diff --git a/src/VTK/dump_vtk.cpp b/src/VTK/dump_vtk.cpp index a7aabe3f51..54dc0d4b0e 100644 --- a/src/VTK/dump_vtk.cpp +++ b/src/VTK/dump_vtk.cpp @@ -31,6 +31,7 @@ #include "domain.h" #include "error.h" #include "fix.h" +#include "fix_store.h" #include "force.h" #include "group.h" #include "input.h" @@ -87,9 +88,9 @@ enum{X,Y,Z, // required for vtk, must come first Q,MUX,MUY,MUZ,MU,RADIUS,DIAMETER, OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ, TQX,TQY,TQZ, - VARIABLE,COMPUTE,FIX,INAME,DNAME, + COMPUTE,FIX,VARIABLE,IVEC,DVEC,IARRAY,DARRAY, ATTRIBUTES}; // must come last -enum{LT,LE,GT,GE,EQ,NEQ}; +enum{LT,LE,GT,GE,EQ,NEQ,XOR}; enum{VTK,VTP,VTU,PVTP,PVTU}; // file formats #define ONEFIELD 32 @@ -119,11 +120,10 @@ DumpVTK::DumpVTK(LAMMPS *lmp, int narg, char **arg) : // ioptional = start of additional optional args // only dump image and dump movie styles process optional args - ioptional = parse_fields(narg,arg); + ioptional = parse_fields(nargnew,earg); - if (ioptional < narg && - strcmp(style,"image") != 0 && strcmp(style,"movie") != 0) - error->all(FLERR,"Invalid attribute in dump vtk command"); + if (ioptional < nargnew) + error->all(FLERR,"Invalid attribute {} in dump vtk command", earg[ioptional]); size_one = pack_choice.size(); current_pack_choice_key = -1; @@ -210,38 +210,40 @@ void DumpVTK::init_style() else write_choice = &DumpVTK::write_vtk; - // find current ptr for each compute,fix,variable + // find current ptr for each compute,fix,variable and custom atom property // check that fix frequency is acceptable - int icompute; for (int i = 0; i < ncompute; i++) { - icompute = modify->find_compute(id_compute[i]); + int icompute = modify->find_compute(id_compute[i]); if (icompute < 0) error->all(FLERR,"Could not find dump vtk compute ID"); compute[i] = modify->compute[icompute]; } - int ifix; for (int i = 0; i < nfix; i++) { - ifix = modify->find_fix(id_fix[i]); + int ifix = modify->find_fix(id_fix[i]); if (ifix < 0) error->all(FLERR,"Could not find dump vtk fix ID"); fix[i] = modify->fix[ifix]; if (nevery % modify->fix[ifix]->peratom_freq) error->all(FLERR,"Dump vtk and fix not computed at compatible times"); } - int ivariable; for (int i = 0; i < nvariable; i++) { - ivariable = input->variable->find(id_variable[i]); + int ivariable = input->variable->find(id_variable[i]); if (ivariable < 0) error->all(FLERR,"Could not find dump vtk variable name"); variable[i] = ivariable; } - int icustom; + int icustom,flag,cols; for (int i = 0; i < ncustom; i++) { - icustom = atom->find_custom(id_custom[i],flag_custom[i]); + icustom = atom->find_custom(id_custom[i],flag,cols); if (icustom < 0) error->all(FLERR,"Could not find custom per-atom property ID"); + custom[i] = icustom; + if (!flag && !cols) custom_flag[i] = IVEC; + else if (flag && !cols) custom_flag[i] = DVEC; + else if (!flag && cols) custom_flag[i] = IARRAY; + else if (flag && cols) custom_flag[i] = DARRAY; } // set index and check validity of region @@ -275,7 +277,7 @@ int DumpVTK::count() // grow choose and variable vbuf arrays if needed - int nlocal = atom->nlocal; + const int nlocal = atom->nlocal; if (atom->nmax > maxlocal) { maxlocal = atom->nmax; @@ -345,10 +347,10 @@ int DumpVTK::count() // un-choose if any threshold criterion isn't met if (nthresh) { - double *ptr; + double *ptr,*ptrhold; + double *values; double value; - int nstride; - int nlocal = atom->nlocal; + int nstride,lastflag; for (int ithresh = 0; ithresh < nthresh; ithresh++) { @@ -635,26 +637,22 @@ int DumpVTK::count() nstride = 1; } else if (thresh_array[ithresh] == MUX) { if (!atom->mu_flag) - error->all(FLERR, - "Threshold for an atom property that isn't allocated"); + error->all(FLERR,"Threshold 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, - "Threshold for an atom property that isn't allocated"); + error->all(FLERR,"Threshold 