + domain->minimum_image(delx,dely,delz); + rsq = delx*delx + dely*dely + delz*delz; + if (rsq < nearsq[rxnID]) { + abortflag = 1; + break; + } + } + if (abortflag) break; + } + } + MPI_Allreduce(MPI_IN_PLACE,&abortflag,1,MPI_INT,MPI_MAX,world); + if (abortflag) { + memory->destroy(coords); + memory->destroy(imageflags); + return 0; + } + } + // check if new atoms are in my sub-box or above it if I am highest proc // if so, add atom to my list via create_atom() // initialize additional info about the atoms @@ -3322,17 +3369,6 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) add_count++; preID = onemol->natoms+add_count; - // apply optimal rotation/translation for created atom coords - // also map coords back into simulation box - if (fitroot == me) { - MathExtra::matvec(rotmat,twomol->x[m],coords[m]); - for (int i = 0; i < 3; i++) coords[m][i] += superposer.T[i]; - imageflags[m] = atom->image[ifit]; - domain->remap(coords[m],imageflags[m]); - } - MPI_Bcast(&imageflags[m],1,MPI_LMP_IMAGEINT,fitroot,world); - MPI_Bcast(coords[m],3,MPI_DOUBLE,fitroot,world); - if (domain->triclinic) { domain->x2lamda(coords[m],lamda); newcoord = lamda; From 337d47ca6cc433cfef26c543865d6accb11343cf Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Tue, 17 Nov 2020 22:46:42 -0500 Subject: [PATCH 27/39] update docs --- doc/src/fix_bond_react.rst | 35 ++++++++++++++++++++++++----------- 1 file changed, 24 insertions(+), 11 deletions(-) diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index cd40828e7d..34d2282312 100755 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -41,7 +41,7 @@ Syntax * template-ID(post-reacted) = ID of a molecule template containing post-reaction topology * map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates * zero or more individual keyword/value pairs may be appended to each react argument -* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges* +* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges* or *modify_create* .. parsed-literal:: @@ -55,9 +55,12 @@ Syntax *custom_charges* value = *no* or *fragmentID* no = update all atomic charges (default) fragmentID = ID of molecule fragment whose charges are updated - *modify_create* value = *no* or *fragmentID* - no = use all eligible atoms for create-atoms fit (default) - fragmentID = ID of molecule fragment used for create-atoms fit + *modify_create* keyword values + *fit* value = *all* or *fragmentID* + all = use all eligible atoms for create-atoms fit (default) + fragmentID = ID of molecule fragment used for create-atoms fit + *near* value = R + R = only insert atom/molecule if further than R from existing particles (distance units) Examples """""""" @@ -362,13 +365,23 @@ pre-reaction template. The inserted positions of created atoms are determined by the coordinates of the post-reaction template, after optimal translation and rotation of the post-reaction template to the reaction site (using a fit with atoms that are neither created nor -deleted). Or, the *modify_create* keyword can be used to specify which -post-reaction atoms are used for this fit. The *fragmentID* value must -be the name of a molecule fragment defined in the post-reaction -:doc:`molecule ` template, and only atoms in this fragment -are used for the fit. The velocity of each created atom is initialized -in a random direction with a magnitude calculated from the -instantaneous temperature of the reaction site. +deleted). The *modify_create* keyword can be used to modify the +default behavior when creating atoms. The *modify_create* keyword has +two sub-keywords, *fit* and *near*. One or more of the sub-keywords +may be used after the *modify_create* keyword. The *fit* sub-keyword +can be used to specify which post-reaction atoms are used for the +optimal translation and rotation of the post-reaction template. The +*fragmentID* value of the *fit* sub-keyword must be the name of a +molecule fragment defined in the post-reaction :doc:`molecule +` template, and only atoms in this fragment are used for the +fit. Atoms are created only if no current atom in the simulation is +within a distance R of any created atom, including the effect of +periodic boundary conditions if applicable. R is defined by the *near* +sub-keyword. Note that the default value for R is 0.0, which will +allow atoms to strongly overlap if you are inserting where other atoms +are present. The velocity of each created atom is initialized in a +random direction with a magnitude calculated from the instantaneous +temperature of the reaction site. The handedness of atoms that are chiral centers can be enforced by listing their IDs in the ChiralIDs section. A chiral atom must be From aa683eca594f15b7ce59b278b58f4a55fb072430 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Wed, 18 Nov 2020 11:47:28 -0500 Subject: [PATCH 28/39] bond/react, create_atom: bugfix when create is aborted --- src/USER-REACTION/fix_bond_react.cpp | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index dd8883fabc..85c265309e 100755 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -3226,12 +3226,6 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) memory->create(coords,twomol->natoms,3,"bond/react:coords"); memory->create(imageflags,twomol->natoms,"bond/react:imageflags"); - // clear ghost count and any ghost bonus data internal to AtomVec - // same logic as beginning of Comm::exchange() - // do it now b/c inserting atoms will overwrite ghost atoms - atom->nghost = 0; - atom->avec->clear_bonus(); - double *sublo,*subhi; if (domain->triclinic == 0) { sublo = domain->sublo; @@ -3357,6 +3351,12 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) } } + // clear ghost count and any ghost bonus data internal to AtomVec + // same logic as beginning of Comm::exchange() + // do it now b/c inserting atoms will overwrite ghost atoms + atom->nghost = 0; + atom->avec->clear_bonus(); + // check if new atoms are in my sub-box or above it if I am highest proc // if so, add atom to my list via create_atom() // initialize additional info about the atoms From 9b7831dc4f71b37076109d37e1117c1c9ef4ad36 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Wed, 18 Nov 2020 11:59:13 -0500 Subject: [PATCH 29/39] rename example folder --- .../8procs_out.lammps | 0 .../chain_plus_styrene_map_create_atoms | 0 .../chain_plus_styrene_reacted.data_template | 0 .../chain_plus_styrene_unreacted_create_atoms.data_template | 0 .../infromdata.class2 | 0 .../trimer.data | 0 6 files changed, 0 insertions(+), 0 deletions(-) rename examples/USER/reaction/{polystyrene_create_atoms => create_atoms_polystyrene}/8procs_out.lammps (100%) rename examples/USER/reaction/{polystyrene_create_atoms => create_atoms_polystyrene}/chain_plus_styrene_map_create_atoms (100%) rename examples/USER/reaction/{polystyrene_create_atoms => create_atoms_polystyrene}/chain_plus_styrene_reacted.data_template (100%) rename examples/USER/reaction/{polystyrene_create_atoms => create_atoms_polystyrene}/chain_plus_styrene_unreacted_create_atoms.data_template (100%) rename examples/USER/reaction/{polystyrene_create_atoms => create_atoms_polystyrene}/infromdata.class2 (100%) rename examples/USER/reaction/{polystyrene_create_atoms => create_atoms_polystyrene}/trimer.data (100%) diff --git a/examples/USER/reaction/polystyrene_create_atoms/8procs_out.lammps b/examples/USER/reaction/create_atoms_polystyrene/8procs_out.lammps similarity index 100% rename from examples/USER/reaction/polystyrene_create_atoms/8procs_out.lammps rename to examples/USER/reaction/create_atoms_polystyrene/8procs_out.lammps diff --git a/examples/USER/reaction/polystyrene_create_atoms/chain_plus_styrene_map_create_atoms b/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_map_create_atoms similarity index 100% rename from examples/USER/reaction/polystyrene_create_atoms/chain_plus_styrene_map_create_atoms rename to examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_map_create_atoms diff --git a/examples/USER/reaction/polystyrene_create_atoms/chain_plus_styrene_reacted.data_template b/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_reacted.data_template similarity index 100% rename from examples/USER/reaction/polystyrene_create_atoms/chain_plus_styrene_reacted.data_template rename to examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_reacted.data_template diff --git a/examples/USER/reaction/polystyrene_create_atoms/chain_plus_styrene_unreacted_create_atoms.data_template b/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_unreacted_create_atoms.data_template similarity index 100% rename from examples/USER/reaction/polystyrene_create_atoms/chain_plus_styrene_unreacted_create_atoms.data_template rename to examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_unreacted_create_atoms.data_template diff --git a/examples/USER/reaction/polystyrene_create_atoms/infromdata.class2 b/examples/USER/reaction/create_atoms_polystyrene/infromdata.class2 similarity index 100% rename from examples/USER/reaction/polystyrene_create_atoms/infromdata.class2 rename to examples/USER/reaction/create_atoms_polystyrene/infromdata.class2 diff --git a/examples/USER/reaction/polystyrene_create_atoms/trimer.data