diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp index 5641b4ea5..2287c10c6 100644 --- a/src/dump_atom.cpp +++ b/src/dump_atom.cpp @@ -1,429 +1,425 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "string.h" #include "dump_atom.h" #include "domain.h" #include "atom.h" #include "update.h" #include "group.h" #include "error.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ DumpAtom::DumpAtom(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg) { if (narg != 5) error->all(FLERR,"Illegal dump atom command"); scale_flag = 1; image_flag = 0; format_default = NULL; } /* ---------------------------------------------------------------------- */ void DumpAtom::init_style() { if (image_flag == 0) size_one = 5; else size_one = 8; // default format depends on image flags delete [] format; if (format_user) { int n = strlen(format_user) + 2; format = new char[n]; strcpy(format,format_user); strcat(format,"\n"); } else { char *str; if (image_flag == 0) str = (char *) "%d %d %g %g %g"; else str = (char *) "%d %d %g %g %g %d %d %d"; int n = strlen(str) + 2; format = new char[n]; strcpy(format,str); strcat(format,"\n"); } // setup boundary string domain->boundary_string(boundstr); // setup column string if (scale_flag == 0 && image_flag == 0) columns = (char *) "id type x y z"; else if (scale_flag == 0 && image_flag == 1) columns = (char *) "id type x y z ix iy iz"; else if (scale_flag == 1 && image_flag == 0) columns = (char *) "id type xs ys zs"; else if (scale_flag == 1 && image_flag == 1) columns = (char *) "id type xs ys zs ix iy iz"; // setup function ptrs if (binary && domain->triclinic == 0) header_choice = &DumpAtom::header_binary; else if (binary && domain->triclinic == 1) header_choice = &DumpAtom::header_binary_triclinic; else if (!binary && domain->triclinic == 0) header_choice = &DumpAtom::header_item; else if (!binary && domain->triclinic == 1) header_choice = &DumpAtom::header_item_triclinic; if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 0) pack_choice = &DumpAtom::pack_scale_noimage; else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 0) pack_choice = &DumpAtom::pack_scale_image; else if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 1) pack_choice = &DumpAtom::pack_scale_noimage_triclinic; else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 1) pack_choice = &DumpAtom::pack_scale_image_triclinic; else if (scale_flag == 0 && image_flag == 0) pack_choice = &DumpAtom::pack_noscale_noimage; else if (scale_flag == 0 && image_flag == 1) pack_choice = &DumpAtom::pack_noscale_image; if (binary) write_choice = &DumpAtom::write_binary; else if (image_flag == 0) write_choice = &DumpAtom::write_noimage; else if (image_flag == 1) write_choice = &DumpAtom::write_image; // open single file, one time only if (multifile == 0) openfile(); } /* ---------------------------------------------------------------------- */ int DumpAtom::modify_param(int narg, char **arg) { if (strcmp(arg[0],"scale") == 0) { if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); if (strcmp(arg[1],"yes") == 0) scale_flag = 1; else if (strcmp(arg[1],"no") == 0) scale_flag = 0; else error->all(FLERR,"Illegal dump_modify command"); return 2; } else if (strcmp(arg[0],"image") == 0) { if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); if (strcmp(arg[1],"yes") == 0) image_flag = 1; else if (strcmp(arg[1],"no") == 0) image_flag = 0; else error->all(FLERR,"Illegal dump_modify command"); return 2; } return 0; } /* ---------------------------------------------------------------------- */ void DumpAtom::write_header(bigint ndump) { if (multiproc) (this->*header_choice)(ndump); else if (me == 0) (this->*header_choice)(ndump); } /* ---------------------------------------------------------------------- */ void DumpAtom::pack(int *ids) { (this->*pack_choice)(ids); } /* ---------------------------------------------------------------------- */ void DumpAtom::write_data(int n, double *mybuf) { (this->*write_choice)(n,mybuf); } /* ---------------------------------------------------------------------- */ void DumpAtom::header_binary(bigint ndump) { fwrite(&update->ntimestep,sizeof(bigint),1,fp); fwrite(&ndump,sizeof(bigint),1,fp); fwrite(&domain->triclinic,sizeof(int),1,fp); fwrite(&domain->boundary[0][0],6*sizeof(int),1,fp); fwrite(&boxxlo,sizeof(double),1,fp); fwrite(&boxxhi,sizeof(double),1,fp); fwrite(&boxylo,sizeof(double),1,fp); fwrite(&boxyhi,sizeof(double),1,fp); fwrite(&boxzlo,sizeof(double),1,fp); fwrite(&boxzhi,sizeof(double),1,fp); fwrite(&size_one,sizeof(int),1,fp); - if (multiproc) { - int one = 1; - fwrite(&one,sizeof(int),1,fp); - } else fwrite(&nprocs,sizeof(int),1,fp); + if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp); + else fwrite(&nprocs,sizeof(int),1,fp); } /* ---------------------------------------------------------------------- */ void DumpAtom::header_binary_triclinic(bigint ndump) { fwrite(&update->ntimestep,sizeof(bigint),1,fp); fwrite(&ndump,sizeof(bigint),1,fp); fwrite(&domain->triclinic,sizeof(int),1,fp); fwrite(&domain->boundary[0][0],6*sizeof(int),1,fp); fwrite(&boxxlo,sizeof(double),1,fp); fwrite(&boxxhi,sizeof(double),1,fp); fwrite(&boxylo,sizeof(double),1,fp); fwrite(&boxyhi,sizeof(double),1,fp); fwrite(&boxzlo,sizeof(double),1,fp); fwrite(&boxzhi,sizeof(double),1,fp); fwrite(&boxxy,sizeof(double),1,fp); fwrite(&boxxz,sizeof(double),1,fp); fwrite(&boxyz,sizeof(double),1,fp); fwrite(&size_one,sizeof(int),1,fp); - if (multiproc) { - int one = 1; - fwrite(&one,sizeof(int),1,fp); - } else fwrite(&nprocs,sizeof(int),1,fp); + if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp); + else fwrite(&nprocs,sizeof(int),1,fp); } /* ---------------------------------------------------------------------- */ void DumpAtom::header_item(bigint ndump) { fprintf(fp,"ITEM: TIMESTEP\n"); fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep); fprintf(fp,"ITEM: NUMBER OF ATOMS\n"); fprintf(fp,BIGINT_FORMAT "\n",ndump); fprintf(fp,"ITEM: BOX BOUNDS %s\n",boundstr); fprintf(fp,"%g %g\n",boxxlo,boxxhi); fprintf(fp,"%g %g\n",boxylo,boxyhi); fprintf(fp,"%g %g\n",boxzlo,boxzhi); fprintf(fp,"ITEM: ATOMS %s\n",columns); } /* ---------------------------------------------------------------------- */ void DumpAtom::header_item_triclinic(bigint ndump) { fprintf(fp,"ITEM: TIMESTEP\n"); fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep); fprintf(fp,"ITEM: NUMBER OF ATOMS\n"); fprintf(fp,BIGINT_FORMAT "\n",ndump); fprintf(fp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr); fprintf(fp,"%g %g %g\n",boxxlo,boxxhi,boxxy); fprintf(fp,"%g %g %g\n",boxylo,boxyhi,boxxz); fprintf(fp,"%g %g %g\n",boxzlo,boxzhi,boxyz); fprintf(fp,"ITEM: ATOMS %s\n",columns); } /* ---------------------------------------------------------------------- */ void DumpAtom::pack_scale_image(int *ids) { int m,n; int *tag = atom->tag; int *type = atom->type; tagint *image = atom->image; int *mask = atom->mask; double **x = atom->x; int nlocal = atom->nlocal; double invxprd = 1.0/domain->xprd; double invyprd = 1.0/domain->yprd; double invzprd = 1.0/domain->zprd; m = n = 00; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { buf[m++] = tag[i]; buf[m++] = type[i]; buf[m++] = (x[i][0] - boxxlo) * invxprd; buf[m++] = (x[i][1] - boxylo) * invyprd; buf[m++] = (x[i][2] - boxzlo) * invzprd; buf[m++] = (image[i] & IMGMASK) - IMGMAX; buf[m++] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; buf[m++] = (image[i] >> IMG2BITS) - IMGMAX; if (ids) ids[n++] = tag[i]; } } /* ---------------------------------------------------------------------- */ void DumpAtom::pack_scale_noimage(int *ids) { int m,n; int *tag = atom->tag; int *type = atom->type; int *mask = atom->mask; double **x = atom->x; int nlocal = atom->nlocal; double invxprd = 1.0/domain->xprd; double invyprd = 1.0/domain->yprd; double invzprd = 1.0/domain->zprd; m = n = 0; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { buf[m++] = tag[i]; buf[m++] = type[i]; buf[m++] = (x[i][0] - boxxlo) * invxprd; buf[m++] = (x[i][1] - boxylo) * invyprd; buf[m++] = (x[i][2] - boxzlo) * invzprd; if (ids) ids[n++] = tag[i]; } } /* ---------------------------------------------------------------------- */ void DumpAtom::pack_scale_image_triclinic(int *ids) { int m,n; int *tag = atom->tag; int *type = atom->type; tagint *image = atom->image; int *mask = atom->mask; double **x = atom->x; int nlocal = atom->nlocal; double lamda[3]; m = n = 0; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { buf[m++] = tag[i]; buf[m++] = type[i]; domain->x2lamda(x[i],lamda); buf[m++] = lamda[0]; buf[m++] = lamda[1]; buf[m++] = lamda[2]; buf[m++] = (image[i] & IMGMASK) - IMGMAX; buf[m++] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; buf[m++] = (image[i] >> IMG2BITS) - IMGMAX; if (ids) ids[n++] = tag[i]; } } /* ---------------------------------------------------------------------- */ void DumpAtom::pack_scale_noimage_triclinic(int *ids) { int m,n; int *tag = atom->tag; int *type = atom->type; int *mask = atom->mask; double **x = atom->x; int nlocal = atom->nlocal; double lamda[3]; m = n = 0; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { buf[m++] = tag[i]; buf[m++] = type[i]; domain->x2lamda(x[i],lamda); buf[m++] = lamda[0]; buf[m++] = lamda[1]; buf[m++] = lamda[2]; if (ids) ids[n++] = tag[i]; } } /* ---------------------------------------------------------------------- */ void DumpAtom::pack_noscale_image(int *ids) { int m,n; int *tag = atom->tag; int *type = atom->type; tagint *image = atom->image; int *mask = atom->mask; double **x = atom->x; int nlocal = atom->nlocal; m = n = 0; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { buf[m++] = tag[i]; buf[m++] = type[i]; buf[m++] = x[i][0]; buf[m++] = x[i][1]; buf[m++] = x[i][2]; buf[m++] = (image[i] & IMGMASK) - IMGMAX; buf[m++] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; buf[m++] = (image[i] >> IMG2BITS) - IMGMAX; if (ids) ids[n++] = tag[i]; } } /* ---------------------------------------------------------------------- */ void DumpAtom::pack_noscale_noimage(int *ids) { int m,n; int *tag = atom->tag; int *type = atom->type; int *mask = atom->mask; double **x = atom->x; int nlocal = atom->nlocal; m = n = 0; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { buf[m++] = tag[i]; buf[m++] = type[i]; buf[m++] = x[i][0]; buf[m++] = x[i][1]; buf[m++] = x[i][2]; if (ids) ids[n++] = tag[i]; } } /* ---------------------------------------------------------------------- */ void DumpAtom::write_binary(int n, double *mybuf) { n *= size_one; fwrite(&n,sizeof(int),1,fp); fwrite(mybuf,sizeof(double),n,fp); } /* ---------------------------------------------------------------------- */ void DumpAtom::write_image(int n, double *mybuf) { int m = 0; for (int i = 0; i < n; i++) { fprintf(fp,format, static_cast<int> (mybuf[m]), static_cast<int> (mybuf[m+1]), mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast<int> (mybuf[m+5]), static_cast<int> (mybuf[m+6]), static_cast<int> (mybuf[m+7])); m += size_one; } } /* ---------------------------------------------------------------------- */ void DumpAtom::write_noimage(int n, double *mybuf) { int m = 0; for (int i = 0; i < n; i++) { fprintf(fp,format, static_cast<int> (mybuf[m]), static_cast<int> (mybuf[m+1]), mybuf[m+2],mybuf[m+3],mybuf[m+4]); m += size_one; } } diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index b2b9cf04c..114666051 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -1,2412 +1,2408 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "math.h" #include "stdlib.h" #include "string.h" #include "dump_custom.h" #include "atom.h" #include "force.h" #include "domain.h" #include "region.h" #include "group.h" #include "input.h" #include "variable.h" #include "update.h" #include "modify.h" #include "compute.h" #include "fix.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; // customize by adding keyword // also customize compute_atom_property.cpp enum{ID,MOL,TYPE,ELEMENT,MASS, X,Y,Z,XS,YS,ZS,XSTRI,YSTRI,ZSTRI,XU,YU,ZU,XUTRI,YUTRI,ZUTRI, XSU,YSU,ZSU,XSUTRI,YSUTRI,ZSUTRI, IX,IY,IZ, VX,VY,VZ,FX,FY,FZ, Q,MUX,MUY,MUZ,MU,RADIUS,DIAMETER, OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ, TQX,TQY,TQZ,SPIN,ERADIUS,ERVEL,ERFORCE, COMPUTE,FIX,VARIABLE}; enum{LT,LE,GT,GE,EQ,NEQ}; enum{INT,DOUBLE,STRING}; #define INVOKED_PERATOM 8 /* ---------------------------------------------------------------------- */ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg) { if (narg == 5) error->all(FLERR,"No dump custom arguments specified"); clearstep = 1; nevery = atoi(arg[3]); // size_one may be shrunk below if additional optional args exist size_one = nfield = narg - 5; pack_choice = new FnPtrPack[nfield]; vtype = new int[nfield]; iregion = -1; idregion = NULL; nthresh = 0; thresh_array = NULL; thresh_op = NULL; thresh_value = NULL; // computes, fixes, variables which the dump accesses memory->create(field2index,nfield,"dump:field2index"); memory->create(argindex,nfield,"dump:argindex"); ncompute = 0; id_compute = NULL; compute = NULL; nfix = 0; id_fix = NULL; fix = NULL; nvariable = 0; id_variable = NULL; variable = NULL; vbuf = NULL; // process attributes // ioptional = start of additional optional args // only dump image style processes optional args ioptional = parse_fields(narg,arg); if (ioptional < narg && strcmp(style,"image") != 0) error->all(FLERR,"Invalid attribute in dump custom command"); size_one = nfield = ioptional - 5; // atom selection arrays maxlocal = 0; choose = NULL; dchoose = NULL; clist = NULL; // element names ntypes = atom->ntypes; typenames = NULL; // setup format strings vformat = new char*[size_one]; format_default = new char[3*size_one+1]; format_default[0] = '\0'; for (int i = 0; i < size_one; i++) { if (vtype[i] == INT) strcat(format_default,"%d "); else if (vtype[i] == DOUBLE) strcat(format_default,"%g "); else if (vtype[i] == STRING) strcat(format_default,"%s "); vformat[i] = NULL; } // setup column string int n = 0; for (int iarg = 5; iarg < narg; iarg++) n += strlen(arg[iarg]) + 2; columns = new char[n]; columns[0] = '\0'; for (int iarg = 5; iarg < narg; iarg++) { strcat(columns,arg[iarg]); strcat(columns," "); } } /* ---------------------------------------------------------------------- */ DumpCustom::~DumpCustom() { delete [] pack_choice; delete [] vtype; memory->destroy(field2index); memory->destroy(argindex); delete [] idregion; memory->destroy(thresh_array); memory->destroy(thresh_op); memory->destroy(thresh_value); for (int i = 0; i < ncompute; i++) delete [] id_compute[i]; memory->sfree(id_compute); delete [] compute; for (int i = 0; i < nfix; i++) delete [] id_fix[i]; memory->sfree(id_fix); delete [] fix; for (int i = 0; i < nvariable; i++) delete [] id_variable[i]; memory->sfree(id_variable); delete [] variable; for (int i = 0; i < nvariable; i++) memory->destroy(vbuf[i]); delete [] vbuf; memory->destroy(choose); memory->destroy(dchoose); memory->destroy(clist); if (typenames) { for (int i = 1; i <= ntypes; i++) delete [] typenames[i]; delete [] typenames; } for (int i = 0; i < size_one; i++) delete [] vformat[i]; delete [] vformat; delete [] columns; } /* ---------------------------------------------------------------------- */ void DumpCustom::init_style() { delete [] format; char *str; if (format_user) str = format_user; else str = format_default; int n = strlen(str) + 1; format = new char[n]; strcpy(format,str); // default for element names = C if (typenames == NULL) { typenames = new char*[ntypes+1]; for (int itype = 1; itype <= ntypes; itype++) { typenames[itype] = new char[2]; strcpy(typenames[itype],"C"); } } // tokenize the format string and add space at end of each format element char *ptr; for (int i = 0; i < size_one; i++) { if (i == 0) ptr = strtok(format," \0"); else ptr = strtok(NULL," \0"); if (ptr == NULL) error->all(FLERR,"Dump_modify format string is too short"); delete [] vformat[i]; vformat[i] = new char[strlen(ptr) + 2]; strcpy(vformat[i],ptr); vformat[i] = strcat(vformat[i]," "); } // setup boundary string domain->boundary_string(boundstr); // setup function ptrs if (binary && domain->triclinic == 0) header_choice = &DumpCustom::header_binary; else if (binary && domain->triclinic == 1) header_choice = &DumpCustom::header_binary_triclinic; else if (!binary && domain->triclinic == 0) header_choice = &DumpCustom::header_item; else if (!binary && domain->triclinic == 1) header_choice = &DumpCustom::header_item_triclinic; if (binary) write_choice = &DumpCustom::write_binary; else write_choice = &DumpCustom::write_text; // find current ptr for each compute,fix,variable // check that fix frequency is acceptable int icompute; for (int i = 0; i < ncompute; i++) { icompute = modify->find_compute(id_compute[i]); if (icompute < 0) error->all(FLERR,"Could not find dump custom compute ID"); compute[i] = modify->compute[icompute]; } int ifix; for (int i = 0; i < nfix; i++) { ifix = modify->find_fix(id_fix[i]); if (ifix < 0) error->all(FLERR,"Could not find dump custom fix ID"); fix[i] = modify->fix[ifix]; if (nevery % modify->fix[ifix]->peratom_freq) error->all(FLERR,"Dump custom and fix not computed at compatible times"); } int ivariable; for (int i = 0; i < nvariable; i++) { ivariable = input->variable->find(id_variable[i]); if (ivariable < 0) error->all(FLERR,"Could not find dump custom variable name"); variable[i] = ivariable; } // set index and check validity of region if (iregion >= 0) { iregion = domain->find_region(idregion); if (iregion == -1) error->all(FLERR,"Region ID for dump custom does not exist"); } // open single file, one time only if (multifile == 0) openfile(); } /* ---------------------------------------------------------------------- */ void DumpCustom::write_header(bigint ndump) { if (multiproc) (this->*header_choice)(ndump); else if (me == 0) (this->*header_choice)(ndump); } /* ---------------------------------------------------------------------- */ void DumpCustom::header_binary(bigint ndump) { fwrite(&update->ntimestep,sizeof(bigint),1,fp); fwrite(&ndump,sizeof(bigint),1,fp); fwrite(&domain->triclinic,sizeof(int),1,fp); fwrite(&domain->boundary[0][0],6*sizeof(int),1,fp); fwrite(&boxxlo,sizeof(double),1,fp); fwrite(&boxxhi,sizeof(double),1,fp); fwrite(&boxylo,sizeof(double),1,fp); fwrite(&boxyhi,sizeof(double),1,fp); fwrite(&boxzlo,sizeof(double),1,fp); fwrite(&boxzhi,sizeof(double),1,fp); fwrite(&size_one,sizeof(int),1,fp); - if (multiproc) { - int one = 1; - fwrite(&one,sizeof(int),1,fp); - } else fwrite(&nprocs,sizeof(int),1,fp); + if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp); + else fwrite(&nprocs,sizeof(int),1,fp); } /* ---------------------------------------------------------------------- */ void DumpCustom::header_binary_triclinic(bigint ndump) { fwrite(&update->ntimestep,sizeof(bigint),1,fp); fwrite(&ndump,sizeof(bigint),1,fp); fwrite(&domain->triclinic,sizeof(int),1,fp); fwrite(&domain->boundary[0][0],6*sizeof(int),1,fp); fwrite(&boxxlo,sizeof(double),1,fp); fwrite(&boxxhi,sizeof(double),1,fp); fwrite(&boxylo,sizeof(double),1,fp); fwrite(&boxyhi,sizeof(double),1,fp); fwrite(&boxzlo,sizeof(double),1,fp); fwrite(&boxzhi,sizeof(double),1,fp); fwrite(&boxxy,sizeof(double),1,fp); fwrite(&boxxz,sizeof(double),1,fp); fwrite(&boxyz,sizeof(double),1,fp); fwrite(&size_one,sizeof(int),1,fp); - if (multiproc) { - int one = 1; - fwrite(&one,sizeof(int),1,fp); - } else fwrite(&nprocs,sizeof(int),1,fp); + if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp); + else fwrite(&nprocs,sizeof(int),1,fp); } /* ---------------------------------------------------------------------- */ void DumpCustom::header_item(bigint ndump) { fprintf(fp,"ITEM: TIMESTEP\n"); fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep); fprintf(fp,"ITEM: NUMBER OF ATOMS\n"); fprintf(fp,BIGINT_FORMAT "\n",ndump); fprintf(fp,"ITEM: BOX BOUNDS %s\n",boundstr); fprintf(fp,"%g %g\n",boxxlo,boxxhi); fprintf(fp,"%g %g\n",boxylo,boxyhi); fprintf(fp,"%g %g\n",boxzlo,boxzhi); fprintf(fp,"ITEM: ATOMS %s\n",columns); } /* ---------------------------------------------------------------------- */ void DumpCustom::header_item_triclinic(bigint ndump) { fprintf(fp,"ITEM: TIMESTEP\n"); fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep); fprintf(fp,"ITEM: NUMBER OF ATOMS\n"); fprintf(fp,BIGINT_FORMAT "\n",ndump); fprintf(fp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr); fprintf(fp,"%g %g %g\n",boxxlo,boxxhi,boxxy); fprintf(fp,"%g %g %g\n",boxylo,boxyhi,boxxz); fprintf(fp,"%g %g %g\n",boxzlo,boxzhi,boxyz); fprintf(fp,"ITEM: ATOMS %s\n",columns); } /* ---------------------------------------------------------------------- */ int DumpCustom::count() { int i; // grow choose and variable vbuf arrays if needed int nlocal = atom->nlocal; if (nlocal > maxlocal) { maxlocal = atom->nmax; memory->destroy(choose); memory->destroy(dchoose); memory->destroy(clist); memory->create(choose,maxlocal,"dump:choose"); memory->create(dchoose,maxlocal,"dump:dchoose"); memory->create(clist,maxlocal,"dump:clist"); for (i = 0; i < nvariable; i++) { memory->destroy(vbuf[i]); memory->create(vbuf[i],maxlocal,"dump:vbuf"); } } // invoke Computes for per-atom quantities if (ncompute) { for (i = 0; i < ncompute; i++) if (!(compute[i]->invoked_flag & INVOKED_PERATOM)) { compute[i]->compute_peratom(); compute[i]->invoked_flag |= INVOKED_PERATOM; } } // evaluate atom-style Variables for per-atom quantities if (nvariable) for (i = 0; i < nvariable; i++) input->variable->compute_atom(variable[i],igroup,vbuf[i],1,0); // choose all local atoms for output for (i = 0; i < nlocal; i++) choose[i] = 1; // un-choose if not in group if (igroup) { int *mask = atom->mask; for (i = 0; i < nlocal; i++) if (!(mask[i] & groupbit)) choose[i] = 0; } // un-choose if not in region if (iregion >= 0) { Region *region = domain->regions[iregion]; double **x = atom->x; for (i = 0; i < nlocal; i++) if (choose[i] && region->match(x[i][0],x[i][1],x[i][2]) == 0) choose[i] = 0; } // un-choose if any threshhold criterion isn't met if (nthresh) { double *ptr; double value; int nstride; int nlocal = atom->nlocal; for (int ithresh = 0; ithresh < nthresh; ithresh++) { // customize by adding to if statement if (thresh_array[ithresh] == ID) { int *tag = atom->tag; for (i = 0; i < nlocal; i++) dchoose[i] = tag[i]; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == MOL) { if (!atom->molecule_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); int *molecule = atom->molecule; for (i = 0; i < nlocal; i++) dchoose[i] = molecule[i]; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == TYPE) { int *type = atom->type; for (i = 0; i < nlocal; i++) dchoose[i] = type[i]; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == ELEMENT) { int *type = atom->type; for (i = 0; i < nlocal; i++) dchoose[i] = type[i]; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == MASS) { if (atom->rmass) { ptr = atom->rmass; nstride = 1; } else { double *mass = atom->mass; int *type = atom->type; for (i = 0; i < nlocal; i++) dchoose[i] = mass[type[i]]; ptr = dchoose; nstride = 1; } } else if (thresh_array[ithresh] == X) { ptr = &atom->x[0][0]; nstride = 3; } else if (thresh_array[ithresh] == Y) { ptr = &atom->x[0][1]; nstride = 3; } else if (thresh_array[ithresh] == Z) { ptr = &atom->x[0][2]; nstride = 3; } else if (thresh_array[ithresh] == XS) { double **x = atom->x; double boxxlo = domain->boxlo[0]; double invxprd = 1.0/domain->xprd; for (i = 0; i < nlocal; i++) dchoose[i] = (x[i][0] - boxxlo) * invxprd; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == YS) { double **x = atom->x; double boxylo = domain->boxlo[1]; double invyprd = 1.0/domain->yprd; for (i = 0; i < nlocal; i++) dchoose[i] = (x[i][1] - boxylo) * invyprd; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == ZS) { double **x = atom->x; double boxzlo = domain->boxlo[2]; double invzprd = 1.0/domain->zprd; for (i = 0; i < nlocal; i++) dchoose[i] = (x[i][2] - boxzlo) * invzprd; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == XSTRI) { double **x = atom->x; double *boxlo = domain->boxlo; double *h_inv = domain->h_inv; for (i = 0; i < nlocal; i++) dchoose[i] = h_inv[0]*(x[i][0]-boxlo[0]) + h_inv[5]*(x[i][1]-boxlo[1]) + h_inv[4]*(x[i][2]-boxlo[2]); ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == YSTRI) { double **x = atom->x; double *boxlo = domain->boxlo; double *h_inv = domain->h_inv; for (i = 0; i < nlocal; i++) dchoose[i] = h_inv[1]*(x[i][1]-boxlo[1]) + h_inv[3]*(x[i][2]-boxlo[2]); ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == ZSTRI) { double **x = atom->x; double *boxlo = domain->boxlo; double *h_inv = domain->h_inv; for (i = 0; i < nlocal; i++) dchoose[i] = h_inv[2]*(x[i][2]-boxlo[2]); ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == XU) { double **x = atom->x; tagint *image = atom->image; double xprd = domain->xprd; for (i = 0; i < nlocal; i++) dchoose[i] = x[i][0] + ((image[i] & IMGMASK) - IMGMAX) * xprd; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == YU) { double **x = atom->x; tagint *image = atom->image; double yprd = domain->yprd; for (i = 0; i < nlocal; i++) dchoose[i] = x[i][1] + ((image[i] >> IMGBITS & IMGMASK) - IMGMAX) * yprd; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == ZU) { double **x = atom->x; tagint *image = atom->image; double zprd = domain->zprd; for (i = 0; i < nlocal; i++) dchoose[i] = x[i][2] + ((image[i] >> IMG2BITS) - IMGMAX) * zprd; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == XUTRI) { double **x = atom->x; tagint *image = atom->image; double *h = domain->h; int xbox,ybox,zbox; for (i = 0; i < nlocal; i++) { xbox = (image[i] & IMGMASK) - IMGMAX; ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; zbox = (image[i] >> IMG2BITS) - IMGMAX; dchoose[i] = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox; } ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == YUTRI) { double **x = atom->x; tagint *image = atom->image; double *h = domain->h; int ybox,zbox; for (i = 0; i < nlocal; i++) { ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; zbox = (image[i] >> IMG2BITS) - IMGMAX; dchoose[i] = x[i][1] + h[1]*ybox + h[3]*zbox; } ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == ZUTRI) { double **x = atom->x; tagint *image = atom->image; double *h = domain->h; int zbox; for (i = 0; i < nlocal; i++) { zbox = (image[i] >> IMG2BITS) - IMGMAX; dchoose[i] = x[i][2] + h[2]*zbox; } ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == XSU) { double **x = atom->x; tagint *image = atom->image; double boxxlo = domain->boxlo[0]; double invxprd = 1.0/domain->xprd; for (i = 0; i < nlocal; i++) dchoose[i] = (x[i][0] - boxxlo) * invxprd + (image[i] & IMGMASK) - IMGMAX; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == YSU) { double **x = atom->x; tagint *image = atom->image; double boxylo = domain->boxlo[1]; double invyprd = 1.0/domain->yprd; for (i = 0; i < nlocal; i++) dchoose[i] = (x[i][1] - boxylo) * invyprd + (image[i] >> IMGBITS & IMGMASK) - IMGMAX; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == ZSU) { double **x = atom->x; tagint *image = atom->image; double boxzlo = domain->boxlo[2]; double invzprd = 1.0/domain->zprd; for (i = 0; i < nlocal; i++) dchoose[i] = (x[i][2] - boxzlo) * invzprd + (image[i] >> IMG2BITS) - IMGMAX; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == XSUTRI) { double **x = atom->x; tagint *image = atom->image; double *boxlo = domain->boxlo; double *h_inv = domain->h_inv; for (i = 0; i < nlocal; i++) dchoose[i] = h_inv[0]*(x[i][0]-boxlo[0]) + h_inv[5]*(x[i][1]-boxlo[1]) + h_inv[4]*(x[i][2]-boxlo[2]) + (image[i] & IMGMASK) - IMGMAX; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == YSUTRI) { double **x = atom->x; tagint *image = atom->image; double *boxlo = domain->boxlo; double *h_inv = domain->h_inv; for (i = 0; i < nlocal; i++) dchoose[i] = h_inv[1]*(x[i][1]-boxlo[1]) + h_inv[3]*(x[i][2]-boxlo[2]) + (image[i] >> IMGBITS & IMGMASK) - IMGMAX; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == ZSUTRI) { double **x = atom->x; tagint *image = atom->image; double *boxlo = domain->boxlo; double *h_inv = domain->h_inv; for (i = 0; i < nlocal; i++) dchoose[i] = h_inv[2]*(x[i][2]-boxlo[2]) + (image[i] >> IMG2BITS) - IMGMAX; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == IX) { tagint *image = atom->image; for (i = 0; i < nlocal; i++) dchoose[i] = (image[i] & IMGMASK) - IMGMAX; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == IY) { tagint *image = atom->image; for (i = 0; i < nlocal; i++) dchoose[i] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == IZ) { tagint *image = atom->image; for (i = 0; i < nlocal; i++) dchoose[i] = (image[i] >> IMG2BITS) - IMGMAX; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == VX) { ptr = &atom->v[0][0]; nstride = 3; } else if (thresh_array[ithresh] == VY) { ptr = &atom->v[0][1]; nstride = 3; } else if (thresh_array[ithresh] == VZ) { ptr = &atom->v[0][2]; nstride = 3; } else if (thresh_array[ithresh] == FX) { ptr = &atom->f[0][0]; nstride = 3; } else if (thresh_array[ithresh] == FY) { ptr = &atom->f[0][1]; nstride = 3; } else if (thresh_array[ithresh] == FZ) { ptr = &atom->f[0][2]; nstride = 3; } else if (thresh_array[ithresh] == Q) { if (!atom->q_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = atom->q; nstride = 1; } else if (thresh_array[ithresh] == MUX) { if (!atom->mu_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = &atom->mu[0][0]; nstride = 4; } else if (thresh_array[ithresh] == MUY) { if (!atom->mu_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = &atom->mu[0][1]; nstride = 4; } else if (thresh_array[ithresh] == MUZ) { if (!atom->mu_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = &atom->mu[0][2]; nstride = 4; } else if (thresh_array[ithresh] == MU) { if (!atom->mu_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = &atom->mu[0][3]; nstride = 4; } else if (thresh_array[ithresh] == RADIUS) { if (!atom->radius_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = atom->radius; nstride = 1; } else if (thresh_array[ithresh] == DIAMETER) { if (!atom->radius_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); double *radius = atom->radius; for (i = 0; i < nlocal; i++) dchoose[i] = 2.0*radius[i]; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == OMEGAX) { if (!atom->omega_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = &atom->omega[0][0]; nstride = 3; } else if (thresh_array[ithresh] == OMEGAY) { if (!atom->omega_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = &atom->omega[0][1]; nstride = 3; } else if (thresh_array[ithresh] == OMEGAZ) { if (!atom->omega_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = &atom->omega[0][2]; nstride = 3; } else if (thresh_array[ithresh] == ANGMOMX) { if (!atom->angmom_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = &atom->angmom[0][0]; nstride = 3; } else if (thresh_array[ithresh] == ANGMOMY) { if (!atom->angmom_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = &atom->angmom[0][1]; nstride = 3; } else if (thresh_array[ithresh] == ANGMOMZ) { if (!atom->angmom_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = &atom->angmom[0][2]; nstride = 3; } else if (thresh_array[ithresh] == TQX) { if (!atom->torque_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = &atom->torque[0][0]; nstride = 3; } else if (thresh_array[ithresh] == TQY) { if (!atom->torque_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = &atom->torque[0][1]; nstride = 3; } else if (thresh_array[ithresh] == TQZ) { if (!atom->torque_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = &atom->torque[0][2]; nstride = 3; } else if (thresh_array[ithresh] == SPIN) { if (!atom->spin_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); int *spin = atom->spin; for (i = 0; i < nlocal; i++) dchoose[i] = spin[i]; ptr = dchoose; nstride = 1; } else if (thresh_array[ithresh] == ERADIUS) { if (!atom->eradius_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = atom->eradius; nstride = 1; } else if (thresh_array[ithresh] == ERVEL) { if (!atom->ervel_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = atom->ervel; nstride = 1; } else if (thresh_array[ithresh] == ERFORCE) { if (!atom->erforce_flag) error->all(FLERR, "Threshhold for an atom property that isn't allocated"); ptr = atom->erforce; nstride = 1; } else if (thresh_array[ithresh] == COMPUTE) { i = nfield + ithresh; if (argindex[i] == 0) { ptr = compute[field2index[i]]->vector_atom; nstride = 1; } else { ptr = &compute[field2index[i]]->array_atom[0][argindex[i]-1]; nstride = compute[field2index[i]]->size_peratom_cols; } } else if (thresh_array[ithresh] == FIX) { i = nfield + ithresh; if (argindex[i] == 0) { ptr = fix[field2index[i]]->vector_atom; nstride = 1; } else { ptr = &fix[field2index[i]]->array_atom[0][argindex[i]-1]; nstride = fix[field2index[i]]->size_peratom_cols; } } else if (thresh_array[ithresh] == VARIABLE) { i = nfield + ithresh; ptr = vbuf[field2index[i]]; nstride = 1; } // unselect atoms that don't meet threshhold criterion value = thresh_value[ithresh]; if (thresh_op[ithresh] == LT) { for (i = 0; i < nlocal; i++, ptr += nstride) if (choose[i] && *ptr >= value) choose[i] = 0; } else if (thresh_op[ithresh] == LE) { for (i = 0; i < nlocal; i++, ptr += nstride) if (choose[i] && *ptr > value) choose[i] = 0; } else if (thresh_op[ithresh] == GT) { for (i = 0; i < nlocal; i++, ptr += nstride) if (choose[i] && *ptr <= value) choose[i] = 0; } else if (thresh_op[ithresh] == GE) { for (i = 0; i < nlocal; i++, ptr += nstride) if (choose[i] && *ptr < value) choose[i] = 0; } else if (thresh_op[ithresh] == EQ) { for (i = 0; i < nlocal; i++, ptr += nstride) if (choose[i] && *ptr != value) choose[i] = 0; } else if (thresh_op[ithresh] == NEQ) { for (i = 0; i < nlocal; i++, ptr += nstride) if (choose[i] && *ptr == value) choose[i] = 0; } } } // compress choose flags into clist // nchoose = # of selected atoms // clist[i] = local index of each selected atom nchoose = 0; for (i = 0; i < nlocal; i++) if (choose[i]) clist[nchoose++] = i; return nchoose; } /* ---------------------------------------------------------------------- */ void DumpCustom::pack(int *ids) { for (int n = 0; n < size_one; n++) (this->*pack_choice[n])(n); if (ids) { int *tag = atom->tag; for (int i = 0; i < nchoose; i++) ids[i] = tag[clist[i]]; } } /* ---------------------------------------------------------------------- */ void DumpCustom::write_data(int n, double *mybuf) { (this->*write_choice)(n,mybuf); } /* ---------------------------------------------------------------------- */ void DumpCustom::write_binary(int n, double *mybuf) { n *= size_one; fwrite(&n,sizeof(int),1,fp); fwrite(mybuf,sizeof(double),n,fp); } /* ---------------------------------------------------------------------- */ void DumpCustom::write_text(int n, double *mybuf) { int i,j; int m = 0; for (i = 0; i < n; i++) { for (j = 0; j < size_one; j++) { if (vtype[j] == INT) fprintf(fp,vformat[j],static_cast<int> (mybuf[m])); else if (vtype[j] == DOUBLE) fprintf(fp,vformat[j],mybuf[m]); else if (vtype[j] == STRING) fprintf(fp,vformat[j],typenames[(int) mybuf[m]]); m++; } fprintf(fp,"\n"); } } /* ---------------------------------------------------------------------- */ int DumpCustom::parse_fields(int narg, char **arg) { // customize by adding to if statement int i; for (int iarg = 5; iarg < narg; iarg++) { i = iarg-5; if (strcmp(arg[iarg],"id") == 0) { pack_choice[i] = &DumpCustom::pack_id; vtype[i] = INT; } else if (strcmp(arg[iarg],"mol") == 0) { if (!atom->molecule_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[i] = &DumpCustom::pack_molecule; vtype[i] = INT; } else if (strcmp(arg[iarg],"type") == 0) { pack_choice[i] = &DumpCustom::pack_type; vtype[i] = INT; } else if (strcmp(arg[iarg],"element") == 0) { pack_choice[i] = &DumpCustom::pack_type; vtype[i] = STRING; } else if (strcmp(arg[iarg],"mass") == 0) { pack_choice[i] = &DumpCustom::pack_mass; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"x") == 0) { pack_choice[i] = &DumpCustom::pack_x; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"y") == 0) { pack_choice[i] = &DumpCustom::pack_y; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"z") == 0) { pack_choice[i] = &DumpCustom::pack_z; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"xs") == 0) { if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_xs_triclinic; else pack_choice[i] = &DumpCustom::pack_xs; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"ys") == 0) { if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_ys_triclinic; else pack_choice[i] = &DumpCustom::pack_ys; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"zs") == 0) { if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_zs_triclinic; else pack_choice[i] = &DumpCustom::pack_zs; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"xu") == 0) { if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_xu_triclinic; else pack_choice[i] = &DumpCustom::pack_xu; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"yu") == 0) { if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_yu_triclinic; else pack_choice[i] = &DumpCustom::pack_yu; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"zu") == 0) { if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_zu_triclinic; else pack_choice[i] = &DumpCustom::pack_zu; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"xsu") == 0) { if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_xsu_triclinic; else pack_choice[i] = &DumpCustom::pack_xsu; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"ysu") == 0) { if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_ysu_triclinic; else pack_choice[i] = &DumpCustom::pack_ysu; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"zsu") == 0) { if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_zsu_triclinic; else pack_choice[i] = &DumpCustom::pack_zsu; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"ix") == 0) { pack_choice[i] = &DumpCustom::pack_ix; vtype[i] = INT; } else if (strcmp(arg[iarg],"iy") == 0) { pack_choice[i] = &DumpCustom::pack_iy; vtype[i] = INT; } else if (strcmp(arg[iarg],"iz") == 0) { pack_choice[i] = &DumpCustom::pack_iz; vtype[i] = INT; } else if (strcmp(arg[iarg],"vx") == 0) { pack_choice[i] = &DumpCustom::pack_vx; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"vy") == 0) { pack_choice[i] = &DumpCustom::pack_vy; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"vz") == 0) { pack_choice[i] = &DumpCustom::pack_vz; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"fx") == 0) { pack_choice[i] = &DumpCustom::pack_fx; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"fy") == 0) { pack_choice[i] = &DumpCustom::pack_fy; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"fz") == 0) { pack_choice[i] = &DumpCustom::pack_fz; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"q") == 0) { if (!atom->q_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[i] = &DumpCustom::pack_q; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"mux") == 0) { if (!atom->mu_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[i] = &DumpCustom::pack_mux; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"muy") == 0) { if (!atom->mu_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[i] = &DumpCustom::pack_muy; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"muz") == 0) { if (!atom->mu_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[i] = &DumpCustom::pack_muz; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"mu") == 0) { if (!atom->mu_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[i] = &DumpCustom::pack_mu; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"radius") == 0) { if (!atom->radius_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[i] = &DumpCustom::pack_radius; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"diameter") == 0) { if (!atom->radius_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[i] = &DumpCustom::pack_diameter; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"omegax") == 0) { if (!atom->omega_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[i] = &DumpCustom::pack_omegax; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"omegay") == 0) { if (!atom->omega_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[i] = &DumpCustom::pack_omegay; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"omegaz") == 0) { if (!atom->omega_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[i] = &DumpCustom::pack_omegaz; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"angmomx") == 0) { if (!atom->angmom_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[i] = &DumpCustom::pack_angmomx; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"angmomy") == 0) { if (!atom->angmom_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[i] = &DumpCustom::pack_angmomy; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"angmomz") == 0) { if (!atom->angmom_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[i] = &DumpCustom::pack_angmomz; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"tqx") == 0) { if (!atom->torque_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[i] = &DumpCustom::pack_tqx; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"tqy") == 0) { if (!atom->torque_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[i] = &DumpCustom::pack_tqy; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"tqz") == 0) { if (!atom->torque_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[i] = &DumpCustom::pack_tqz; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"spin") == 0) { if (!atom->spin_flag) error->all(FLERR,"Dumping an atom quantity that isn't allocated"); pack_choice[i] = &DumpCustom::pack_spin; vtype[i] = INT; } else if (strcmp(arg[iarg],"eradius") == 0) { if (!atom->eradius_flag) error->all(FLERR,"Dumping an atom quantity that isn't allocated"); pack_choice[i] = &DumpCustom::pack_eradius; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"ervel") == 0) { if (!atom->ervel_flag) error->all(FLERR,"Dumping an atom quantity that isn't allocated"); pack_choice[i] = &DumpCustom::pack_ervel; vtype[i] = DOUBLE; } else if (strcmp(arg[iarg],"erforce") == 0) { if (!atom->erforce_flag) error->all(FLERR,"Dumping an atom quantity that isn't allocated"); pack_choice[i] = &DumpCustom::pack_erforce; vtype[i] = DOUBLE; // compute value = c_ID // if no trailing [], then arg is set to 0, else arg is int between [] } else if (strncmp(arg[iarg],"c_",2) == 0) { pack_choice[i] = &DumpCustom::pack_compute; vtype[i] = DOUBLE; int n = strlen(arg[iarg]); char *suffix = new char[n]; strcpy(suffix,&arg[iarg][2]); char *ptr = strchr(suffix,'['); if (ptr) { if (suffix[strlen(suffix)-1] != ']') error->all(FLERR,"Invalid attribute in dump custom command"); argindex[i] = atoi(ptr+1); *ptr = '\0'; } else argindex[i] = 0; n = modify->find_compute(suffix); if (n < 0) error->all(FLERR,"Could not find dump custom compute ID"); if (modify->compute[n]->peratom_flag == 0) error->all(FLERR,"Dump custom compute does not compute per-atom info"); if (argindex[i] == 0 && modify->compute[n]->size_peratom_cols > 0) error->all(FLERR,"Dump custom compute does not calculate per-atom vector"); if (argindex[i] > 0 && modify->compute[n]->size_peratom_cols == 0) error->all(FLERR,"Dump custom compute does not calculate per-atom array"); if (argindex[i] > 0 && argindex[i] > modify->compute[n]->size_peratom_cols) error->all(FLERR,"Dump custom compute vector is accessed out-of-range"); field2index[i] = add_compute(suffix); delete [] suffix; // fix value = f_ID // if no trailing [], then arg is set to 0, else arg is between [] } else if (strncmp(arg[iarg],"f_",2) == 0) { pack_choice[i] = &DumpCustom::pack_fix; vtype[i] = DOUBLE; int n = strlen(arg[iarg]); char *suffix = new char[n]; strcpy(suffix,&arg[iarg][2]); char *ptr = strchr(suffix,'['); if (ptr) { if (suffix[strlen(suffix)-1] != ']') error->all(FLERR,"Invalid attribute in dump custom command"); argindex[i] = atoi(ptr+1); *ptr = '\0'; } else argindex[i] = 0; n = modify->find_fix(suffix); if (n < 0) error->all(FLERR,"Could not find dump custom fix ID"); if (modify->fix[n]->peratom_flag == 0) error->all(FLERR,"Dump custom fix does