add support for custom properties to dump custom
This commit is contained in:
Axel Kohlmeyer
@ -42,7 +42,7 @@ enum{ID,MOL,PROC,TYPE,ELEMENT,MASS,
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Q,MUX,MUY,MUZ,MU,RADIUS,DIAMETER,
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OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ,
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TQX,TQY,TQZ,
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COMPUTE,FIX,VARIABLE};
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COMPUTE,FIX,VARIABLE,INAME,DNAME};
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enum{LT,LE,GT,GE,EQ,NEQ};
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enum{INT,DOUBLE,STRING,BIGINT}; // same as in DumpCFG
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@ -94,6 +94,10 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
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variable = NULL;
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vbuf = NULL;
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ncustom = 0;
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id_custom = NULL;
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flag_custom = NULL;
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// process attributes
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// ioptional = start of additional optional args
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// only dump image and dump movie styles process optional args
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@ -172,6 +176,10 @@ DumpCustom::~DumpCustom()
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for (int i = 0; i < nvariable; i++) memory->destroy(vbuf[i]);
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delete [] vbuf;
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for (int i = 0; i < ncustom; i++) delete [] id_custom[i];
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memory->sfree(id_custom);
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delete [] flag_custom;
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memory->destroy(choose);
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memory->destroy(dchoose);
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memory->destroy(clist);
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@ -269,6 +277,13 @@ void DumpCustom::init_style()
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variable[i] = ivariable;
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}
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int icustom;
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for (int i = 0; i < ncustom; i++) {
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icustom = atom->find_custom(id_custom[i],flag_custom[i]);
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if (icustom < 0)
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error->all(FLERR,"Could not find custom per-atom property ID");
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}
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// set index and check validity of region
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if (iregion >= 0) {
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@ -1241,6 +1256,50 @@ int DumpCustom::parse_fields(int narg, char **arg)
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field2index[i] = add_variable(suffix);
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delete [] suffix;
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// custom per-atom floating point value = d_ID
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} else if (strncmp(arg[iarg],"d_",2) == 0) {
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pack_choice[i] = &DumpCustom::pack_custom;
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vtype[i] = DOUBLE;
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int n = strlen(arg[iarg]);
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char *suffix = new char[n];
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strcpy(suffix,&arg[iarg][2]);
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argindex[i] = 0;
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int tmp = -1;
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n = atom->find_custom(suffix,tmp);
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if (n < 0)
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error->all(FLERR,"Could not find custom per-atom property ID");
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if (tmp != 1)
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error->all(FLERR,"Custom per-atom property ID is not floating point");
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field2index[i] = add_custom(suffix,1);
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delete [] suffix;
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// custom per-atom integer value = i_ID
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} else if (strncmp(arg[iarg],"i_",2) == 0) {
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pack_choice[i] = &DumpCustom::pack_custom;
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vtype[i] = INT;
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int n = strlen(arg[iarg]);
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char *suffix = new char[n];
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strcpy(suffix,&arg[iarg][2]);
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argindex[i] = 0;
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int tmp = -1;
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n = atom->find_custom(suffix,tmp);
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if (n < 0)
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error->all(FLERR,"Could not find custom per-atom property ID");
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if (tmp != 0)
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error->all(FLERR,"Custom per-atom property ID is not integer");
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field2index[i] = add_custom(suffix,0);
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delete [] suffix;
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} else return iarg;
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}
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@ -1326,6 +1385,34 @@ int DumpCustom::add_variable(char *id)
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return nvariable-1;
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}
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/* ----------------------------------------------------------------------
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add custom atom property to list used by dump
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return index of where this property is in list
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if already in list, do not add, just return index, else add to list
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------------------------------------------------------------------------- */
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int DumpCustom::add_custom(char *id, int flag)
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{
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int icustom;
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for (icustom = 0; icustom < ncustom; icustom++)
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if ((strcmp(id,id_custom[icustom]) == 0)
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&& (flag == flag_custom[icustom])) break;
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if (icustom < ncustom) return icustom;
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id_custom = (char **)
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memory->srealloc(id_custom,(ncustom+1)*sizeof(char *),"dump:id_custom");
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flag_custom = (int *)
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memory->srealloc(flag_custom,(ncustom+1)*sizeof(int),"dump:flag_custom");
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int n = strlen(id) + 1;
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id_custom[ncustom] = new char[n];
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strcpy(id_custom[ncustom],id);
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flag_custom[ncustom] = flag;
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ncustom++;
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return ncustom-1;
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}
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/* ---------------------------------------------------------------------- */
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int DumpCustom::modify_param(int narg, char **arg)
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@ -1566,6 +1653,48 @@ int DumpCustom::modify_param(int narg, char **arg)
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field2index[nfield+nthresh] = add_variable(suffix);
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delete [] suffix;
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// custom per atom floating point value = d_ID
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// must grow field2index and argindex arrays, since access is beyond nfield
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} else if (strncmp(arg[1],"d_",2) == 0) {
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thresh_array[nthresh] = DNAME;
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memory->grow(field2index,nfield+nthresh+1,"dump:field2index");
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memory->grow(argindex,nfield+nthresh+1,"dump:argindex");
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int n = strlen(arg[1]);
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char *suffix = new char[n];
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strcpy(suffix,&arg[1][2]);
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argindex[nfield+nthresh] = 0;
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int tmp = -1;
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n = atom->find_custom(suffix,tmp);
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if ((n < 0) || (tmp != 1))
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error->all(FLERR,"Could not find dump modify "
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"custom atom floating point property ID");
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field2index[nfield+nthresh] = add_custom(suffix,1);
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delete [] suffix;
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// custom per atom integer value = i_ID
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// must grow field2index and argindex arrays, since access is beyond nfield
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} else if (strncmp(arg[1],"i_",2) == 0) {
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thresh_array[nthresh] = INAME;
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memory->grow(field2index,nfield+nthresh+1,"dump:field2index");
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memory->grow(argindex,nfield+nthresh+1,"dump:argindex");
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int n = strlen(arg[1]);
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char *suffix = new char[n];
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strcpy(suffix,&arg[1][2]);
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argindex[nfield+nthresh] = 0;
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int tmp = -1;
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n = atom->find_custom(suffix,tmp);
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if ((n < 0) || (tmp != 0))
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error->all(FLERR,"Could not find dump modify "
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"custom atom integer property ID");
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field2index[nfield+nthresh] = add_custom(suffix,0);
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delete [] suffix;
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} else error->all(FLERR,"Invalid dump_modify threshhold operator");
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// set operation type of threshhold
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@ -1661,6 +1790,34 @@ void DumpCustom::pack_variable(int n)
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpCustom::pack_custom(int n)
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{
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int index = field2index[n];
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if (flag_custom[index] == 0) { // integer
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int iwhich,tmp;
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iwhich = atom->find_custom(id_custom[index],tmp);
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int *ivector = atom->ivector[iwhich];
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for (int i = 0; i < nchoose; i++) {
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buf[n] = ivector[clist[i]];
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n += size_one;
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}
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} else if (flag_custom[index] == 1) { // double
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int iwhich,tmp;
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iwhich = atom->find_custom(id_custom[index],tmp);
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double *dvector = atom->dvector[iwhich];
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for (int i = 0; i < nchoose; i++) {
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buf[n] = dvector[clist[i]];
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n += size_one;
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}
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}
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}
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/* ----------------------------------------------------------------------
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one method for every attribute dump custom can output
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the atom property is packed into buf starting at n with stride size_one
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