b/examples/USER/reaction/create_atoms_polystyrene/trimer.data similarity index 100% rename from examples/USER/reaction/polystyrene_create_atoms/trimer.data rename to examples/USER/reaction/create_atoms_polystyrene/trimer.data From 95c267c21bad16c0b58714b55c5f4966f71e9b91 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Wed, 18 Nov 2020 12:02:19 -0500 Subject: [PATCH 30/39] update example with new syntax --- .../USER/reaction/create_atoms_polystyrene/infromdata.class2 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/USER/reaction/create_atoms_polystyrene/infromdata.class2 b/examples/USER/reaction/create_atoms_polystyrene/infromdata.class2 index 3affb24904..b6e63d5365 100755 --- a/examples/USER/reaction/create_atoms_polystyrene/infromdata.class2 +++ b/examples/USER/reaction/create_atoms_polystyrene/infromdata.class2 @@ -32,7 +32,7 @@ molecule mol4 chain_plus_styrene_reacted.data_template fix rxn1 all bond/react stabilization yes statted_grp .03 & react rxn2 all 1 0 3.0 mol3 mol4 chain_plus_styrene_map_create_atoms & - modify_create create_fit stabilize_steps 100 max_rxn 50 + modify_create fit create_fit near 2.0 stabilize_steps 100 max_rxn 50 fix 1 statted_grp_REACT nvt temp $T $T 100 #iso 1 1 1000 From 0927e52dea30dbe7feea35954380aec294bd2f2e Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Wed, 18 Nov 2020 16:18:34 -0500 Subject: [PATCH 31/39] cleanup dead code --- src/USER-REACTION/fix_bond_react.cpp | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 85c265309e..08542b518e 100755 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -3416,11 +3416,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) atom->molecule[n] = maxmol_all + 1; } } - if (atom->molecular == 2) { - atom->molindex[n] = 0; - atom->molatom[n] = m; - } - + atom->mask[n] = 1 | groupbit; atom->image[n] = imageflags[m]; From de5ba601f214eab3f26e87693f666821d82c5a51 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 4 Feb 2021 13:41:58 -0500 Subject: [PATCH 32/39] Update fix_bond_react.rst manual rebase --- doc/src/fix_bond_react.rst | 170 +++++++++++++++++++++++-------------- 1 file changed, 106 insertions(+), 64 deletions(-) diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index 34d2282312..f54ba29bd3 100755 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -35,13 +35,13 @@ Syntax * react-ID = user-assigned name for the reaction * react-group-ID = only atoms in this group are considered for the reaction * Nevery = attempt reaction every this many steps -* Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) -* Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) +* Rmin = initiator atoms must be separated by more than Rmin to initiate reaction (distance units) +* Rmax = initiator atoms must be separated by less than Rmax to initiate reaction (distance units) * template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology * template-ID(post-reacted) = ID of a molecule template containing post-reaction topology * map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates * zero or more individual keyword/value pairs may be appended to each react argument -* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges* or *modify_create* +* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges* or *molecule* or *modify_create* .. parsed-literal:: @@ -55,6 +55,10 @@ Syntax *custom_charges* value = *no* or *fragmentID* no = update all atomic charges (default) fragmentID = ID of molecule fragment whose charges are updated + *molecule* value = *off* or *inter* or *intra* + off = allow both inter- and intramolecular reactions (default) + inter = search for reactions between molecules with different IDs + intra = search for reactions within the same molecule *modify_create* keyword values *fit* value = *all* or *fragmentID* all = use all eligible atoms for create-atoms fit (default) @@ -180,17 +184,19 @@ timesteps. *Nevery* can be specified with an equal-style integer. Three physical conditions must be met for a reaction to occur. First, -a bonding atom pair must be identified within the reaction distance -cutoffs. Second, the topology surrounding the bonding atom pair must -match the topology of the pre-reaction template. Finally, any reaction -constraints listed in the map file (see below) must be satisfied. If -all of these conditions are met, the reaction site is eligible to be -modified to match the post-reaction template. +an initiator atom pair must be identified within the reaction distance +cutoffs. Second, the topology surrounding the initiator atom pair must +match the topology of the pre-reaction template. Only atom types and +bond connectivity are used to identify a valid reaction site (not bond +types, etc.). Finally, any reaction constraints listed in the map file +(see below) must be satisfied. If all of these conditions are met, the +reaction site is eligible to be modified to match the post-reaction +template. -A bonding atom pair will be identified if several conditions are met. -First, a pair of atoms I,J within the specified react-group-ID of type -itype and jtype must be separated by a distance between *Rmin* and -*Rmax*\ . *Rmin* and *Rmax* can be specified with equal-style +An initiator atom pair will be identified if several conditions are +met. First, a pair of atoms I,J within the specified react-group-ID of +type itype and jtype must be separated by a distance between *Rmin* +and *Rmax*\ . *Rmin* and *Rmax* can be specified with equal-style :doc:`variables `. For example, these reaction cutoffs can be a function of the reaction conversion using the following commands: @@ -200,23 +206,30 @@ be a function of the reaction conversion using the following commands: fix myrxn all bond/react react myrxn1 all 1 0 v_rmax mol1 mol2 map_file.txt variable rmax equal 3+f_myrxn[1]/100 # arbitrary function of reaction count -It is possible that multiple bonding atom pairs are identified: if the -bonding atoms in the pre-reacted template are 1-2 neighbors, i.e. -directly bonded, the farthest bonding atom partner is set as its -bonding partner; otherwise, the closest potential partner is chosen. -Then, if both an atom I and atom J have each other as their bonding -partners, these two atoms are identified as the bonding atom pair of -the reaction site. Once this unique bonding atom pair is identified -for each reaction, there could two or more reactions that involve a -given atom on the same timestep. If this is the case, only one such -reaction is permitted to occur. This reaction is chosen randomly from -all potential reactions. This capability allows e.g. for different -reaction pathways to proceed from identical reaction sites with -user-specified probabilities. +The following criteria are used if multiple candidate initiator atom +pairs are identified within the cutoff distance: 1) If the initiator +atoms in the pre-reaction template are not 1-2 neighbors (i.e. not +directly bonded) the closest potential partner is chosen. 2) +Otherwise, if the initiator atoms in the pre-reaction template are 1-2 +neighbors (i.e. directly bonded) the farthest potential partner is +chosen. 3) Then, if both an atom I and atom J have each other as their +initiator partners, these two atoms are identified as the initiator +atom pair of the reaction site. Note that it can be helpful to select +unique atom types for the initiator atoms: if an initiator atom pair +is identified, as described in the previous steps, but does not +correspond to the same pair specified in the pre-reaction template, an +otherwise eligible reaction could be prevented from occurring. Once +this unique initiator atom pair is identified for each reaction, there +could be two or more reactions that involve the same atom on the same +timestep. If this is the case, only one such reaction is permitted to +occur. This reaction is chosen randomly from all potential reactions +involving the overlapping atom. This capability allows e.g. for +different reaction pathways to proceed from identical reaction sites +with user-specified probabilities. The pre-reacted molecule template is specified by a molecule command. This molecule template file contains a sample reaction site and its -surrounding topology. As described below, the bonding atom pairs of +surrounding topology. As described below, the initiator atom pairs of the pre-reacted template are specified by atom ID in the map file. The pre-reacted molecule template should contain as few atoms as possible while still completely describing the topology of all atoms affected @@ -230,18 +243,18 @@ missing topology with respect to the simulation. For example, the pre-reacted template may contain an atom that, in the simulation, is currently connected to the rest of a long polymer chain. These are referred to as edge atoms, and are also specified in the map file. All -pre-reaction template atoms should be linked to a bonding atom, via at -least one path that does not involve edge atoms. When the pre-reaction -template contains edge atoms, not all atoms, bonds, charges, etc. -specified in the reaction templates will be updated. Specifically, -topology that involves only atoms that are 'too near' to template -edges will not be updated. The definition of 