not compute per-atom info"); if (argindex[i] == 0 && modify->fix[n]->size_peratom_cols > 0) error->all(FLERR,"Dump custom fix does not compute per-atom vector"); if (argindex[i] > 0 && modify->fix[n]->size_peratom_cols == 0) error->all(FLERR,"Dump custom fix does not compute per-atom array"); if (argindex[i] > 0 && argindex[i] > modify->fix[n]->size_peratom_cols) error->all(FLERR,"Dump custom fix vector is accessed out-of-range"); field2index[i] = add_fix(suffix); delete [] suffix; // variable value = v_name } else if (strncmp(arg[iarg],"v_",2) == 0) { pack_choice[i] = &DumpCustom::pack_variable; vtype[i] = DOUBLE; int n = strlen(arg[iarg]); char *suffix = new char[n]; strcpy(suffix,&arg[iarg][2]); argindex[i] = 0; n = input->variable->find(suffix); if (n < 0) error->all(FLERR,"Could not find dump custom variable name"); if (input->variable->atomstyle(n) == 0) error->all(FLERR,"Dump custom variable is not atom-style variable"); field2index[i] = add_variable(suffix); delete [] suffix; } else return iarg; } return narg; } /* ---------------------------------------------------------------------- add Compute to list of Compute objects used by dump return index of where this Compute is in list if already in list, do not add, just return index, else add to list ------------------------------------------------------------------------- */ int DumpCustom::add_compute(char *id) { int icompute; for (icompute = 0; icompute < ncompute; icompute++) if (strcmp(id,id_compute[icompute]) == 0) break; if (icompute < ncompute) return icompute; id_compute = (char **) memory->srealloc(id_compute,(ncompute+1)*sizeof(char *),"dump:id_compute"); delete [] compute; compute = new Compute*[ncompute+1]; int n = strlen(id) + 1; id_compute[ncompute] = new char[n]; strcpy(id_compute[ncompute],id); ncompute++; return ncompute-1; } /* ---------------------------------------------------------------------- add Fix to list of Fix objects used by dump return index of where this Fix is in list if already in list, do not add, just return index, else add to list ------------------------------------------------------------------------- */ int DumpCustom::add_fix(char *id) { int ifix; for (ifix = 0; ifix < nfix; ifix++) if (strcmp(id,id_fix[ifix]) == 0) break; if (ifix < nfix) return ifix; id_fix = (char **) memory->srealloc(id_fix,(nfix+1)*sizeof(char *),"dump:id_fix"); delete [] fix; fix = new Fix*[nfix+1]; int n = strlen(id) + 1; id_fix[nfix] = new char[n]; strcpy(id_fix[nfix],id); nfix++; return nfix-1; } /* ---------------------------------------------------------------------- add Variable to list of Variables used by dump return index of where this Variable is in list if already in list, do not add, just return index, else add to list ------------------------------------------------------------------------- */ int DumpCustom::add_variable(char *id) { int ivariable; for (ivariable = 0; ivariable < nvariable; ivariable++) if (strcmp(id,id_variable[ivariable]) == 0) break; if (ivariable < nvariable) return ivariable; id_variable = (char **) memory->srealloc(id_variable,(nvariable+1)*sizeof(char *), "dump:id_variable"); delete [] variable; variable = new int[nvariable+1]; delete [] vbuf; vbuf = new double*[nvariable+1]; for (int i = 0; i <= nvariable; i++) vbuf[i] = NULL; int n = strlen(id) + 1; id_variable[nvariable] = new char[n]; strcpy(id_variable[nvariable],id); nvariable++; return nvariable-1; } /* ---------------------------------------------------------------------- */ int DumpCustom::modify_param(int narg, char **arg) { if (strcmp(arg[0],"region") == 0) { if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); if (strcmp(arg[1],"none") == 0) iregion = -1; else { iregion = domain->find_region(arg[1]); if (iregion == -1) error->all(FLERR,"Dump_modify region ID does not exist"); int n = strlen(arg[1]) + 1; idregion = new char[n]; strcpy(idregion,arg[1]); } return 2; } if (strcmp(arg[0],"element") == 0) { if (narg < ntypes+1) error->all(FLERR,"Dump modify element names do not match atom types"); if (typenames) { for (int i = 1; i <= ntypes; i++) delete [] typenames[i]; delete [] typenames; typenames = NULL; } typenames = new char*[ntypes+1]; for (int itype = 1; itype <= ntypes; itype++) { int n = strlen(arg[itype]) + 1; typenames[itype] = new char[n]; strcpy(typenames[itype],arg[itype]); } return ntypes+1; } if (strcmp(arg[0],"thresh") == 0) { if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); if (strcmp(arg[1],"none") == 0) { if (nthresh) { memory->destroy(thresh_array); memory->destroy(thresh_op); memory->destroy(thresh_value); thresh_array = NULL; thresh_op = NULL; thresh_value = NULL; } nthresh = 0; return 2; } if (narg < 4) error->all(FLERR,"Illegal dump_modify command"); // grow threshhold arrays memory->grow(thresh_array,nthresh+1,"dump:thresh_array"); memory->grow(thresh_op,(nthresh+1),"dump:thresh_op"); memory->grow(thresh_value,(nthresh+1),"dump:thresh_value"); // set attribute type of threshhold // customize by adding to if statement if (strcmp(arg[1],"id") == 0) thresh_array[nthresh] = ID; else if (strcmp(arg[1],"mol") == 0) thresh_array[nthresh] = MOL; else if (strcmp(arg[1],"type") == 0) thresh_array[nthresh] = TYPE; else if (strcmp(arg[1],"mass") == 0) thresh_array[nthresh] = MASS; else if (strcmp(arg[1],"x") == 0) thresh_array[nthresh] = X; else if (strcmp(arg[1],"y") == 0) thresh_array[nthresh] = Y; else if (strcmp(arg[1],"z") == 0) thresh_array[nthresh] = Z; else if (strcmp(arg[1],"xs") == 0 && domain->triclinic == 0) thresh_array[nthresh] = XS; else if (strcmp(arg[1],"xs") == 0 && domain->triclinic == 1) thresh_array[nthresh] = XSTRI; else if (strcmp(arg[1],"ys") == 0 && domain->triclinic == 0) thresh_array[nthresh] = YS; else if (strcmp(arg[1],"ys") == 0 && domain->triclinic == 1) thresh_array[nthresh] = YSTRI; else if (strcmp(arg[1],"zs") == 0 && domain->triclinic == 0) thresh_array[nthresh] = ZS; else if (strcmp(arg[1],"zs") == 0 && domain->triclinic == 1) thresh_array[nthresh] = ZSTRI; else if (strcmp(arg[1],"xu") == 0 && domain->triclinic == 0) thresh_array[nthresh] = XU; else if (strcmp(arg[1],"xu") == 0 && domain->triclinic == 1) thresh_array[nthresh] = XUTRI; else if (strcmp(arg[1],"yu") == 0 && domain->triclinic == 0) thresh_array[nthresh] = YU; else if (strcmp(arg[1],"yu") == 0 && domain->triclinic == 1) thresh_array[nthresh] = YUTRI; else if (strcmp(arg[1],"zu") == 0 && domain->triclinic == 0) thresh_array[nthresh] = ZU; else if (strcmp(arg[1],"zu") == 0 && domain->triclinic == 1) thresh_array[nthresh] = ZUTRI; else if (strcmp(arg[1],"xsu") == 0 && domain->triclinic == 0) thresh_array[nthresh] = XSU; else if (strcmp(arg[1],"xsu") == 0 && domain->triclinic == 1) thresh_array[nthresh] = XSUTRI; else if (strcmp(arg[1],"ysu") == 0 && domain->triclinic == 0) thresh_array[nthresh] = YSU; else if (strcmp(arg[1],"ysu") == 0 && domain->triclinic == 1) thresh_array[nthresh] = YSUTRI; else if (strcmp(arg[1],"zsu") == 0 && domain->triclinic == 0) thresh_array[nthresh] = ZSU; else if (strcmp(arg[1],"zsu") == 0 && domain->triclinic == 1) thresh_array[nthresh] = ZSUTRI; else if (strcmp(arg[1],"ix") == 0) thresh_array[nthresh] = IX; else if (strcmp(arg[1],"iy") == 0) thresh_array[nthresh] = IY; else if (strcmp(arg[1],"iz") == 0) thresh_array[nthresh] = IZ; else if (strcmp(arg[1],"vx") == 0) thresh_array[nthresh] = VX; else if (strcmp(arg[1],"vy") == 0) thresh_array[nthresh] = VY; else if (strcmp(arg[1],"vz") == 0) thresh_array[nthresh] = VZ; else if (strcmp(arg[1],"fx") == 0) thresh_array[nthresh] = FX; else if (strcmp(arg[1],"fy") == 0) thresh_array[nthresh] = FY; else if (strcmp(arg[1],"fz") == 0) thresh_array[nthresh] = FZ; else if (strcmp(arg[1],"q") == 0) thresh_array[nthresh] = Q; else if (strcmp(arg[1],"mux") == 0) thresh_array[nthresh] = MUX; else if (strcmp(arg[1],"muy") == 0) thresh_array[nthresh] = MUY; else if (strcmp(arg[1],"muz") == 0) thresh_array[nthresh] = MUZ; else if (strcmp(arg[1],"mu") == 0) thresh_array[nthresh] = MU; else if (strcmp(arg[1],"radius") == 0) thresh_array[nthresh] = RADIUS; else if (strcmp(arg[1],"diameter") == 0) thresh_array[nthresh] = DIAMETER; else if (strcmp(arg[1],"omegax") == 0) thresh_array[nthresh] = OMEGAX; else if (strcmp(arg[1],"omegay") == 0) thresh_array[nthresh] = OMEGAY; else if (strcmp(arg[1],"omegaz") == 0) thresh_array[nthresh] = OMEGAZ; else if (strcmp(arg[1],"angmomx") == 0) thresh_array[nthresh] = ANGMOMX; else if (strcmp(arg[1],"angmomy") == 0) thresh_array[nthresh] = ANGMOMY; else if (strcmp(arg[1],"angmomz") == 0) thresh_array[nthresh] = ANGMOMZ; else if (strcmp(arg[1],"tqx") == 0) thresh_array[nthresh] = TQX; else if (strcmp(arg[1],"tqy") == 0) thresh_array[nthresh] = TQY; else if (strcmp(arg[1],"tqz") == 0) thresh_array[nthresh] = TQZ; else if (strcmp(arg[1],"spin") == 0) thresh_array[nthresh] = SPIN; else