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, - "Threshold for an atom property that isn't allocated"); + error->all(FLERR,"Threshold 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, - "Threshold for an atom property that isn't allocated"); + error->all(FLERR,"Threshold for an atom property that isn't allocated"); ptr = &atom->mu[0][3]; nstride = 4; @@ -753,9 +751,8 @@ int DumpVTK::count() nstride = 1; } else if (thresh_array[ithresh] == IVEC) { - int iwhich,flag,cols i = ATTRIBUTES + nfield + ithresh; - iwhich = atom->find_custom(id_custom[field2index[i]],flag,cols); + int iwhich = custom[field2index[i]]; int *ivector = atom->ivector[iwhich]; for (i = 0; i < nlocal; i++) dchoose[i] = ivector[i]; @@ -763,16 +760,14 @@ int DumpVTK::count() nstride = 1; } else if (thresh_array[ithresh] == DVEC) { - int iwhich,flag,cols; i = ATTRIBUTES + nfield + ithresh; - iwhich = atom->find_custom(id_custom[field2index[i]],flag,cols); + int iwhich = custom[field2index[i]]; ptr = atom->dvector[iwhich]; nstride = 1; } else if (thresh_array[ithresh] == IARRAY) { - int iwhich,flag,cols; i = ATTRIBUTES + nfield + ithresh; - iwhich = atom->find_custom(id_custom[field2index[i]],flag,cols); + int iwhich = custom[field2index[i]]; int **iarray = atom->iarray[iwhich]; int icol = argindex[i] - 1; for (i = 0; i < nlocal; i++) @@ -781,43 +776,99 @@ int DumpVTK::count() nstride = 1; } else if (thresh_array[ithresh] == DARRAY) { - int iwhich,flag,cols; i = ATTRIBUTES + nfield + ithresh; - iwhich = atom->find_custom(id_custom[field2index[i]],flag,cols) + int iwhich = custom[field2index[i]]; double **darray = atom->darray[iwhich]; ptr = &darray[0][argindex[i]-1]; nstride = atom->dcols[iwhich]; } // unselect atoms that don't meet threshold criterion + // compare to single value or values stored in threshfix + // copy ptr attribute into thresh_fix if this is first comparison - value = thresh_value[ithresh]; + if (thresh_last[ithresh] < 0) { + lastflag = 0; + value = thresh_value[ithresh]; + } else { + lastflag = 1; + int ilast = thresh_last[ithresh]; + values = thresh_fix[ilast]->vstore; + ptrhold = ptr; + if (thresh_first[ilast]) { + thresh_first[ilast] = 0; + for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr; + ptr = ptrhold; + } + } - switch (thresh_op[ithresh]) { - case LT: - for (i = 0; i < nlocal; i++, ptr += nstride) - if (choose[i] && *ptr >= value) choose[i] = 0; - break; - case LE: - for (i = 0; i < nlocal; i++, ptr += nstride) - if (choose[i] && *ptr > value) choose[i] = 0; - break; - case GT: - for (i = 0; i < nlocal; i++, ptr += nstride) - if (choose[i] && *ptr <= value) choose[i] = 0; - break; - case GE: - for (i = 0; i < nlocal; i++, ptr += nstride) - if (choose[i] && *ptr < value) choose[i] = 0; - break; - case EQ: - for (i = 0; i < nlocal; i++, ptr += nstride) - if (choose[i] && *ptr != value) choose[i] = 0; - break; - case NEQ: - for (i = 0; i < nlocal; i++, ptr += nstride) - if (choose[i] && *ptr == value) choose[i] = 0; - break; + if (thresh_op[ithresh] == LT) { + if (lastflag) { + for (i = 0; i < nlocal; i++, ptr += nstride) + if (choose[i] && *ptr >= values[i]) choose[i] = 0; + } else { + for (i = 0; i < nlocal; i++, ptr += nstride) + if (choose[i] && *ptr >= value) choose[i] = 0; + } + } else if (thresh_op[ithresh] == LE) { + if (lastflag) { + for (i = 0; i < nlocal; i++, ptr += nstride) + if (choose[i] && *ptr > values[i]) choose[i] = 0; + } else { + for (i = 0; i < nlocal; i++, ptr += nstride) + if (choose[i] && *ptr > value) choose[i] = 0; + } + } else if (thresh_op[ithresh] == GT) { + if (lastflag) { + for (i = 0; i < nlocal; i++, ptr += nstride) + if (choose[i] && *ptr <= values[i]) choose[i] = 0; + } else { + for (i = 0; i < nlocal; i++, ptr += nstride) + if (choose[i] && *ptr <= value) choose[i] = 0; + } + } else if (thresh_op[ithresh] == GE) { + if (lastflag) { + for (i = 0; i < nlocal; i++, ptr += nstride) + if (choose[i] && *ptr < values[i]) choose[i] = 0; + } else { + for (i = 0; i < nlocal; i++, ptr += nstride) + if (choose[i] && *ptr < value) choose[i] = 0; + } + } else if (thresh_op[ithresh] == EQ) { + if (lastflag) { + for (i = 0; i < nlocal; i++, ptr += nstride) + if (choose[i] && *ptr != values[i]) choose[i] = 0; + } else { + for (i = 0; i < nlocal; i++, ptr += nstride) + if (choose[i] && *ptr != value) choose[i] = 0; + } + } else if (thresh_op[ithresh] == NEQ) { + if (lastflag) { + for (i = 0; i < nlocal; i++, ptr += nstride) + if (choose[i] && *ptr == values[i]) choose[i] = 0; + } else { + for (i = 0; i < nlocal; i++, ptr += nstride) + if (choose[i] && *ptr == value) choose[i] = 0; + } + } else if (thresh_op[ithresh] == XOR) { + if (lastflag) { + for (i = 0; i < nlocal; i++, ptr += nstride) + if ((choose[i] && *ptr == 0.0 && values[i] == 0.0) || + (*ptr != 0.0 && values[i] != 0.0)) + choose[i] = 0; + } else { + for (i = 0; i < nlocal; i++, ptr += nstride) + if ((choose[i] && *ptr == 0.0 && value == 0.0) || + (*ptr != 0.0 && value != 0.0)) + choose[i] = 0; + } + } + + // update values stored in threshfix + + if (lastflag) { + ptr = ptrhold; + for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr; } } } @@ -1754,15 +1805,16 @@ int DumpVTK::parse_fields(int narg, char **arg) } else { - int n,tmp; + int n,flag,cols; ArgInfo argi(arg[iarg],ArgInfo::COMPUTE|ArgInfo::FIX|ArgInfo::VARIABLE - |ArgInfo::DVEC|ArgInfo::IVEC); + |ArgInfo::DNAME|ArgInfo::INAME); argindex[ATTRIBUTES+i] = argi.get_index1(); + auto aname = argi.get_name(); switch (argi.get_type()) { case ArgInfo::UNKNOWN: - error->all(FLERR,"Invalid attribute in dump vtk command"); + error->all(FLERR,"Invalid attribute in dump vtk command: {}",arg[iarg]); break; // compute value = c_ID @@ -1772,21 +1824,19 @@ int DumpVTK::parse_fields(int narg, char **arg) pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_compute; vtype[ATTRIBUTES+i] = Dump::DOUBLE; - n = modify->find_compute(argi.get_name()); - if (n < 0) error->all(FLERR,"Could not find dump vtk compute ID"); + n = modify->find_compute(aname); + if (n < 0) error->all(FLERR,"Could not find dump vtk compute ID: {}",aname); if (modify->compute[n]->peratom_flag == 0) - error->all(FLERR,"Dump vtk compute does not compute per-atom info"); + error->all(FLERR,"Dump vtk compute {} does not compute per-atom info",aname); if (argi.get_dim() == 0 && modify->compute[n]->size_peratom_cols > 0) - error->all(FLERR, - "Dump vtk compute does not calculate per-atom vector"); + error->all(FLERR,"Dump vtk compute {} does not calculate per-atom vector",aname); if (argi.get_dim() > 0 && modify->compute[n]->size_peratom_cols == 0) - error->all(FLERR, - "Dump vtk compute does not calculate per-atom array"); + error->all(FLERR,"Dump vtk compute {} does not calculate per-atom array",aname); if (argi.get_dim() > 0 && argi.get_index1() > modify->compute[n]->size_peratom_cols) - error->all(FLERR,"Dump vtk compute vector is accessed out-of-range"); + error->all(FLERR,"Dump vtk compute {} vector is accessed out-of-range",aname); - field2index[ATTRIBUTES+i] = add_compute(argi.get_name()); + field2index[ATTRIBUTES+i] = add_compute(aname); name[ATTRIBUTES+i] = arg[iarg]; break; @@ -1797,19 +1847,19 @@ int DumpVTK::parse_fields(int narg, char **arg) pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_fix; vtype[ATTRIBUTES+i] = Dump::DOUBLE; - n = modify->find_fix(argi.get_name()); - if (n < 0) error->all(FLERR,"Could not find dump vtk fix ID"); + n = modify->find_fix(aname); + if (n < 0) error->all(FLERR,"Could not find dump vtk fix ID: {}",aname); if (modify->fix[n]->peratom_flag == 0) - error->all(FLERR,"Dump vtk fix does not compute per-atom info"); + error->all(FLERR,"Dump vtk fix {} does not compute per-atom info",aname); if (argi.get_dim() == 0 && modify->fix[n]->size_peratom_cols > 0) - error->all(FLERR,"Dump vtk fix does not compute per-atom vector"); + error->all(FLERR,"Dump vtk fix {} does not compute per-atom vector",aname); if (argi.get_dim() > 0 && modify->fix[n]->size_peratom_cols == 0) - error->all(FLERR,"Dump vtk fix does not compute per-atom array"); + error->all(FLERR,"Dump vtk fix {} does not compute per-atom array",aname); if (argi.get_dim() > 0 && argi.get_index1() > modify->fix[n]->size_peratom_cols) - error->all(FLERR,"Dump vtk fix vector is accessed out-of-range"); + error->all(FLERR,"Dump vtk fix {} vector is accessed out-of-range",aname); - field2index[ATTRIBUTES+i] = add_fix(argi.get_name()); + field2index[ATTRIBUTES+i] = add_fix(aname); name[ATTRIBUTES+i] = arg[iarg]; break; @@ -1819,61 +1869,62 @@ int DumpVTK::parse_fields(int narg, char **arg) pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_variable; vtype[ATTRIBUTES+i] = Dump::DOUBLE; - n = input->variable->find(argi.get_name()); - if (n < 0) error->all(FLERR,"Could not find dump vtk variable name"); + n = input->variable->find(aname); + if (n < 0) error->all(FLERR,"Could not find dump vtk variable name {}",aname); if (input->variable->atomstyle(n) == 0) - error->all(FLERR,"Dump vtk variable is not atom-style variable"); + error->all(FLERR,"Dump vtk variable {} is not atom-style variable",aname); - field2index[ATTRIBUTES+i] = add_variable(argi.get_name()); + field2index[ATTRIBUTES+i] = add_variable(aname); name[ATTRIBUTES+i] = arg[iarg]; break; - // custom per-atom integer vector = i_ID - - case ArgInfo::INAME: - pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_custom; - vtype[ATTRIBUTES+i] = Dump::INT; - - tmp = -1; - n = atom->find_custom(argi.get_name(),tmp); - if (n < 0) - error->all(FLERR,"Could not find custom per-atom property ID"); - - if (tmp != 0) - error->all(FLERR,"Custom per-atom property ID is not integer"); - - field2index[ATTRIBUTES+i] = add_custom(argi.get_name(),0); - name[ATTRIBUTES+i] = arg[iarg]; - break; - - // custom per-atom floating point vector = d_ID + // custom per-atom floating point vector or array = d_ID d2_ID case ArgInfo::DNAME: pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_custom; vtype[ATTRIBUTES+i] = Dump::DOUBLE; - tmp = -1; - n = atom->find_custom(argi.get_name(),tmp); + n = atom->find_custom(aname,flag,cols); + if (n < 0) - error->all(FLERR,"Could not find custom per-atom property ID"); - - if (tmp != 1) - error->all(FLERR,"Custom per-atom property ID is not floating point"); - - field2index[ATTRIBUTES+i] = add_custom(argi.get_name(),1); + error->all(FLERR,"Could not find custom per-atom property ID: {}", aname); + if (argindex[ATTRIBUTES+i] == 0) { + if (!flag || cols) + error->all(FLERR,"Property double vector {} for dump vtk does not exist",aname); + } else { + if (!flag || !cols) + error->all(FLERR,"Property double array {} for dump vtk does not exist",aname); + if (argindex[ATTRIBUTES+i] > atom->dcols[n]) + error->all(FLERR,"Dump vtk property array {} is accessed out-of-range",aname); + } + field2index[ATTRIBUTES+i] = add_custom(aname,1); name[ATTRIBUTES+i] = arg[iarg]; break; - // NEWSTYLE - // custom per-atom integer array = i2_ID + // custom per-atom integer vector or array = i_ID or i2_ID - case ArgInfo::IARRAY: - return iarg; + case ArgInfo::INAME: + pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_custom; + vtype[ATTRIBUTES+i] = Dump::INT; - // custom per-atom floating point array = d2_ID + n = atom->find_custom(aname,flag,cols); - case ArgInfo::DARRAY: - return iarg; + if (n < 0) + error->all(FLERR,"Could not find custom per-atom property ID: {}", aname); + if (argindex[ATTRIBUTES+i] == 0) { + if (flag || cols) + error->all(FLERR,"Property integer vector {} for dump vtk does not exist",aname); + } else { + if (flag || !cols) + error->all(FLERR,"Property integer array {} for dump vtk does not exist",aname); + if (argindex[ATTRIBUTES+i] > atom->icols[n]) + error->all(FLERR,"Dump vtk property array {} is accessed out-of-range",aname); + } + field2index[ATTRIBUTES+i] = add_custom(aname,0); + name[ATTRIBUTES+i] = arg[iarg]; + break; + + // no match default: return iarg; @@ -1948,12 +1999,10 @@ int DumpVTK::add_compute(const char *id) id_compute = (char **) memory->srealloc(id_compute,(ncompute+1)*sizeof(char *),"dump:id_compute"); - delete [] compute; + delete[] compute; compute = new Compute*[ncompute+1]; - int n = strlen(id) + 1; - id_compute[ncompute] = new char[n]; - strcpy(id_compute[ncompute],id); + id_compute[ncompute] = utils::strdup(id); ncompute++; return ncompute-1; } @@ -1973,12 +2022,10 @@ int DumpVTK::add_fix(const char *id) id_fix = (char **) memory->srealloc(id_fix,(nfix+1)*sizeof(char *),"dump:id_fix"); - delete [] fix; + delete[] fix; fix = new Fix*[nfix+1]; - int n = strlen(id) + 1; - id_fix[nfix] = new char[n]; - strcpy(id_fix[nfix],id); + id_fix[nfix] = utils::strdup(id); nfix++; return nfix-1; } @@ -1999,22 +2046,20 @@ int DumpVTK::add_variable(const char *id) id_variable = (char **) memory->srealloc(id_variable,(nvariable+1)*sizeof(char *), "dump:id_variable"); - delete [] variable; + delete[] variable; variable = new int[nvariable+1]; - delete [] vbuf; + delete[] vbuf; vbuf = new double*[nvariable+1]; for (int i = 0; i <= nvariable; i++) vbuf[i] = nullptr; - int n = strlen(id) + 1; - id_variable[nvariable] = new char[n]; - strcpy(id_variable[nvariable],id); + id_variable[nvariable] = utils::strdup(id); nvariable++; return nvariable-1; } /* ---------------------------------------------------------------------- add custom atom property to list used by dump - return index of where this property is in list + return index of where this property is in Atom class custom lists if already in list, do not add, just return index, else add to list ------------------------------------------------------------------------- */ @@ -2022,21 +2067,17 @@ int DumpVTK::add_custom(const char *id, int flag) { int icustom; for (icustom = 0; icustom < ncustom; icustom++) - if ((strcmp(id,id_custom[icustom]) == 0) - && (flag == flag_custom[icustom])) break; + if (strcmp(id,id_custom[icustom]) == 0) break; if (icustom < ncustom) return icustom; - id_custom = (char **) - memory->srealloc(id_custom,(ncustom+1)*sizeof(char *),"dump:id_custom"); - flag_custom = (int *) - memory->srealloc(flag_custom,(ncustom+1)*sizeof(int),"dump:flag_custom"); - - int n = strlen(id) + 1; - id_custom[ncustom] = new char[n]; - strcpy(id_custom[ncustom],id); - flag_custom[ncustom] = flag; + id_custom = (char **) memory->srealloc(id_custom,(ncustom+1)*sizeof(char *),"dump:id_custom"); + custom = (int *) memory->srealloc(custom,(ncustom+1)*sizeof(int),"dump:custom"); + custom_flag = (int *) memory->srealloc(custom_flag,(ncustom+1)*sizeof(int),"dump:custom_flag"); + id_custom[ncustom] = utils::strdup(id); + custom_flag[ncustom] = flag; ncustom++; + return ncustom-1; } @@ -2050,21 +2091,17 @@ int DumpVTK::modify_param(int narg, char **arg) else { iregion = domain->find_region(arg[1]); if (iregion == -1) - error->all(FLERR,"Dump_modify region ID does not exist"); - delete [] idregion; - int n = strlen(arg[1]) + 1; - idregion = new char[n]; - strcpy(idregion,arg[1]); + error->all(FLERR,"Dump_modify region ID {} does not exist",arg[1]); + delete[] idregion; + idregion = utils::strdup(arg[1]); } return 2; } if (strcmp(arg[0],"label") == 0) { if (narg < 2) error->all(FLERR,"Illegal dump_modify command [label]"); - delete [] label; - int n = strlen(arg[1]) + 1; - label = new char[n]; - strcpy(label,arg[1]); + delete[] label; + label = utils::strdup(arg[1]); return 2; } @@ -2076,23 +2113,29 @@ int DumpVTK::modify_param(int narg, char **arg) if (strcmp(arg[0],"element") == 0) { if (narg < ntypes+1) - error->all(FLERR,"Dump modify: number of element names do not match atom types"); - - if (typenames) { - for (int i = 1; i <= ntypes; i++) delete [] typenames[i]; - delete [] typenames; - typenames = nullptr; - } + error->all(FLERR,"Number of dump_modify element names does not match number of atom types"); + for (int i = 1; i <= ntypes; i++) delete[] typenames[i]; + delete[] typenames; 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]); + typenames[itype] = utils::strdup(arg[itype]); } return ntypes+1; } + if (strcmp(arg[0],"refresh") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + ArgInfo argi(arg[1],ArgInfo::COMPUTE); + if ((argi.get_type() != ArgInfo::COMPUTE) || (argi.get_dim() != 0)) + error->all(FLERR,"Illegal dump_modify command"); + if (refreshflag) error->all(FLERR,"Dump_modify can only have one refresh"); + + refreshflag = 1; + refresh = argi.copy_name(); + return 2; + } + if (strcmp(arg[0],"thresh") == 0) { if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); if (strcmp(arg[1],"none") == 0) { @@ -2103,8 +2146,16 @@ int DumpVTK::modify_param(int narg, char **arg) thresh_array = nullptr; thresh_op = nullptr; thresh_value = nullptr; + thresh_last = nullptr; + for (int i = 0; i < nthreshlast; i++) { + modify->delete_fix(thresh_fixID[i]); + delete[] thresh_fixID[i]; + } + thresh_fix = nullptr; + thresh_fixID = nullptr; + thresh_first = nullptr; } - nthresh = 0; + nthresh = nthreshlast = 0; return 2; } @@ -2115,6 +2166,7 @@ int DumpVTK::modify_param(int narg, char **arg) 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"); + memory->grow(thresh_last,(nthresh+1),"dump:thresh_last"); // set attribute type of threshold // customize by adding to if statement @@ -2197,98 +2249,125 @@ int DumpVTK::modify_param(int narg, char **arg) else if (strcmp(arg[1],"tqy") == 0) thresh_array[nthresh] = TQY; else if (strcmp(arg[1],"tqz") == 0) thresh_array[nthresh] = TQZ; - // compute value = c_ID - // if no trailing [], then arg is set to 0, else arg is between [] + // compute or fix or variable or custom vector/array - else if (strncmp(arg[1],"c_",2) == 0) { - thresh_array[nthresh] = COMPUTE; - int n = strlen(arg[1]); - char *suffix = new char[n]; - strcpy(suffix,&arg[1][2]); + else { + int n,flag,cols; + ArgInfo argi(arg[1],ArgInfo::COMPUTE|ArgInfo::FIX|ArgInfo::VARIABLE + |ArgInfo::DNAME|ArgInfo::INAME); + argindex[ATTRIBUTES+nfield+nthresh] = argi.get_index1(); + auto aname = argi.get_name(); - char *ptr = strchr(suffix,'['); - if (ptr) { - if (suffix[strlen(suffix)-1] != ']') - error->all(FLERR,"Invalid attribute in dump modify command"); - argindex[ATTRIBUTES+nfield+nthresh] = atoi(ptr+1); - *ptr = '\0'; - } else argindex[ATTRIBUTES+nfield+nthresh] = 0; + switch (argi.get_type()) { - n = modify->find_compute(suffix); - if (n < 0) error->all(FLERR,"Could not find dump modify compute ID"); + case ArgInfo::UNKNOWN: + error->all(FLERR,"Invalid attribute in dump modify command"); + break; - if (modify->compute[n]->peratom_flag == 0) - error->all(FLERR, - "Dump modify compute ID does not compute per-atom info"); - if (argindex[ATTRIBUTES+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[ATTRIBUTES+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[ATTRIBUTES+nfield+nthresh] > 0 && - argindex[ATTRIBUTES+nfield+nthresh] > modify->compute[n]->size_peratom_cols) - error->all(FLERR,"Dump modify compute ID vector is not large enough"); + // compute value = c_ID + // if no trailing [], then arg is set to 0, else arg is between [] - field2index[ATTRIBUTES+nfield+nthresh] = add_compute(suffix); - delete [] suffix; + case ArgInfo::COMPUTE: + thresh_array[nthresh] = COMPUTE; + n = modify->find_compute(aname); + if (n < 0) error->all(FLERR,"Could not find dump modify compute ID: {}",aname); - // fix value = f_ID - // if no trailing [], then arg is set to 0, else arg is between [] + if (modify->compute[n]->peratom_flag == 