'too near the edge' -depends on which interactions are defined in the simulation. If the -simulation has defined dihedrals, atoms within two bonds of edge atoms -are considered 'too near the edge.' If the simulation defines angles, -but not dihedrals, atoms within one bond of edge atoms are considered -'too near the edge.' If just bonds are defined, only edge atoms are -considered 'too near the edge.' +pre-reaction template atoms should be linked to an initiator atom, via +at least one path that does not involve edge atoms. When the +pre-reaction template contains edge atoms, not all atoms, bonds, +charges, etc. specified in the reaction templates will be updated. +Specifically, topology that involves only atoms that are 'too near' to +template edges will not be updated. The definition of 'too near the +edge' depends on which interactions are defined in the simulation. If +the simulation has defined dihedrals, atoms within two bonds of edge +atoms are considered 'too near the edge.' If the simulation defines +angles, but not dihedrals, atoms within one bond of edge atoms are +considered 'too near the edge.' If just bonds are defined, only edge +atoms are considered 'too near the edge.' .. note:: @@ -298,25 +311,25 @@ The optional keywords are 'edgeIDs', 'deleteIDs', 'chiralIDs' and The body of the map file contains two mandatory sections and five optional sections. The first mandatory section begins with the keyword -'BondingIDs' and lists the atom IDs of the bonding atom pair in the -pre-reacted molecule template. The second mandatory section begins -with the keyword 'Equivalences' and lists a one-to-one correspondence -between atom IDs of the pre- and post-reacted templates. The first -column is an atom ID of the pre-reacted molecule template, and the -second column is the corresponding atom ID of the post-reacted -molecule template. The first optional section begins with the keyword -'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted -molecule template. The second optional section begins with the keyword -'DeleteIDs' and lists the atom IDs of pre-reaction template atoms to -delete. The third optional section begins with the keyword 'CreateIDs' -and lists the atom IDs of the post-reaction template atoms to create. -The fourth optional section begins with the keyword 'ChiralIDs' lists -the atom IDs of chiral atoms whose handedness should be enforced. The -fifth optional section begins with the keyword 'Constraints' and lists -additional criteria that must be satisfied in order for the reaction -to occur. Currently, there are five types of constraints available, as -discussed below: 'distance', 'angle', 'dihedral', 'arrhenius', and -'rmsd'. +'InitiatorIDs' and lists the two atom IDs of the initiator atom pair +in the pre-reacted molecule template. The second mandatory section +begins with the keyword 'Equivalences' and lists a one-to-one +correspondence between atom IDs of the pre- and post-reacted +templates. The first column is an atom ID of the pre-reacted molecule +template, and the second column is the corresponding atom ID of the +post-reacted molecule template. The first optional section begins with +the keyword 'EdgeIDs' and lists the atom IDs of edge atoms in the +pre-reacted molecule template. The second optional section begins with +the keyword 'DeleteIDs' and lists the atom IDs of pre-reaction +template atoms to delete. The third optional section begins with the +keyword 'CreateIDs' and lists the atom IDs of the post-reaction +template atoms to create. The fourth optional section begins with the +keyword 'ChiralIDs' lists the atom IDs of chiral atoms whose +handedness should be enforced. The fifth optional section begins with +the keyword 'Constraints' and lists additional criteria that must be +satisfied in order for the reaction to occur. Currently, there are +five types of constraints available, as discussed below: 'distance', +'angle', 'dihedral', 'arrhenius', and 'rmsd'. A sample map file is given below: @@ -329,7 +342,7 @@ A sample map file is given below: 7 equivalences 2 edgeIDs - BondingIDs + InitiatorIDs 3 5 @@ -487,6 +500,23 @@ example, the molecule fragment could consist of only the backbone atoms of a polymer chain. This constraint can be used to enforce a specific relative position and orientation between reacting molecules. +By default, all constraints must be satisfied for the reaction to +occur. In other words, constraints are evaluated as a series of +logical values using the logical AND operator "&&". More complex logic +can be achieved by explicitly adding the logical AND operator "&&" or +the logical OR operator "||" after a given constraint command. If a +logical operator is specified after a constraint, it must be placed +after all constraint parameters, on the same line as the constraint +(one per line). Similarly, parentheses can be used to group +constraints. The expression that results from concatenating all +constraints should be a valid logical expression that can be read by +the :doc:`variable ` command after converting each +constraint to a logical value. Because exactly one constraint is +allowed per line, having a valid logical expression implies that left +parentheses "(" should only appear before a constraint, and right +parentheses ")" should only appear after a constraint and before any +logical operator. + Once a reaction site has been successfully identified, data structures within LAMMPS that store bond topology are updated to reflect the post-reacted molecule template. All force fields with fixed bonds, @@ -496,7 +526,7 @@ A few capabilities to note: 1) You may specify as many *react* arguments as desired. For example, you could break down a complicated reaction mechanism into several reaction steps, each defined by its own *react* argument. 2) While typically a bond is formed or removed -between the bonding atom pairs specified in the pre-reacted molecule +between the initiator atoms specified in the pre-reacted molecule template, this is not required. 3) By reversing the order of the pre- and post- reacted molecule templates in another *react* argument, you can allow for the possibility of one or more reverse reactions. @@ -525,12 +555,20 @@ situations, decreasing rather than increasing this parameter will result in an increase in stability. The *custom_charges* keyword can be used to specify which atoms' -atomic charges are updated. When the value is set to 'no,' all atomic +atomic charges are updated. When the value is set to 'no', all atomic charges are updated to those specified by the post-reaction template (default). Otherwise, the value should be the name of a molecule fragment defined in the pre-reaction molecule template. In this case, only the atomic charges of atoms in the molecule fragment are updated. +The *molecule* keyword can be used to force the reaction to be +intermolecular, intramolecular or either. When the value is set to +'off', molecule IDs are not considered when searching for reactions +(default). When the value is set to 'inter', the initiator atoms must +have different molecule IDs in order to be considered for the +reaction. When the value is set to 'intra', only initiator atoms with +the same molecule ID are considered for the reaction. + A few other considerations: Optionally, you can enforce additional behaviors on reacting atoms. @@ -583,7 +621,7 @@ These is 1 quantity for each react argument: No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. -When fix bond/react is 'unfixed,' all internally-created groups are +When fix bond/react is 'unfixed', all internally-created groups are deleted. Therefore, fix bond/react can only be unfixed after unfixing all other fixes that use any group created by fix bond/react. @@ -606,10 +644,14 @@ Default """"""" The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, -reset_mol_ids = yes, custom_charges = no, modify_create = no +reset_mol_ids = yes, custom_charges = no, molecule = off, modify_create = no ---------- .. _Gissinger: -**(Gissinger)** Gissinger, Jensen and Wise, Polymer, 128, 211 (2017). +**(Gissinger)** Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017). + +.. _Gissinger2020: + +**(Gissinger)** Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020). From e5ead83c8f45ff14bcfee333db954d584e9e5452 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 4 Feb 2021 15:33:45 -0500 Subject: [PATCH 33/39] near->overlap keyword update --- doc/src/fix_bond_react.rst | 14 +++++++------- src/USER-REACTION/fix_bond_react.cpp | 16 ++++++++-------- src/USER-REACTION/fix_bond_react.h | 2 +- 3 files changed, 16 insertions(+), 16 deletions(-) diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index f54ba29bd3..b995239d08 100755 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -63,7 +63,7 @@ Syntax *fit* value = *all* or *fragmentID* all = use all eligible atoms for create-atoms fit (default) fragmentID = ID of molecule fragment used for create-atoms fit - *near* value = R + *overlap* value = R R = only insert atom/molecule if further than R from existing particles (distance units) Examples @@ -380,7 +380,7 @@ optimal translation and rotation of the post-reaction template to the reaction