if (strcmp(arg[1],"eradius") == 0) thresh_array[nthresh] = ERADIUS; else if (strcmp(arg[1],"ervel") == 0) thresh_array[nthresh] = ERVEL; else if (strcmp(arg[1],"erforce") == 0) thresh_array[nthresh] = ERFORCE; // compute value = c_ID // if no trailing [], then arg is set to 0, else arg is between [] // must grow field2index and argindex arrays, since access is beyond nfield else if (strncmp(arg[1],"c_",2) == 0) { thresh_array[nthresh] = COMPUTE; memory->grow(field2index,nfield+nthresh+1,"dump:field2index"); memory->grow(argindex,nfield+nthresh+1,"dump:argindex"); int n = strlen(arg[1]); char *suffix = new char[n]; strcpy(suffix,&arg[1][2]); char *ptr = strchr(suffix,'['); if (ptr) { if (suffix[strlen(suffix)-1] != ']') error->all(FLERR,"Invalid attribute in dump modify command"); argindex[nfield+nthresh] = atoi(ptr+1); *ptr = '\0'; } else argindex[nfield+nthresh] = 0; n = modify->find_compute(suffix); if (n < 0) error->all(FLERR,"Could not find dump modify compute ID"); if (modify->compute[n]->peratom_flag == 0) error->all(FLERR, "Dump modify compute ID does not compute per-atom info"); if (argindex[nfield+nthresh] == 0 && modify->compute[n]->size_peratom_cols > 0) error->all(FLERR, "Dump modify compute ID does not compute per-atom vector"); if (argindex[nfield+nthresh] > 0 && modify->compute[n]->size_peratom_cols == 0) error->all(FLERR, "Dump modify compute ID does not compute per-atom array"); if (argindex[nfield+nthresh] > 0 && argindex[nfield+nthresh] > modify->compute[n]->size_peratom_cols) error->all(FLERR,"Dump modify compute ID vector is not large enough"); field2index[nfield+nthresh] = add_compute(suffix); delete [] suffix; // fix value = f_ID // if no trailing [], then arg is set to 0, else arg is between [] // must grow field2index and argindex arrays, since access is beyond nfield } else if (strncmp(arg[1],"f_",2) == 0) { thresh_array[nthresh] = FIX; memory->grow(field2index,nfield+nthresh+1,"dump:field2index"); memory->grow(argindex,nfield+nthresh+1,"dump:argindex"); int n = strlen(arg[1]); char *suffix = new char[n]; strcpy(suffix,&arg[1][2]); char *ptr = strchr(suffix,'['); if (ptr) { if (suffix[strlen(suffix)-1] != ']') error->all(FLERR,"Invalid attribute in dump modify command"); argindex[nfield+nthresh] = atoi(ptr+1); *ptr = '\0'; } else argindex[nfield+nthresh] = 0; n = modify->find_fix(suffix); if (n < 0) error->all(FLERR,"Could not find dump modify fix ID"); if (modify->fix[n]->peratom_flag == 0) error->all(FLERR,"Dump modify fix ID does not compute per-atom info"); if (argindex[nfield+nthresh] == 0 && modify->fix[n]->size_peratom_cols > 0) error->all(FLERR,"Dump modify fix ID does not compute per-atom vector"); if (argindex[nfield+nthresh] > 0 && modify->fix[n]->size_peratom_cols == 0) error->all(FLERR,"Dump modify fix ID does not compute per-atom array"); if (argindex[nfield+nthresh] > 0 && argindex[nfield+nthresh] > modify->fix[n]->size_peratom_cols) error->all(FLERR,"Dump modify fix ID vector is not large enough"); field2index[nfield+nthresh] = add_fix(suffix); delete [] suffix; // variable value = v_ID // must grow field2index and argindex arrays, since access is beyond nfield } else if (strncmp(arg[1],"v_",2) == 0) { thresh_array[nthresh] = VARIABLE; memory->grow(field2index,nfield+nthresh+1,"dump:field2index"); memory->grow(argindex,nfield+nthresh+1,"dump:argindex"); int n = strlen(arg[1]); char *suffix = new char[n]; strcpy(suffix,&arg[1][2]); argindex[nfield+nthresh] = 0; n = input->variable->find(suffix); if (n < 0) error->all(FLERR,"Could not find dump modify variable name"); if (input->variable->atomstyle(n) == 0) error->all(FLERR,"Dump modify variable is not atom-style variable"); field2index[nfield+nthresh] = add_variable(suffix); delete [] suffix; } else error->all(FLERR,"Invalid dump_modify threshhold operator"); // set operation type of threshhold if (strcmp(arg[2],"<") == 0) thresh_op[nthresh] = LT; else if (strcmp(arg[2],"<=") == 0) thresh_op[nthresh] = LE; else if (strcmp(arg[2],">") == 0) thresh_op[nthresh] = GT; else if (strcmp(arg[2],">=") == 0) thresh_op[nthresh] = GE; else if (strcmp(arg[2],"==") == 0) thresh_op[nthresh] = EQ; else if (strcmp(arg[2],"!=") == 0) thresh_op[nthresh] = NEQ; else error->all(FLERR,"Invalid dump_modify threshhold operator"); // set threshhold value thresh_value[nthresh] = atof(arg[3]); nthresh++; return 4; } return 0; } /* ---------------------------------------------------------------------- return # of bytes of allocated memory in buf, choose, variable arrays ------------------------------------------------------------------------- */ bigint DumpCustom::memory_usage() { bigint bytes = Dump::memory_usage(); bytes += memory->usage(choose,maxlocal); bytes += memory->usage(dchoose,maxlocal); bytes += memory->usage(clist,maxlocal); bytes += memory->usage(vbuf,nvariable,maxlocal); return bytes; } /* ---------------------------------------------------------------------- extraction of Compute, Fix, Variable results ------------------------------------------------------------------------- */ void DumpCustom::pack_compute(int n) { double *vector = compute[field2index[n]]->vector_atom; double **array = compute[field2index[n]]->array_atom; int index = argindex[n]; if (index == 0) { for (int i = 0; i < nchoose; i++) { buf[n] = vector[clist[i]]; n += size_one; } } else { index--; for (int i = 0; i < nchoose; i++) { buf[n] = array[clist[i]][index]; n += size_one; } } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_fix(int n) { double *vector = fix[field2index[n]]->vector_atom; double **array = fix[field2index[n]]->array_atom; int index = argindex[n]; if (index == 0) { for (int i = 0; i < nchoose; i++) { buf[n] = vector[clist[i]]; n += size_one; } } else { index--; for (int i = 0; i < nchoose; i++) { buf[n] = array[clist[i]][index]; n += size_one; } } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_variable(int n) { double *vector = vbuf[field2index[n]]; for (int i = 0; i < nchoose; i++) { buf[n] = vector[clist[i]]; n += size_one; } } /* ---------------------------------------------------------------------- one method for every attribute dump custom can output the atom property is packed into buf starting at n with stride size_one customize a new attribute by adding a method ------------------------------------------------------------------------- */ void DumpCustom::pack_id(int n) { int *tag = atom->tag; for (int i = 0; i < nchoose; i++) { buf[n] = tag[clist[i]]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_molecule(int n) { int *molecule = atom->molecule; for (int i = 0; i < nchoose; i++) { buf[n] = molecule[clist[i]]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_type(int n) { int *type = atom->type; for (int i = 0; i < nchoose; i++) { buf[n] = type[clist[i]]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_mass(int n) { int *type = atom->type; double *mass = atom->mass; double *rmass = atom->rmass; if (rmass) { for (int i = 0; i < nchoose; i++) { buf[n] = rmass[clist[i]]; n += size_one; } } else { for (int i = 0; i < nchoose; i++) { buf[n] = mass[type[clist[i]]]; n += size_one; } } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_x(int n) { double **x = atom->x; for (int i = 0; i < nchoose; i++) { buf[n] = x[clist[i]][0]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_y(int n) { double **x = atom->x; for (int i = 0; i < nchoose; i++) { buf[n] = x[clist[i]][1]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_z(int n) { double **x = atom->x; for (int i = 0; i < nchoose; i++) { buf[n] = x[clist[i]][2]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_xs(int n) { double **x = atom->x; double boxxlo = domain->boxlo[0]; double invxprd = 1.0/domain->xprd; for (int i = 0; i < nchoose; i++) { buf[n] = (x[clist[i]][0] - boxxlo) * invxprd; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_ys(int n) { double **x = atom->x; double boxylo = domain->boxlo[1]; double invyprd = 1.0/domain->yprd; for (int i = 0; i < nchoose; i++) { buf[n] = (x[clist[i]][1] - boxylo) * invyprd; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_zs(int n) { double **x = atom->x; double boxzlo = domain->boxlo[2]; double invzprd = 1.0/domain->zprd; for (int i = 0; i < nchoose; i++) { buf[n] = (x[clist[i]][2] - boxzlo) * invzprd; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_xs_triclinic(int n) { int j; double **x = atom->x; double *boxlo = domain->boxlo; double *h_inv = domain->h_inv; for (int i = 0; i < nchoose; i++) { j = clist[i]; buf[n] = h_inv[0]*(x[j][0]-boxlo[0]) + h_inv[5]*(x[j][1]-boxlo[1]) + h_inv[4]*(x[j][2]-boxlo[2]); n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_ys_triclinic(int n) { int j; double **x = atom->x; double *boxlo = domain->boxlo; double *h_inv = domain->h_inv; for (int i = 0; i < nchoose; i++) { j = clist[i]; buf[n] = h_inv[1]*(x[j][1]-boxlo[1]) + h_inv[3]*(x[j][2]-boxlo[2]); n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_zs_triclinic(int n) { double **x = atom->x; double *boxlo = domain->boxlo; double *h_inv = domain->h_inv; for (int i = 0; i < nchoose; i++) { buf[n] = h_inv[2]*(x[clist[i]][2]-boxlo[2]); n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_xu(int n) { int j; double **x = atom->x; tagint *image = atom->image; double xprd = domain->xprd; for (int i = 0; i < nchoose; i++) { j = clist[i]; buf[n] = x[j][0] + ((image[j] & IMGMASK) - IMGMAX) * xprd; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_yu(int n) { int j; double **x = atom->x; tagint *image = atom->image; double yprd = domain->yprd; for (int i = 0; i < nchoose; i++) { j = clist[i]; buf[n] = x[j][1] + ((image[j] >> IMGBITS & IMGMASK) - IMGMAX) * yprd; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_zu(int n) { int j; double **x = atom->x; tagint *image = atom->image; double zprd = domain->zprd; for (int i = 0; i < nchoose; i++) { j = clist[i]; buf[n] = x[j][2] + ((image[j] >> IMG2BITS) - IMGMAX) * zprd; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_xu_triclinic(int n) { int j; double **x = atom->x; tagint *image = atom->image; double *h = domain->h; int xbox,ybox,zbox; for (int i = 0; i < nchoose; i++) { j = clist[i]; xbox = (image[j] & IMGMASK) - IMGMAX; ybox = (image[j] >> IMGBITS & IMGMASK) - IMGMAX; zbox = (image[j] >> IMG2BITS) - IMGMAX; buf[n] = x[j][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_yu_triclinic(int n) { int j; double **x = atom->x; tagint *image = atom->image; double *h = domain->h; int ybox,zbox; for (int i = 0; i < nchoose; i++) { j = clist[i]; ybox = (image[j] >> IMGBITS & IMGMASK) - IMGMAX; zbox = (image[j] >> IMG2BITS) - IMGMAX; buf[n] = x[j][1] + h[1]*ybox + h[3]*zbox; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_zu_triclinic(int n) { int j; double **x = atom->x; tagint *image = atom->image; double *h = domain->h; int zbox; for (int i = 0; i < nchoose; i++) { j = clist[i]; zbox = (image[j] >> IMG2BITS) - IMGMAX; buf[n] = x[j][2] + h[2]*zbox; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_xsu(int n) { int j; double **x = atom->x; tagint *image = atom->image; double boxxlo = domain->boxlo[0]; double invxprd = 1.0/domain->xprd; for (int i = 0; i < nchoose; i++) { j = clist[i]; buf[n] = (x[j][0] - boxxlo) * invxprd + (image[j] & IMGMASK) - IMGMAX; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_ysu(int n) { int j; double **x = atom->x; tagint *image = atom->image; double boxylo = domain->boxlo[1]; double invyprd = 1.0/domain->yprd; for (int i = 0; i < nchoose; i++) { j = clist[i]; buf[n] = (x[j][1] - boxylo) * invyprd + (image[j] >> IMGBITS & IMGMASK) - IMGMAX; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_zsu(int n) { int j; double **x = atom->x; tagint *image = atom->image; double boxzlo = domain->boxlo[2]; double invzprd = 1.0/domain->zprd; for (int i = 0; i < nchoose; i++) { j = clist[i]; buf[n] = (x[j][2] - boxzlo) * invzprd + (image[j] >> IMG2BITS) - IMGMAX; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_xsu_triclinic(int n) { int j; double **x = atom->x; tagint *image = atom->image; double *boxlo = domain->boxlo; double *h_inv = domain->h_inv; for (int i = 0; i < nchoose; i++) { j = clist[i]; buf[n] = h_inv[0]*(x[j][0]-boxlo[0]) + h_inv[5]*(x[j][1]-boxlo[1]) + h_inv[4]*(x[j][2]-boxlo[2]) + (image[j] & IMGMASK) - IMGMAX; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_ysu_triclinic(int n) { int j; double **x = atom->x; tagint *image = atom->image; double *boxlo = domain->boxlo; double *h_inv = domain->h_inv; for (int i = 0; i < nchoose; i++) { j = clist[i]; buf[n] = h_inv[1]*(x[j][1]-boxlo[1]) + h_inv[3]*(x[j][2]-boxlo[2]) + (image[j] >> IMGBITS & IMGMASK) - IMGMAX; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_zsu_triclinic(int n) { int j; double **x = atom->x; tagint *image = atom->image; double *boxlo = domain->boxlo; double *h_inv = domain->h_inv; for (int i = 0; i < nchoose; i++) { j = clist[i]; buf[n] = h_inv[2]*(x[j][2]-boxlo[2]) + (image[j] >> IMG2BITS) - IMGMAX; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_ix(int n) { tagint *image = atom->image; for (int i = 0; i < nchoose; i++) { buf[n] = (image[clist[i]] & IMGMASK) - IMGMAX; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_iy(int n) { tagint *image = atom->image; for (int i = 0; i < nchoose; i++) { buf[n] = (image[clist[i]] >> IMGBITS & IMGMASK) - IMGMAX; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_iz(int n) { tagint *image = atom->image; for (int i = 0; i < nchoose; i++) { buf[n] = (image[clist[i]] >> IMG2BITS) - IMGMAX; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_vx(int n) { double **v = atom->v; for (int i = 0; i < nchoose; i++) { buf[n] = v[clist[i]][0]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_vy(int n) { double **v = atom->v; for (int i = 0; i < nchoose; i++) { buf[n] = v[clist[i]][1]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_vz(int n) { double **v = atom->v; for (int i = 0; i < nchoose; i++) { buf[n] = v[clist[i]][2]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_fx(int n) { double **f = atom->f; for (int i = 0; i < nchoose; i++) { buf[n] = f[clist[i]][0]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_fy(int n) { double **f = atom->f; for (int i = 0; i < nchoose; i++) { buf[n] = f[clist[i]][1]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_fz(int n) { double **f = atom->f; for (int i = 0; i < nchoose; i++) { buf[n] = f[clist[i]][2]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_q(int n) { double *q = atom->q; for (int i = 0; i < nchoose; i++) { buf[n] = q[clist[i]]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_mux(int n) { double **mu = atom->mu; for (int i = 0; i < nchoose; i++) { buf[n] = mu[clist[i]][0]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_muy(int n) { double **mu = atom->mu; for (int i = 0; i < nchoose; i++) { buf[n] = mu[clist[i]][1]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_muz(int n) { double **mu = atom->mu; for (int i = 0; i < nchoose; i++) { buf[n] = mu[clist[i]][2]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_mu(int n) { double **mu = atom->mu; for (int i = 0; i < nchoose; i++) { buf[n] = mu[clist[i]][3]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_radius(int n) { double *radius = atom->radius; for (int i = 0; i < nchoose; i++) { buf[n] = radius[clist[i]]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_diameter(int n) { double *radius = atom->radius; for (int i = 0; i < nchoose; i++) { buf[n] = 2.0*radius[clist[i]]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_omegax(int n) { double **omega = atom->omega; for (int i = 0; i < nchoose; i++) { buf[n] = omega[clist[i]][0]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_omegay(int n) { double **omega = atom->omega; for (int i = 0; i < nchoose; i++) { buf[n] = omega[clist[i]][1]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_omegaz(int n) { double **omega = atom->omega; for (int i = 0; i < nchoose; i++) { buf[n] = omega[clist[i]][2]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_angmomx(int n) { double **angmom = atom->angmom; for (int i = 0; i < nchoose; i++) { buf[n] = angmom[clist[i]][0]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_angmomy(int n) { double **angmom = atom->angmom; for (int i = 0; i < nchoose; i++) { buf[n] = angmom[clist[i]][1]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_angmomz(int n) { double **angmom = atom->angmom; for (int i = 0; i < nchoose; i++) { buf[n] = angmom[clist[i]][2]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_tqx(int n) { double **torque = atom->torque; for (int i = 0; i < nchoose; i++) { buf[n] = torque[clist[i]][0]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_tqy(int n) { double **torque = atom->torque; for (int i = 0; i < nchoose; i++) { buf[n] = torque[clist[i]][1]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_tqz(int n) { double **torque = atom->torque; for (int i = 0; i < nchoose; i++) { buf[n] = torque[clist[i]][2]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_spin(int n) { int *spin = atom->spin; for (int i = 0; i < nchoose; i++) { buf[n] = spin[clist[i]]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_eradius(int n) { double *eradius = atom->eradius; for (int i = 0; i < nchoose; i++) { buf[n] = eradius[clist[i]]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_ervel(int n) { double *ervel = atom->ervel; for (int i = 0; i < nchoose; i++) { buf[n] = ervel[clist[i]]; n += size_one; } } /* ---------------------------------------------------------------------- */ void DumpCustom::pack_erforce(int n) { double *erforce = atom->erforce; for (int i = 0; i < nchoose; i++) { buf[n] = erforce[clist[i]]; n += size_one; } }