0) + error->all(FLERR,"Dump modify compute ID {} does not compute per-atom info",aname); + if (argi.get_dim() == 0 && modify->compute[n]->size_peratom_cols > 0) + error->all(FLERR,"Dump modify compute ID {} does not compute per-atom vector",aname); + if (argi.get_index1() > 0 && modify->compute[n]->size_peratom_cols == 0) + error->all(FLERR,"Dump modify compute ID {} does not compute per-atom array",aname); + if (argi.get_index1() > 0 && + argi.get_index1() > modify->compute[n]->size_peratom_cols) + error->all(FLERR,"Dump modify compute ID {} vector is not large enough",aname); - } else if (strncmp(arg[1],"f_",2) == 0) { - thresh_array[nthresh] = FIX; - int n = strlen(arg[1]); - char *suffix = new char[n]; - strcpy(suffix,&arg[1][2]); + field2index[ATTRIBUTES+nfield+nthresh] = add_compute(aname); + break; - char *ptr = strchr(suffix,'['); - if (ptr) { - if (suffix[strlen(suffix)-1] != ']') - error->all(FLERR,"Invalid attribute in dump modify command"); - argindex[ATTRIBUTES+nfield+nthresh] = atoi(ptr+1); - *ptr = '\0'; - } else argindex[ATTRIBUTES+nfield+nthresh] = 0; + // fix value = f_ID + // if no trailing [], then arg is set to 0, else arg is between [] - n = modify->find_fix(suffix); - if (n < 0) error->all(FLERR,"Could not find dump modify fix ID"); + case ArgInfo::FIX: + thresh_array[nthresh] = FIX; + n = modify->find_fix(aname); + if (n < 0) error->all(FLERR,"Could not find dump modify fix ID: {}",aname); - if (modify->fix[n]->peratom_flag == 0) - error->all(FLERR,"Dump modify fix ID does not compute per-atom info"); - if (argindex[ATTRIBUTES+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[ATTRIBUTES+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[ATTRIBUTES+nfield+nthresh] > 0 && - argindex[ATTRIBUTES+nfield+nthresh] > modify->fix[n]->size_peratom_cols) - error->all(FLERR,"Dump modify fix ID vector is not large enough"); + if (modify->fix[n]->peratom_flag == 0) + error->all(FLERR,"Dump modify fix ID {} does not compute per-atom info",aname); + if (argi.get_dim() == 0 && modify->fix[n]->size_peratom_cols > 0) + error->all(FLERR,"Dump modify fix ID {} does not compute per-atom vector",aname); + if (argi.get_index1() > 0 && modify->fix[n]->size_peratom_cols == 0) + error->all(FLERR,"Dump modify fix ID {} does not compute per-atom array",aname); + if (argi.get_index1() > 0 && argi.get_index1() > modify->fix[n]->size_peratom_cols) + error->all(FLERR,"Dump modify fix ID {} vector is not large enough",aname); - field2index[ATTRIBUTES+nfield+nthresh] = add_fix(suffix); - delete [] suffix; + field2index[ATTRIBUTES+nfield+nthresh] = add_fix(aname); + break; - // variable value = v_ID + // variable value = v_ID - } else if (strncmp(arg[1],"v_",2) == 0) { - thresh_array[nthresh] = VARIABLE; - int n = strlen(arg[1]); - char *suffix = new char[n]; - strcpy(suffix,&arg[1][2]); + case ArgInfo::VARIABLE: + thresh_array[nthresh] = VARIABLE; + n = input->variable->find(aname); + if (n < 0) error->all(FLERR,"Could not find dump modify variable name: {}",aname); + if (input->variable->atomstyle(n) == 0) + error->all(FLERR,"Dump modify variable {} is not atom-style variable",aname); - argindex[ATTRIBUTES+nfield+nthresh] = 0; + field2index[ATTRIBUTES+nfield+nthresh] = add_variable(aname); + break; - 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"); + // custom per atom floating point vector or array - field2index[ATTRIBUTES+nfield+nthresh] = add_variable(suffix); - delete [] suffix; + case ArgInfo::DNAME: + n = atom->find_custom(aname,flag,cols); - } else error->all(FLERR,"Invalid dump_modify threshold operator"); + if (n < 0) + error->all(FLERR,"Could not find custom per-atom property ID: {}", aname); + if (argindex[ATTRIBUTES+nfield+nthresh] == 0) { + if (!flag || cols) + error->all(FLERR,"Property double vector for dump custom does not exist"); + thresh_array[nthresh] = DVEC; + } else { + if (!flag || !cols) + error->all(FLERR,"Property double array for dump custom does not exist"); + if (argindex[ATTRIBUTES+nfield+nthresh] > atom->dcols[n]) + error->all(FLERR,"Dump custom property array is accessed out-of-range"); + thresh_array[nthresh] = DARRAY; + } + + field2index[ATTRIBUTES+nfield+nthresh] = add_custom(aname,thresh_array[nthresh]); + break; + + // custom per atom integer vector or array + + case ArgInfo::INAME: + n = atom->find_custom(aname,flag,cols); + + if (n < 0) + error->all(FLERR,"Could not find custom per-atom property ID: {}", aname); + if (argindex[ATTRIBUTES+nfield+nthresh] == 0) { + if (flag || cols) + error->all(FLERR,"Property integer vector for dump custom does not exist"); + thresh_array[nthresh] = IVEC; + } else { + if (flag || !cols) + error->all(FLERR,"Property integer array for dump custom does not exist"); + if (argindex[ATTRIBUTES+nfield+nthresh] > atom->icols[n]) + error->all(FLERR,"Dump custom property array is accessed out-of-range"); + thresh_array[nthresh] = IARRAY; + } + + field2index[ATTRIBUTES+nfield+nthresh] = add_custom(aname,thresh_array[nthresh]); + break; + + // no match + + default: + error->all(FLERR,"Invalid dump_modify thresh attribute: {}",aname); + break; + } + } // set operation type of threshold @@ -2298,11 +2377,32 @@ int DumpVTK::modify_param(int narg, char **arg) 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 threshold operator"); + else if (strcmp(arg[2],"|^") == 0) thresh_op[nthresh] = XOR; + else error->all(FLERR,"Invalid dump_modify thresh operator"); - // set threshold value + // set threshold value as number or special LAST keyword + // create FixStore to hold LAST values, should work with restart + // id = dump-ID + nthreshlast + DUMP_STORE, fix group = dump group - thresh_value[nthresh] = utils::numeric(FLERR,arg[3],false,lmp); + if (strcmp(arg[3],"LAST") != 0) { + thresh_value[nthresh] = utils::numeric(FLERR,arg[3],false,lmp); + thresh_last[nthresh] = -1; + } else { + thresh_fix = (FixStore **) + memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStore *),"dump:thresh_fix"); + thresh_fixID = (char **) + memory->srealloc(thresh_fixID,(nthreshlast+1)*sizeof(char *),"dump:thresh_fixID"); + memory->grow(thresh_first,(nthreshlast+1),"dump:thresh_first"); + + std::string threshid = fmt::format("{}{}_DUMP_STORE",id,nthreshlast); + thresh_fixID[nthreshlast] = utils::strdup(threshid); + threshid += fmt::format(" {} STORE peratom 1 1", group->names[igroup]); + thresh_fix[nthreshlast] = (FixStore *) modify->add_fix(threshid); + + thresh_last[nthreshlast] = nthreshlast; + thresh_first[nthreshlast] = 1; + nthreshlast++; + } nthresh++; return 4; @@ -2387,25 +2487,35 @@ void DumpVTK::pack_variable(int n) void DumpVTK::pack_custom(int n) { - int index = field2index[n]; - - if (flag_custom[index] == 0) { // integer - int iwhich,tmp; - iwhich = atom->find_custom(id_custom[index],tmp); + int flag = custom_flag[field2index[current_pack_choice_key]]; + int iwhich = custom[field2index[current_pack_choice_key]]; + int index = argindex[current_pack_choice_key]; + if (flag == IVEC) { int *ivector = atom->ivector[iwhich]; for (int i = 0; i < nchoose; i++) { buf[n] = ivector[clist[i]]; n += size_one; } - } else if (flag_custom[index] == 1) { // double - int iwhich,tmp; - iwhich = atom->find_custom(id_custom[index],tmp); - + } else if (flag == DVEC) { double *dvector = atom->dvector[iwhich]; for (int i = 0; i < nchoose; i++) { buf[n] = dvector[clist[i]]; n += size_one; } + } else if (flag == IARRAY) { + index--; + int **iarray = atom->iarray[iwhich]; + for (int i = 0; i < nchoose; i++) { + buf[n] = iarray[clist[i]][index]; + n += size_one; + } + } else if (flag == DARRAY) { + index--; + double **darray = atom->darray[iwhich]; + for (int i = 0; i < nchoose; i++) { + buf[n] = darray[clist[i]][index]; + n += size_one; + } } }