site (using a fit with atoms that are neither created nor deleted). The *modify_create* keyword can be used to modify the default behavior when creating atoms. The *modify_create* keyword has -two sub-keywords, *fit* and *near*. One or more of the sub-keywords +two sub-keywords, *fit* and *overlap*. One or more of the sub-keywords may be used after the *modify_create* keyword. The *fit* sub-keyword can be used to specify which post-reaction atoms are used for the optimal translation and rotation of the post-reaction template. The @@ -389,11 +389,11 @@ molecule fragment defined in the post-reaction :doc:`molecule ` template, and only atoms in this fragment are used for the fit. Atoms are created only if no current atom in the simulation is within a distance R of any created atom, including the effect of -periodic boundary conditions if applicable. R is defined by the *near* -sub-keyword. Note that the default value for R is 0.0, which will -allow atoms to strongly overlap if you are inserting where other atoms -are present. The velocity of each created atom is initialized in a -random direction with a magnitude calculated from the instantaneous +periodic boundary conditions if applicable. R is defined by the +*overlap* sub-keyword. Note that the default value for R is 0.0, which +will allow atoms to strongly overlap if you are inserting where other +atoms are present. The velocity of each created atom is initialized in +a random direction with a magnitude calculated from the instantaneous temperature of the reaction site. The handedness of atoms that are chiral centers can be enforced by diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index de1a0a1a41..5b298be18d 100755 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -213,7 +213,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : memory->create(custom_charges_fragid,nreacts,"bond/react:custom_charges_fragid"); memory->create(create_atoms_flag,nreacts,"bond/react:create_atoms_flag"); memory->create(modify_create_fragid,nreacts,"bond/react:modify_create_fragid"); - memory->create(nearsq,nreacts,"bond/react:nearsq"); + memory->create(overlapsq,nreacts,"bond/react:overlapsq"); memory->create(molecule_keyword,nreacts,"bond/react:molecule_keyword"); memory->create(nconstraints,nreacts,"bond/react:nconstraints"); memory->create(constraintstr,nreacts,MAXLINE,"bond/react:constraintstr"); @@ -239,7 +239,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : custom_charges_fragid[i] = -1; create_atoms_flag[i] = 0; modify_create_fragid[i] = -1; - nearsq[i] = 0; + overlapsq[i] = 0; molecule_keyword[i] = OFF; nconstraints[i] = 0; // set default limit duration to 60 timesteps @@ -419,11 +419,11 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : "'modify_create' keyword does not exist"); } iarg += 2; - } else if (strcmp(arg[iarg],"near") == 0) { + } else if (strcmp(arg[iarg],"overlap") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: " "'modify_create' has too few arguments"); - nearsq[rxn] = utils::numeric(FLERR,arg[iarg+1],false,lmp); - nearsq[rxn] *= nearsq[rxn]; + overlapsq[rxn] = utils::numeric(FLERR,arg[iarg+1],false,lmp); + overlapsq[rxn] *= overlapsq[rxn]; iarg += 2; } else break; } @@ -616,7 +616,7 @@ FixBondReact::~FixBondReact() // need to delete rxn_name and constraintstr memory->destroy(create_atoms_flag); memory->destroy(modify_create_fragid); - memory->destroy(nearsq); + memory->destroy(overlapsq); memory->destroy(iatomtype); memory->destroy(jatomtype); @@ -3379,7 +3379,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) // check distance between any existing atom and inserted atom // if less than near, abort - if (nearsq[rxnID] > 0) { + if (overlapsq[rxnID] > 0) { int abortflag = 0; for (int m = 0; m < twomol->natoms; m++) { if (create_atoms[m][rxnID] == 1) { @@ -3389,7 +3389,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) delz = coords[m][2] - x[i][2]; domain->minimum_image(delx,dely,delz); rsq = delx*delx + dely*dely + delz*delz; - if (rsq < nearsq[rxnID]) { + if (rsq < overlapsq[rxnID]) { abortflag = 1; break; } diff --git a/src/USER-REACTION/fix_bond_react.h b/src/USER-REACTION/fix_bond_react.h index d0b3d52625..87a5945d45 100755 --- a/src/USER-REACTION/fix_bond_react.h +++ b/src/USER-REACTION/fix_bond_react.h @@ -69,7 +69,7 @@ class FixBondReact : public Fix { int *custom_charges_fragid; int *create_atoms_flag; int *modify_create_fragid; - double *nearsq; + double *overlapsq; int *molecule_keyword; int maxnconstraints; int *nconstraints; From c1292598544613e520e3f7e747de24606f4fe12d Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 4 Feb 2021 15:49:16 -0500 Subject: [PATCH 34/39] rebase correction --- src/USER-REACTION/fix_bond_react.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 5b298be18d..0ef302137e 100755 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -1956,7 +1956,7 @@ int FixBondReact::check_constraints() } if (ANDgate != 1) satisfied[i] = 0; } else if (constraints[i][rxnID].type == ARRHENIUS) { - t = get_temperature(); + t = get_temperature(glove,0,1); prrhob = constraints[i][rxnID].par[1]*pow(t,constraints[i][rxnID].par[2])* exp(-constraints[i][rxnID].par[3]/(force->boltz*t)); if (prrhob < rrhandom[(int) constraints[i][rxnID].par[0]]->uniform()) satisfied[i] = 0; From bd1cc91bddba31b6564058a324e40cf72d9a34fd Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 4 Feb 2021 20:20:18 -0500 Subject: [PATCH 35/39] update create atoms example --- .../chain_plus_styrene_map_create_atoms | 12 ++++---- .../chain_plus_styrene_reacted.data_template | 4 +-- ...yrene_unreacted_create_atoms.data_template | 4 +-- .../infromdata.class2 | 30 ++++++++----------- .../create_atoms_polystyrene/trimer.data | 2 +- 5 files changed, 23 insertions(+), 29 deletions(-) diff --git a/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_map_create_atoms b/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_map_create_atoms index a90f1528bb..88d282690c 100644 --- a/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_map_create_atoms +++ b/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_map_create_atoms @@ -1,18 +1,18 @@ -this is a map file +map file: styrene growth 1 edgeIDs 30 equivalences 16 createIDs -EdgeIDs - -30 - -BondingIDs +InitiatorIDs 4 13 +EdgeIDs + +30 + CreateIDs 1 diff --git a/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_reacted.data_template b/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_reacted.data_template index 83f04899b1..de0c2383bb 100755 --- a/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_reacted.data_template +++ b/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_reacted.data_template @@ -1,4 +1,4 @@ -LAMMPS data file. msi2lmp v3.9.8 / 06 Oct 2016 / CGCMM for chain_plus_styrene_reacted +molecule template: end of chain plus polymerized styrene 46 atoms 48 bonds @@ -9,7 +9,7 @@ LAMMPS data file. msi2lmp v3.9.8 / 06 Oct 2016 / CGCMM for chain_plus_styrene_re Fragments -create_fit 34 44 +create_fit 34 44 Types diff --git a/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_unreacted_create_atoms.data_template b/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_unreacted_create_atoms.data_template index f85b928f1e..d04fefccf5 100644 --- a/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_unreacted_create_atoms.data_template +++ b/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_unreacted_create_atoms.data_template @@ -1,4 +1,4 @@ -LAMMPS data file via write_data, version 18 Sep 2020, timestep = 0 +molecule template: end of styrene chain 30 atoms 31 bonds @@ -69,7 +69,7 @@ Coords 26 53.86061213540014 61.09506223825291 58.69441939855832 27 55.94906007539648 61.56969281804616 59.039933529456256 28 56.2513193202326 60.54265974655139 59.15389588713244 -29 58.35468332440925 64.79274880895268 59.64495986218142 +29 58.35468332440925 64.79274880895268 59.64495986218142 30 57.07961929431883 66.29987186904283 58.394030287459465 Charges diff --git a/examples/USER/reaction/create_atoms_polystyrene/infromdata.class2 b/examples/USER/reaction/create_atoms_polystyrene/infromdata.class2 index b6e63d5365..4331bf60b7 100755 --- a/examples/USER/reaction/create_atoms_polystyrene/infromdata.class2 +++ b/examples/USER/reaction/create_atoms_polystyrene/infromdata.class2 @@ -1,4 +1,4 @@ -# Jake practice run +# use bond/react 'create atoms' feature to add 50 new styrene monomers to chain units real @@ -20,30 +20,24 @@ improper_style class2 variable T equal 530 -read_data trimer.data & - extra/bond/per/atom 5 & - extra/angle/per/atom 15 & - extra/dihedral/per/atom 15 & - extra/improper/per/atom 25 & - extra/special/per/atom 25 +read_data trimer.data -molecule mol3 chain_plus_styrene_unreacted_create_atoms.data_template -molecule mol4 chain_plus_styrene_reacted.data_template +molecule mol1 grow_styrene_pre.data_template +molecule mol2 grow_styrene_post.data_template -fix rxn1 all bond/react stabilization yes statted_grp .03 & - react rxn2 all 1 0 3.0 mol3 mol4 chain_plus_styrene_map_create_atoms & - modify_create fit create_fit near 2.0 stabilize_steps 100 max_rxn 50 +fix myrxns all bond/react stabilization yes statted_grp .03 & + react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map & + modify_create fit create_fit overlap 2.0 & + stabilize_steps 100 max_rxn 50 -fix 1 statted_grp_REACT nvt temp $T $T 100 #iso 1 1 1000 +fix 1 statted_grp_REACT nvt temp $T $T 100 fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1 -thermo_style custom step temp press density f_rxn1[1] +thermo_style custom step temp press density f_myrxns[1] -#restart 1 restart1 restart2 - -thermo 2 +thermo 100 run 8000 -write_data restart_longrun.data nofix +# write_data final.data nofix diff --git a/examples/USER/reaction/create_atoms_polystyrene/trimer.data b/examples/USER/reaction/create_atoms_polystyrene/trimer.data index 8bd81f0600..b3ad132f03 100644 --- a/examples/USER/reaction/create_atoms_polystyrene/trimer.data +++ b/examples/USER/reaction/create_atoms_polystyrene/trimer.data @@ -1,4 +1,4 @@ -LAMMPS data file via write_data, version 15 May 2019, timestep = 500 +polystyrene trimer 48 atoms 7 atom types From 9a0805529c5f06a08862ee4b9a9dfdd702467437 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 4 Feb 2021 20:25:26 -0500 Subject: [PATCH 36/39] rename example files --- .../{chain_plus_styrene_map_create_atoms => grow_styrene.map} | 0 ...rene_reacted.data_template => grow_styrene_post.data_template} | 0 ..._create_atoms.data_template => grow_styrene_pre.data_template} | 0 .../{infromdata.class2 => in.grow_styrene} | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename examples/USER/reaction/create_atoms_polystyrene/{chain_plus_styrene_map_create_atoms => grow_styrene.map} (100%) rename examples/USER/reaction/create_atoms_polystyrene/{chain_plus_styrene_reacted.data_template => grow_styrene_post.data_template} (100%) rename examples/USER/reaction/create_atoms_polystyrene/{chain_plus_styrene_unreacted_create_atoms.data_template => grow_styrene_pre.data_template} (100%) rename examples/USER/reaction/create_atoms_polystyrene/{infromdata.class2 => in.grow_styrene} (100%) diff --git a/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_map_create_atoms b/examples/USER/reaction/create_atoms_polystyrene/grow_styrene.map similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_map_create_atoms rename to examples/USER/reaction/create_atoms_polystyrene/grow_styrene.map diff --git a/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_reacted.data_template b/examples/USER/reaction/create_atoms_polystyrene/grow_styrene_post.data_template similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_reacted.data_template rename to examples/USER/reaction/create_atoms_polystyrene/grow_styrene_post.data_template diff --git a/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_unreacted_create_atoms.data_template b/examples/USER/reaction/create_atoms_polystyrene/grow_styrene_pre.data_template similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_unreacted_create_atoms.data_template rename to examples/USER/reaction/create_atoms_polystyrene/grow_styrene_pre.data_template diff --git a/examples/USER/reaction/create_atoms_polystyrene/infromdata.class2 b/examples/USER/reaction/create_atoms_polystyrene/in.grow_styrene similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/infromdata.class2 rename to examples/USER/reaction/create_atoms_polystyrene/in.grow_styrene From dde3a8cebba81d634238b49645f528e1f3120753 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 4 Feb 2021 21:00:46 -0500 Subject: [PATCH 37/39] update log files --- .../8procs_out.lammps | 4137 ----------------- .../create_atoms_polystyrene/in.grow_styrene | 11 +- .../log.24Dec20.grow_styrene.g++.1 | 196 + .../log.24Dec20.grow_styrene.g++.4 | 196 + 4 files changed, 400 insertions(+), 4140 deletions(-) delete mode 100644 examples/USER/reaction/create_atoms_polystyrene/8procs_out.lammps create mode 100644 examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 create mode 100644 examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 diff --git a/examples/USER/reaction/create_atoms_polystyrene/8procs_out.lammps b/examples/USER/reaction/create_atoms_polystyrene/8procs_out.lammps deleted file mode 100644 index 953a32394a..0000000000 --- a/examples/USER/reaction/create_atoms_polystyrene/8procs_out.lammps +++ /dev/null @@ -1,4137 +0,0 @@ -LAMMPS (22 Oct 2020) -Reading data file ... - orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 48 atoms - reading velocities ... - 48 velocities - scanning bonds ... - 8 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 33 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 50 bonds - reading angles ... - 84 angles - reading dihedrals ... - 127 dihedrals - reading impropers ... - 36 impropers -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0.0 0.0 0.0 - special bond factors coul: 0.0 0.0 0.0 - 4 = max # of 1-2 neighbors - 8 = max # of 1-3 neighbors - 17 = max # of 1-4 neighbors - 46 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.022 seconds -Read molecule template mol3: - 1 molecules - 30 atoms with max type 6 - 31 bonds with max type 10 - 51 angles with max type 16 - 73 dihedrals with max type 19 - 21 impropers with max type 7 -Read molecule template mol4: - 1 molecules - 46 atoms with max type 6 - 48 bonds with max type 13 - 81 angles with max type 22 - 121 dihedrals with max type 36 - 35 impropers with max type 9 -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp_REACT defined -PPPM initialization ... -WARNING: System is not charge neutral, net charge = -0.0006 (../kspace.cpp:313) - using 12-bit tables for long-range coulomb (../kspace.cpp:328) - G vector (1/distance) = 0.20144813 - grid = 45 45 45 - stencil order = 5 - estimated absolute RMS force accuracy = 0.00053712952 - estimated relative force accuracy = 1.6175496e-06 - using double precision KISS FFT - 3d grid and FFT values/proc = 21952 12167 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10.5 - ghost atom cutoff = 10.5 - binsize = 5.25, bins = 39 39 39 - 2 neighbor lists, perpetual/occasional/extra = 1 1 0 - (1) pair lj/class2/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard - (2) fix bond/react, occasional, copy from (1) - attributes: half, newton on - pair build: copy - stencil: none - bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 1.0 -WARNING: Inconsistent image flags (../domain.cpp:812) -Per MPI rank memory allocation (min/avg/max) = 37.97 | 38.12 | 38.70 Mbytes -Step Temp Press Density f_rxn1[1] - 0 496.23742 0.9983211 6.4856516e-05 0 - 2 672.73362 -516.54985 8.6475354e-05 1 - 4 667.5039 -434.77386 8.6475354e-05 1 - 6 672.39598 -362.84027 8.6475354e-05 1 - 8 685.87152 -299.54792 8.6475354e-05 1 - 10 691.00305 -244.43255 8.6475354e-05 1 - 12 669.95405 -197.53983 8.6475354e-05 1 - 14 646.37761 -158.31437 8.6475354e-05 1 - 16 643.66763 -125.39769 8.6475354e-05 1 - 18 667.56644 -97.573538 8.6475354e-05 1 - 20 703.91664 -74.339207 8.6475354e-05 1 - 22 720.06237 -55.689578 8.6475354e-05 1 - 24 697.20697 -41.333247 8.6475354e-05 1 - 26 674.83509 -30.383402 8.6475354e-05 1 - 28 670.01312 -21.803547 8.6475354e-05 1 - 30 679.49765 -15.012223 8.6475354e-05 1 - 32 700.25949 -9.9961585 8.6475354e-05 1 - 34 700.57498 -6.7727869 8.6475354e-05 1 - 36 685.11304 -4.9950196 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3893.4144 -0.80375709 0.00045399561 18 - 1816 3892.8065 -0.43723593 0.00045399561 18 - 1818 3879.6317 -0.27127498 0.00045399561 18 - 1820 3863.231 -0.26927869 0.00045399561 18 - 1822 3839.1828 -0.16469626 0.00045399561 18 - 1824 3817.7643 0.17259437 0.00045399561 18 - 1826 3814.5806 0.55900288 0.00045399561 18 - 1828 3814.4881 0.73981688 0.00045399561 18 - 1830 3826.593 0.61721493 0.00045399561 18 - 1832 3850.1378 0.38603904 0.00045399561 18 - 1834 3867.6612 0.31140301 0.00045399561 18 - 1836 3881.9933 0.36675857 0.00045399561 18 - 1838 4088.212 261434.69 0.00047561445 19 - 1840 4096.5564 27676.737 0.00047561445 19 - 1842 4116.6104 4562.7115 0.00047561445 19 - 1844 4138.3331 942.30407 0.00047561445 19 - 1846 4157.8346 171.41233 0.00047561445 19 - 1848 4189.7389 -26.014237 0.00047561445 19 - 1850 4203.2273 -76.212233 0.00047561445 19 - 1852 4206.7084 -81.595913 0.00047561445 19 - 1854 4214.7407 -72.613587 0.00047561445 19 - 1856 4219.541 -59.566243 0.00047561445 19 - 1858 4238.5637 -46.274295 0.00047561445 19 - 1860 4268.5595 -34.588591 0.00047561445 19 - 1862 4277.6539 -25.225003 0.00047561445 19 - 1864 4285.3854 -18.06534 0.00047561445 19 - 1866 4276.8633 -12.627639 0.00047561445 19 - 1868 4255.485 -8.5283892 0.00047561445 19 - 1870 4248.7917 -5.6394153 0.00047561445 19 - 1872 4232.7796 -3.7373251 0.00047561445 19 - 1874 4213.674 -2.5982718 0.00047561445 19 - 1876 4196.3767 -1.8849709 0.00047561445 19 - 1878 4154.9323 -1.2753507 0.00047561445 19 - 1880 4121.2743 -0.82249822 0.00047561445 19 - 1882 4101.6239 -0.60366804 0.00047561445 19 - 1884 4076.731 -0.62133231 0.00047561445 19 - 1886 4071.191 -0.92478991 0.00047561445 19 - 1888 4070.5745 -1.3485064 0.00047561445 19 - 1890 4073.0041 -1.8304913 0.00047561445 19 - 1892 4099.534 -2.4147085 0.00047561445 19 - 1894 4122.2249 -3.0099619 0.00047561445 19 - 1896 4134.95 -3.5440729 0.00047561445 19 - 1898 4138.662 -3.8951738 0.00047561445 19 - 1900 4119.9803 -3.9477528 0.00047561445 19 - 1902 4105.9779 -3.7437217 0.00047561445 19 - 1904 4103.6993 -3.3264299 0.00047561445 19 - 1906 4099.5993 -2.7195122 0.00047561445 19 - 1908 4099.0927 -2.0152229 0.00047561445 19 - 1910 4092.7303 -1.3051093 0.00047561445 19 - 1912 4079.7989 -0.70887774 0.00047561445 19 - 1914 4070.1861 -0.30814281 0.00047561445 19 - 1916 4064.2331 -0.12483815 0.00047561445 19 - 1918 4057.4172 -0.14863786 0.00047561445 19 - 1920 4045.7673 -0.36919485 0.00047561445 19 - 1922 4025.2377 -0.75787503 0.00047561445 19 - 1924 3997.6829 -1.2270004 0.00047561445 19 - 1926 3973.4154 -1.6380242 0.00047561445 19 - 1928 3967.2261 -1.8579591 0.00047561445 19 - 1930 3984.008 -1.8481876 0.00047561445 19 - 1932 4014.2028 -1.695545 0.00047561445 19 - 1934 4040.7038 -1.4466441 0.00047561445 19 - 1936 4046.6823 -1.0457806 0.00047561445 19 - 1938 4050.3414 -0.43691244 0.00047561445 19 - 1940 4158.8456 -485.87062 0.00049723329 20 - 1942 4138.6859 -406.83847 0.00049723329 20 - 1944 4122.6253 -337.57463 0.00049723329 20 - 1946 4101.6274 -277.34116 0.00049723329 20 - 1948 4085.2854 -225.34082 0.00049723329 20 - 1950 4088.9637 -181.0183 0.00049723329 20 - 1952 4109.9585 -143.74698 0.00049723329 20 - 1954 4141.6977 -112.7839 0.00049723329 20 - 1956 4173.9013 -87.397165 0.00049723329 20 - 1958 4185.8014 -66.686886 0.00049723329 20 - 1960 4182.5342 -49.929089 0.00049723329 20 - 1962 4173.7911 -36.539866 0.00049723329 20 - 1964 4164.6792 -26.055513 0.00049723329 20 - 1966 4166.91 -18.173563 0.00049723329 20 - 1968 4170.7606 -12.411793 0.00049723329 20 - 1970 4168.2387 -8.2434854 0.00049723329 20 - 1972 4167.5496 -5.3241601 0.00049723329 20 - 1974 4165.6717 -3.4268698 0.00049723329 20 - 1976 4171.0255 -2.459824 0.00049723329 20 - 1978 4186.2281 -2.210817 0.00049723329 20 - 1980 4200.046 -2.2265372 0.00049723329 20 - 1982 4214.8919 -2.1835848 0.00049723329 20 - 1984 4230.6418 -1.9876854 0.00049723329 20 - 1986 4242.4071 -1.7430167 0.00049723329 20 - 1988 4252.8222 -1.6283597 0.00049723329 20 - 1990 4255.8615 -1.5968122 0.00049723329 20 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0.0011457984 50 - 7622 9410.5734 7.5124718 0.0011457984 50 - 7624 9483.015 6.434736 0.0011457984 50 - 7626 9417.367 5.8180565 0.0011457984 50 - 7628 9504.2707 4.8808406 0.0011457984 50 - 7630 9708.7689 3.1972208 0.0011457984 50 - 7632 9705.0142 1.4578035 0.0011457984 50 - 7634 9712.5013 0.041948151 0.0011457984 50 - 7636 9729.5345 -0.061359152 0.0011457984 50 - 7638 9603.3866 1.3424057 0.0011457984 50 - 7640 9659.7375 2.5412485 0.0011457984 50 - 7642 9653.7578 3.3597609 0.0011457984 50 - 7644 9526.3277 4.5019132 0.0011457984 50 - 7646 9522.1426 6.4723916 0.0011457984 50 - 7648 9551.1617 9.4539084 0.0011457984 50 - 7650 9448.6486 12.17887 0.0011457984 50 - 7652 9441.6445 12.73528 0.0011457984 50 - 7654 9372.3016 11.623139 0.0011457984 50 - 7656 9353.7281 10.159189 0.0011457984 50 - 7658 9533.6437 9.1148105 0.0011457984 50 - 7660 9720.4729 8.2979611 0.0011457984 50 - 7662 9687.7535 6.5903069 0.0011457984 50 - 7664 9679.7651 3.1582718 0.0011457984 50 - 7666 9506.8095 -0.16657303 0.0011457984 50 - 7668 9432.2748 -1.9647403 0.0011457984 50 - 7670 9562.3452 -2.0511502 0.0011457984 50 - 7672 9603.1776 -1.1215214 0.0011457984 50 - 7674 9614.5799 -0.73355736 0.0011457984 50 - 7676 9717.1466 -0.97171895 0.0011457984 50 - 7678 9660.4746 -0.065105035 0.0011457984 50 - 7680 9652.4727 2.1105705 0.0011457984 50 - 7682 9632.6572 4.7124033 0.0011457984 50 - 7684 9459.4445 6.5506091 0.0011457984 50 - 7686 9459.2384 6.5399378 0.0011457984 50 - 7688 9527.0273 5.8950819 0.0011457984 50 - 7690 9552.6913 5.8727872 0.0011457984 50 - 7692 9594.6979 6.1402731 0.0011457984 50 - 7694 9507.6571 6.0382366 0.0011457984 50 - 7696 9435.6211 4.6987185 0.0011457984 50 - 7698 9593.5298 2.4864572 0.0011457984 50 - 7700 9649.3417 1.3774067 0.0011457984 50 - 7702 9733.9587 1.3621968 0.0011457984 50 - 7704 9748.2134 1.6826187 0.0011457984 50 - 7706 9607.2673 1.730675 0.0011457984 50 - 7708 9570.3284 1.056172 0.0011457984 50 - 7710 9623.4646 0.68062243 0.0011457984 50 - 7712 9584.1504 1.5492829 0.0011457984 50 - 7714 9727.4828 2.3647176 0.0011457984 50 - 7716 9768.0882 2.5188312 0.0011457984 50 - 7718 9675.8436 1.915033 0.0011457984 50 - 7720 9742.4159 0.98004134 0.0011457984 50 - 7722 9729.339 1.348188 0.0011457984 50 - 7724 9737.0089 2.3572792 0.0011457984 50 - 7726 9867.0438 2.3334077 0.0011457984 50 - 7728 9685.1497 1.779699 0.0011457984 50 - 7730 9541.5463 1.0959201 0.0011457984 50 - 7732 9601.3202 1.360164 0.0011457984 50 - 7734 9511.1979 3.3763173 0.0011457984 50 - 7736 9691.0676 4.6273168 0.0011457984 50 - 7738 9841.6024 4.2729278 0.0011457984 50 - 7740 9648.3216 3.3438312 0.0011457984 50 - 7742 9644.2115 2.2183629 0.0011457984 50 - 7744 9588.828 2.5300306 0.0011457984 50 - 7746 9341.8422 3.7987816 0.0011457984 50 - 7748 9547.0139 3.0814107 0.0011457984 50 - 7750 9527.4193 1.3593932 0.0011457984 50 - 7752 9489.3054 -0.4087885 0.0011457984 50 - 7754 9740.3405 -1.2673367 0.0011457984 50 - 7756 9721.0147 0.00428777 0.0011457984 50 - 7758 9702.5241 0.82419258 0.0011457984 50 - 7760 9859.071 -0.6228219 0.0011457984 50 - 7762 9650.9663 -2.3957203 0.0011457984 50 - 7764 9706.9729 -3.6785526 0.0011457984 50 - 7766 9818.8903 -2.8392329 0.0011457984 50 - 7768 9663.4435 -0.34323863 0.0011457984 50 - 7770 9803.2456 0.38943494 0.0011457984 50 - 7772 9820.2274 -0.39394936 0.0011457984 50 - 7774 9713.4768 -1.0733572 0.0011457984 50 - 7776 9852.736 -0.42363135 0.0011457984 50 - 7778 9886.2509 2.3769023 0.0011457984 50 - 7780 9832.7358 4.9166992 0.0011457984 50 - 7782 9932.8973 4.712252 0.0011457984 50 - 7784 9796.5384 3.1448764 0.0011457984 50 - 7786 9753.7015 1.9309203 0.0011457984 50 - 7788 9839.8416 2.3899169 0.0011457984 50 - 7790 9872.1501 3.7655463 0.0011457984 50 - 7792 9953.7516 3.4859888 0.0011457984 50 - 7794 10034.369 1.1698958 0.0011457984 50 - 7796 9944.3003 -0.92549906 0.0011457984 50 - 7798 9965.518 -1.1278296 0.0011457984 50 - 7800 10012.5 0.80938361 0.0011457984 50 - 7802 10034.925 2.8840295 0.0011457984 50 - 7804 10097.202 3.1108041 0.0011457984 50 - 7806 10109.566 2.2692514 0.0011457984 50 - 7808 10070.186 2.6683711 0.0011457984 50 - 7810 10086.066 5.1330175 0.0011457984 50 - 7812 10101.889 8.1779122 0.0011457984 50 - 7814 9955.2551 9.6584018 0.0011457984 50 - 7816 9924.9784 8.6108988 0.0011457984 50 - 7818 9892.9233 7.3026856 0.0011457984 50 - 7820 9940.0085 7.6562588 0.0011457984 50 - 7822 10043.889 9.2169653 0.0011457984 50 - 7824 10040.433 10.071061 0.0011457984 50 - 7826 9888.6625 8.8793367 0.0011457984 50 - 7828 9843.2339 6.2958302 0.0011457984 50 - 7830 9769.9935 4.9813275 0.0011457984 50 - 7832 9817.1369 5.5036474 0.0011457984 50 - 7834 9908.1863 6.5022137 0.0011457984 50 - 7836 9836.952 6.5533027 0.0011457984 50 - 7838 9823.5066 5.1861522 0.0011457984 50 - 7840 9842.244 4.290555 0.0011457984 50 - 7842 9807.8307 5.4702915 0.0011457984 50 - 7844 9866.4119 7.5011118 0.0011457984 50 - 7846 9948.1838 8.4741237 0.0011457984 50 - 7848 9929.854 7.7316361 0.0011457984 50 - 7850 10067.409 5.8569645 0.0011457984 50 - 7852 10032.145 5.2165212 0.0011457984 50 - 7854 9899.4962 6.0924898 0.0011457984 50 - 7856 9921.7169 6.719158 0.0011457984 50 - 7858 9916.003 6.389409 0.0011457984 50 - 7860 9870.0171 5.3824146 0.0011457984 50 - 7862 9982.1614 4.6911758 0.0011457984 50 - 7864 9885.8857 5.9014244 0.0011457984 50 - 7866 9833.4896 7.7602131 0.0011457984 50 - 7868 9945.8481 8.582649 0.0011457984 50 - 7870 9940.9251 8.4512902 0.0011457984 50 - 7872 9955.2114 7.7609086 0.0011457984 50 - 7874 9947.7609 7.5875024 0.0011457984 50 - 7876 9824.999 8.1626806 0.0011457984 50 - 7878 9821.2327 8.0188501 0.0011457984 50 - 7880 9842.1396 6.8799344 0.0011457984 50 - 7882 9763.4974 5.6291783 0.0011457984 50 - 7884 9830.8014 4.8298768 0.0011457984 50 - 7886 9864.651 5.1057619 0.0011457984 50 - 7888 9897.6271 5.4523732 0.0011457984 50 - 7890 9969.4632 4.8645946 0.0011457984 50 - 7892 9905.2637 4.0683578 0.0011457984 50 - 7894 9867.218 3.7625675 0.0011457984 50 - 7896 9964.8143 4.1222515 0.0011457984 50 - 7898 9970.8383 4.8135178 0.0011457984 50 - 7900 9960.2843 4.6528207 0.0011457984 50 - 7902 9929.1614 4.0045485 0.0011457984 50 - 7904 9732.7455 4.4197682 0.0011457984 50 - 7906 9784.6307 5.46138 0.0011457984 50 - 7908 9902.0578 6.4536086 0.0011457984 50 - 7910 9835.8696 6.5806316 0.0011457984 50 - 7912 9816.4882 5.2605278 0.0011457984 50 - 7914 9678.3646 4.2597874 0.0011457984 50 - 7916 9495.2316 4.5265141 0.0011457984 50 - 7918 9625.0995 4.6607196 0.0011457984 50 - 7920 9667.4185 3.9419695 0.0011457984 50 - 7922 9602.5767 1.8452379 0.0011457984 50 - 7924 9714.4671 -0.78549348 0.0011457984 50 - 7926 9600.4719 -1.3021957 0.0011457984 50 - 7928 9595.5944 -0.40978783 0.0011457984 50 - 7930 9671.4849 0.18383962 0.0011457984 50 - 7932 9427.9403 0.13097094 0.0011457984 50 - 7934 9336.0891 -0.75045689 0.0011457984 50 - 7936 9377.7418 -0.37773788 0.0011457984 50 - 7938 9313.8567 2.3838933 0.0011457984 50 - 7940 9563.9378 4.7263846 0.0011457984 50 - 7942 9725.0125 5.1314861 0.0011457984 50 - 7944 9526.2488 3.8387064 0.0011457984 50 - 7946 9567.6993 1.6692464 0.0011457984 50 - 7948 9454.276 1.4617733 0.0011457984 50 - 7950 9353.5637 2.4804377 0.0011457984 50 - 7952 9601.2572 1.7746058 0.0011457984 50 - 7954 9621.3707 -0.54877445 0.0011457984 50 - 7956 9545.5258 -3.3532832 0.0011457984 50 - 7958 9635.7985 -4.5615531 0.0011457984 50 - 7960 9426.8802 -2.4111311 0.0011457984 50 - 7962 9415.5196 0.10777037 0.0011457984 50 - 7964 9525.2541 0.98550692 0.0011457984 50 - 7966 9409.782 1.0022769 0.0011457984 50 - 7968 9501.2728 1.0925635 0.0011457984 50 - 7970 9566.9142 2.9916085 0.0011457984 50 - 7972 9434.188 5.8343619 0.0011457984 50 - 7974 9543.452 6.3023867 0.0011457984 50 - 7976 9515.7435 4.393159 0.0011457984 50 - 7978 9397.8265 1.67238 0.0011457984 50 - 7980 9518.8853 -0.26214002 0.0011457984 50 - 7982 9464.9738 -0.20322159 0.0011457984 50 - 7984 9411.3658 -0.34294737 0.0011457984 50 - 7986 9480.5763 -2.2898799 0.0011457984 50 - 7988 9346.0022 -4.3015335 0.0011457984 50 - 7990 9323.7758 -4.7818874 0.0011457984 50 - 7992 9447.4591 -2.8155787 0.0011457984 50 - 7994 9370.0301 0.86042184 0.0011457984 50 - 7996 9414.3206 3.209964 0.0011457984 50 - 7998 9443.2413 3.7897264 0.0011457984 50 - 8000 9337.5805 4.2404387 0.0011457984 50 -Loop time of 107.636 on 8 procs for 8000 steps with 848 atoms - -Performance: 6.422 ns/day, 3.737 hours/ns, 74.325 timesteps/s -93.6% CPU use with 8 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0071581 | 0.99286 | 4.3913 | 151.9 | 0.92 -Bond | 0.023263 | 2.2103 | 10.081 | 229.9 | 2.05 -Kspace | 28.814 | 39.764 | 42.853 | 76.0 | 36.94 -Neigh | 6.4084 | 6.4395 | 6.4689 | 1.0 | 5.98 -Comm | 0.19227 | 0.25072 | 0.36267 | 12.4 | 0.23 -Output | 56.437 | 56.509 | 56.849 | 1.7 | 52.50 -Modify | 0.78657 | 1.4521 | 1.6493 | 23.1 | 1.35 -Other | | 0.0172 | | | 0.02 - -Nlocal: 106.000 ave 407 max 0 min -Histogram: 5 0 0 0 1 0 1 0 0 1 -Nghost: 71.1250 ave 338 max 0 min -Histogram: 5 0 1 0 1 0 0 0 0 1 -Neighs: 7377.88 ave 29891 max 0 min -Histogram: 5 0 0 0 1 1 0 0 0 1 - -Total # of neighbors = 59023 -Ave neighs/atom = 69.602594 -Ave special neighs/atom = 11.443396 -Neighbor list builds = 8000 -Dangerous builds = 0 -System init for write_data ... -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:328) - G vector (1/distance) = 0.20144813 - grid = 45 45 45 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0022576485 - estimated relative force accuracy = 6.7988414e-06 - using double precision KISS FFT - 3d grid and FFT values/proc = 21952 12167 -System init for write_data ... -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:328) - G vector (1/distance) = 0.20144813 - grid = 45 45 45 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0022576485 - estimated relative force accuracy = 6.7988414e-06 - using double precision KISS FFT - 3d grid and FFT values/proc = 21952 12167 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:01:48 diff --git a/examples/USER/reaction/create_atoms_polystyrene/in.grow_styrene b/examples/USER/reaction/create_atoms_polystyrene/in.grow_styrene index 4331bf60b7..8950cec614 100755 --- a/examples/USER/reaction/create_atoms_polystyrene/in.grow_styrene +++ b/examples/USER/reaction/create_atoms_polystyrene/in.grow_styrene @@ -1,4 +1,4 @@ -# use bond/react 'create atoms' feature to add 50 new styrene monomers to chain +# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain units real @@ -20,7 +20,12 @@ improper_style class2 variable T equal 530 -read_data trimer.data +read_data trimer.data & + extra/bond/per/atom 5 & + extra/angle/per/atom 15 & + extra/dihedral/per/atom 15 & + extra/improper/per/atom 25 & + extra/special/per/atom 25 molecule mol1 grow_styrene_pre.data_template molecule mol2 grow_styrene_post.data_template @@ -28,7 +33,7 @@ molecule mol2 grow_styrene_post.data_template fix myrxns all bond/react stabilization yes statted_grp .03 & react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map & modify_create fit create_fit overlap 2.0 & - stabilize_steps 100 max_rxn 50 + stabilize_steps 100 max_rxn 30 fix 1 statted_grp_REACT nvt temp $T $T 100 diff --git a/examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 b/examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 new file mode 100644 index 0000000000..5f1f2c6698 --- /dev/null +++ b/examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 @@ -0,0 +1,196 @@ +LAMMPS (24 Dec 2020) +Reading data file ... + orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 48 atoms + reading velocities ... + 48 velocities + scanning bonds ... + 8 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 33 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 50 bonds + reading angles ... + 84 angles + reading dihedrals ... + 127 dihedrals + reading impropers ... + 36 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 8 = max # of 1-3 neighbors + 17 = max # of 1-4 neighbors + 46 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.077 seconds +Read molecule template mol1: + 1 molecules + 30 atoms with max type 6 + 31 bonds with max type 10 + 51 angles with max type 16 + 73 dihedrals with max type 19 + 21 impropers with max type 7 +Read molecule template mol2: + 1 molecules + 46 atoms with max type 6 + 48 bonds with max type 13 + 81 angles with max type 22 + 121 dihedrals with max type 36 + 35 impropers with max type 9 +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined +PPPM initialization ... +WARNING: System is not charge neutral, net charge = -0.00060000000 (../kspace.cpp:324) + using 12-bit tables for long-range coulomb (../kspace.cpp:339) + G vector (1/distance) = 0.20144813 + grid = 45 45 45 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00053712952 + estimated relative force accuracy = 1.6175496e-06 + using double precision KISS FFT + 3d grid and FFT values/proc = 125000 91125 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 39 39 39 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 48.02 | 48.02 | 48.02 Mbytes +Step Temp Press Density f_myrxns[1] + 0 496.23742 0.9983211 6.4856516e-05 0 + 100 534.05394 -0.76952227 6.4856516e-05 0 + 200 552.2225 -0.55375493 6.4856516e-05 0 + 300 857.52834 -0.4272061 8.6475354e-05 1 + 400 714.10681 1.5004615 8.6475354e-05 1 + 500 678.19171 0.21965471 8.6475354e-05 1 + 600 572.3234 0.87879933 8.6475354e-05 1 + 700 996.17398 -0.24269717 0.00010809419 2 + 800 904.50395 1.3662054 0.00010809419 2 + 900 1097.1568 -2.2909907 0.00012971303 3 + 1000 954.08892 1.7705672 0.00012971303 3 + 1100 1102.0377 -1.7018446 0.00015133187 4 + 1200 1239.785 -0.30442903 0.00015133187 4 + 1300 1388.4127 1.3301175 0.00017295071 5 + 1400 1559.3853 1.6709729 0.00017295071 5 + 1500 1471.8623 0.8268427 0.00017295071 5 + 1600 1543.6793 2.1987908 0.00019456955 6 + 1700 1694.5595 0.48852817 0.00019456955 6 + 1800 1632.7737 -1.4617692 0.00021618839 7 + 1900 1922.6502 1.1664257 0.00021618839 7 + 2000 2223.503 -0.95799878 0.00023780722 8 + 2100 2142.6035 0.88444463 0.00025942606 9 + 2200 2298.8636 3.4239313 0.00025942606 9 + 2300 2252.4355 0.82167302 0.00025942606 9 + 2400 2321.0788 1.7499714 0.00025942606 9 + 2500 2095.6715 0.55288444 0.00025942606 9 + 2600 2136.0316 -3.833114 0.00025942606 9 + 2700 2466.3134 -2.2519511 0.00025942606 9 + 2800 2294.3454 1.0637304 0.00025942606 9 + 2900 2340.3891 1.3997049 0.0002810449 10 + 3000 2272.0013 -0.27591886 0.0002810449 10 + 3100 2333.9696 -0.11772138 0.0002810449 10 + 3200 2409.0946 -1.025473 0.0002810449 10 + 3300 2148.023 1.6752329 0.0002810449 10 + 3400 2267.636 -0.45297583 0.0002810449 10 + 3500 2457.622 0.35627297 0.0002810449 10 + 3600 2288.008 -15.516626 0.00030266374 11 + 3700 2458.2681 1.4571773 0.00030266374 11 + 3800 2566.7623 -29.140553 0.00032428258 12 + 3900 2839.4062 0.64583638 0.00032428258 12 + 4000 2893.9852 -52.954497 0.00034590142 13 + 4100 3021.3611 -65.03731 0.00036752025 14 + 4200 3002.7136 1.5750081 0.00036752025 14 + 4300 3218.6248 -120.74039 0.00038913909 15 + 4400 3345.1482 -0.96545269 0.00038913909 15 + 4500 3603.2429 1.2438833 0.00038913909 15 + 4600 3129.8814 -249.91806 0.00041075793 16 + 4700 3769.052 -289.24351 0.00043237677 17 + 4800 3560.4714 -3.1655406 0.00043237677 17 + 4900 3452.2717 -2.1270765 0.00043237677 17 + 5000 3594.3247 -523.48506 0.00045399561 18 + 5100 3578.4199 1.0009097 0.00045399561 18 + 5200 3822.1566 1.0526914 0.00047561445 19 + 5300 3901.8883 -0.14607602 0.00047561445 19 + 5400 4059.3644 -1.7789927 0.00049723329 20 + 5500 4163.6847 1.0240127 0.00049723329 20 + 5600 4109.1649 0.80199787 0.00049723329 20 + 5700 4391.2091 2.8730036 0.00049723329 20 + 5800 4279.6579 -0.36499822 0.00051885212 21 + 5900 4296.2695 -1.3064528 0.00051885212 21 + 6000 4065.3758 -2.0483224 0.00051885212 21 + 6100 4772.5362 -2.6814694 0.00054047096 22 + 6200 4627.029 2.999215 0.0005620898 23 + 6300 5120.7881 0.65372968 0.00058370864 24 + 6400 4588.9559 3.7570705 0.00058370864 24 + 6500 5008.7814 2.3595833 0.00060532748 25 + 6600 5195.0053 1.4641612 0.00060532748 25 + 6700 5622.293 -0.33396047 0.00062694632 26 + 6800 5515.1957 -4.234874 0.00062694632 26 + 6900 5156.7455 0.40171954 0.00064856516 27 + 7000 5120.1639 -1.6065245 0.00064856516 27 + 7100 5650.0327 0.94436323 0.00067018399 28 + 7200 5985.1115 -3.8940347 0.00069180283 29 + 7300 5983.197 0.5293568 0.00069180283 29 + 7400 6001.1559 -0.13712834 0.00071342167 30 + 7500 5889.2134 0.17230892 0.00071342167 30 + 7600 5797.31 2.0920058 0.00071342167 30 + 7700 5865.2783 -0.18556395 0.00071342167 30 + 7800 6207.0659 -5.6237083 0.00071342167 30 + 7900 5627.5108 -2.3718942 0.00071342167 30 + 8000 5823.9502 -0.85418578 0.00071342167 30 +Loop time of 184.87 on 1 procs for 8000 steps with 528 atoms + +Performance: 3.739 ns/day, 6.419 hours/ns, 43.274 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 | 3.3043 | 3.3043 | 3.3043 | 0.0 | 1.79 +Bond | 8.0003 | 8.0003 | 8.0003 | 0.0 | 4.33 +Kspace | 168.33 | 168.33 | 168.33 | 0.0 | 91.05 +Neigh | 4.6322 | 4.6322 | 4.6322 | 0.0 | 2.51 +Comm | 0.077927 | 0.077927 | 0.077927 | 0.0 | 0.04 +Output | 0.0020548 | 0.0020548 | 0.0020548 | 0.0 | 0.00 +Modify | 0.5005 | 0.5005 | 0.5005 | 0.0 | 0.27 +Other | | 0.02483 | | | 0.01 + +Nlocal: 528.000 ave 528 max 528 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 341.000 ave 341 max 341 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 35111.0 ave 35111 max 35111 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 35111 +Ave neighs/atom = 66.498106 +Ave special neighs/atom = 11.409091 +Neighbor list builds = 8000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:03:05 diff --git a/examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 b/examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 new file mode 100644 index 0000000000..8daa6d8161 --- /dev/null +++ b/examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 @@ -0,0 +1,196 @@ +LAMMPS (24 Dec 2020) +Reading data file ... + orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 48 atoms + reading velocities ... + 48 velocities + scanning bonds ... + 8 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 33 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 50 bonds + reading angles ... + 84 angles + reading dihedrals ... + 127 dihedrals + reading impropers ... + 36 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 8 = max # of 1-3 neighbors + 17 = max # of 1-4 neighbors + 46 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.007 seconds +Read molecule template mol1: + 1 molecules + 30 atoms with max type 6 + 31 bonds with max type 10 + 51 angles with max type 16 + 73 dihedrals with max type 19 + 21 impropers with max type 7 +Read molecule template mol2: + 1 molecules + 46 atoms with max type 6 + 48 bonds with max type 13 + 81 angles with max type 22 + 121 dihedrals with max type 36 + 35 impropers with max type 9 +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined +PPPM initialization ... +WARNING: System is not charge neutral, net charge = -0.00060000000 (../kspace.cpp:324) + using 12-bit tables for long-range coulomb (../kspace.cpp:339) + G vector (1/distance) = 0.20144813 + grid = 45 45 45 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00053712952 + estimated relative force accuracy = 1.6175496e-06 + using double precision KISS FFT + 3d grid and FFT values/proc = 39200 24300 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 39 39 39 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 38.70 | 38.92 | 39.43 Mbytes +Step Temp Press Density f_myrxns[1] + 0 496.23742 0.9983211 6.4856516e-05 0 + 100 534.05394 -0.76952227 6.4856516e-05 0 + 200 552.2225 -0.55375493 6.4856516e-05 0 + 300 857.52834 -0.4272061 8.6475354e-05 1 + 400 714.10681 1.5004615 8.6475354e-05 1 + 500 678.19171 0.21965471 8.6475354e-05 1 + 600 572.3234 0.87879933 8.6475354e-05 1 + 700 996.17398 -0.24269717 0.00010809419 2 + 800 904.50395 1.3662054 0.00010809419 2 + 900 1097.1568 -2.2909907 0.00012971303 3 + 1000 954.08892 1.7705672 0.00012971303 3 + 1100 1102.0377 -1.7018446 0.00015133187 4 + 1200 1239.785 -0.30442903 0.00015133187 4 + 1300 1388.4127 1.3301175 0.00017295071 5 + 1400 1559.3853 1.6709729 0.00017295071 5 + 1500 1471.8623 0.8268427 0.00017295071 5 + 1600 1543.6793 2.1987908 0.00019456955 6 + 1700 1694.5595 0.48852817 0.00019456955 6 + 1800 1632.7737 -1.4617692 0.00021618839 7 + 1900 1922.6502 1.1664257 0.00021618839 7 + 2000 2223.503 -0.95799878 0.00023780722 8 + 2100 2142.6035 0.88444463 0.00025942606 9 + 2200 2298.8636 3.4239313 0.00025942606 9 + 2300 2252.4355 0.82167302 0.00025942606 9 + 2400 2321.0788 1.7499714 0.00025942606 9 + 2500 2095.6715 0.55288444 0.00025942606 9 + 2600 2136.0316 -3.833114 0.00025942606 9 + 2700 2466.3134 -2.2519511 0.00025942606 9 + 2800 2294.3454 1.0637304 0.00025942606 9 + 2900 2340.3891 1.3997049 0.0002810449 10 + 3000 2272.0013 -0.27591886 0.0002810449 10 + 3100 2333.9696 -0.11772138 0.0002810449 10 + 3200 2409.0946 -1.025473 0.0002810449 10 + 3300 2148.023 1.6752329 0.0002810449 10 + 3400 2267.636 -0.45297583 0.0002810449 10 + 3500 2457.622 0.35627297 0.0002810449 10 + 3600 2288.008 -15.516626 0.00030266374 11 + 3700 2458.2681 1.4571773 0.00030266374 11 + 3800 2566.7623 -29.140553 0.00032428258 12 + 3900 2839.4062 0.64583638 0.00032428258 12 + 4000 2893.2204 -53.187892 0.00034590142 13 + 4100 3024.6375 -65.068146 0.00036752025 14 + 4200 3004.6784 1.4155214 0.00036752025 14 + 4300 3033.1895 1.8572273 0.00036752025 14 + 4400 3157.2542 -0.92462977 0.00036752025 14 + 4500 3557.7137 -194.46498 0.00038913909 15 + 4600 3096.485 -1.830492 0.00038913909 15 + 4700 3488.088 -286.81055 0.00041075793 16 + 4800 3390.5493 -372.77818 0.00043237677 17 + 4900 3773.7226 -446.58574 0.00045399561 18 + 5000 3703.0159 -0.81188551 0.00045399561 18 + 5100 4051.3067 1.2567439 0.00045399561 18 + 5200 3813.3682 0.92945737 0.00047561445 19 + 5300 4036.0078 -2.5336258 0.00049723329 20 + 5400 4219.803 -0.96928261 0.00049723329 20 + 5500 4433.7447 -0.026762463 0.00051885212 21 + 5600 4477.4505 -1.417316 0.00054047096 22 + 5700 4500.0306 -1.0551443 0.00054047096 22 + 5800 4600.3507 -4.9580056 0.00054047096 22 + 5900 4765.4978 -2.2546941 0.0005620898 23 + 6000 5442.6193 0.91161284 0.00058370864 24 + 6100 5086.8047 -0.9875332 0.00060532748 25 + 6200 5485.3437 -2.8296626 0.00062694632 26 + 6300 4988.0396 -0.15179023 0.00064856516 27 + 6400 5597.3703 4.2941885 0.00067018399 28 + 6500 5677.0263 -2.8611595 0.00069180283 29 + 6600 6058.0009 1.4111778 0.00071342167 30 + 6700 5859.0817 -2.5782466 0.00071342167 30 + 6800 5879.3941 -4.5681807 0.00071342167 30 + 6900 6398.288 2.5259412 0.00071342167 30 + 7000 6250.1096 -2.6049627 0.00071342167 30 + 7100 5849.651 -0.44062578 0.00071342167 30 + 7200 5778.6532 -0.27299118 0.00071342167 30 + 7300 5977.6661 4.2483639 0.00071342167 30 + 7400 5862.4231 1.0289519 0.00071342167 30 + 7500 6482.376 7.5412373 0.00071342167 30 + 7600 5810.4325 1.0343075 0.00071342167 30 + 7700 5916.7304 2.304302 0.00071342167 30 + 7800 5869.9504 -0.5946555 0.00071342167 30 + 7900 5804.0522 -4.1207689 0.00071342167 30 + 8000 6077.1704 0.52211243 0.00071342167 30 +Loop time of 60.5603 on 4 procs for 8000 steps with 528 atoms + +Performance: 11.413 ns/day, 2.103 hours/ns, 132.100 timesteps/s +99.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0041695 | 0.90113 | 2.3423 | 102.8 | 1.49 +Bond | 0.011606 | 2.1188 | 5.8107 | 163.9 | 3.50 +Kspace | 47.987 | 52.817 | 55.679 | 43.7 | 87.21 +Neigh | 3.5961 | 3.6262 | 3.6496 | 1.2 | 5.99 +Comm | 0.11097 | 0.16569 | 0.26369 | 15.3 | 0.27 +Output | 0.0020366 | 0.0023427 | 0.0032469 | 1.1 | 0.00 +Modify | 0.62302 | 0.91659 | 1.1227 | 21.5 | 1.51 +Other | | 0.0126 | | | 0.02 + +Nlocal: 132.000 ave 295 max 0 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 133.000 ave 349 max 0 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Neighs: 8383.50 ave 20143 max 0 min +Histogram: 2 0 0 0 0 0 1 0 0 1 + +Total # of neighbors = 33534 +Ave neighs/atom = 63.511364 +Ave special neighs/atom = 11.409091 +Neighbor list builds = 8000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:00 From 89e47e7aaecc94010d9d51ddd55271f90f6af88d Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 4 Feb 2021 22:31:15 -0500 Subject: [PATCH 38/39] memory fix --- src/USER-REACTION/fix_bond_react.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 0ef302137e..6739e20ac6 100755 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -596,6 +596,7 @@ FixBondReact::~FixBondReact() memory->destroy(create_atoms); memory->destroy(chiral_atoms); + memory->destroy(rxn_name); memory->destroy(nevery); memory->destroy(cutsq); memory->destroy(unreacted_mol); @@ -613,7 +614,7 @@ FixBondReact::~FixBondReact() memory->destroy(molecule_keyword); memory->destroy(constraints); memory->destroy(nconstraints); - // need to delete rxn_name and constraintstr + memory->destroy(constraintstr); memory->destroy(create_atoms_flag); memory->destroy(modify_create_fragid); memory->destroy(overlapsq); From 9995bef9112d424a2926eb2862fd48ba36bb3d04 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Fri, 5 Feb 2021 17:50:23 -0500 Subject: [PATCH 39/39] file permissions --- doc/src/fix_bond_react.rst | 0 src/USER-REACTION/fix_bond_react.cpp | 0 src/USER-REACTION/fix_bond_react.h | 0 3 files changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 doc/src/fix_bond_react.rst mode change 100755 => 100644 src/USER-REACTION/fix_bond_react.cpp mode change 100755 => 100644 src/USER-REACTION/fix_bond_react.h diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst old mode 100755 new mode 100644 diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp old mode 100755 new mode 100644 diff --git a/src/USER-REACTION/fix_bond_react.h b/src/USER-REACTION/fix_bond_react.h old mode 100755 new mode 100644