mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@136 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
89edd8589c
commit
658d2c7669
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@ -15,6 +15,7 @@
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#include "string.h"
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#include "dump_custom.h"
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#include "atom.h"
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#include "force.h"
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#include "domain.h"
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#include "region.h"
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#include "group.h"
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@ -30,7 +31,8 @@
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// customize by adding to 1st enum
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enum{TAG,MOL,TYPE,X,Y,Z,XS,YS,ZS,XU,YU,ZU,IX,IY,IZ,VX,VY,VZ,FX,FY,FZ,
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Q,MUX,MUY,MUZ,TQX,TQY,TQZ,CENTRO,ENG,SXX,SYY,SZZ,SXY,SXZ,SYZ};
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Q,MUX,MUY,MUZ,TQX,TQY,TQZ,
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ETOTAL,KE,EPAIR,CENTRO,SXX,SYY,SZZ,SXY,SXZ,SYZ};
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enum{LT,LE,GT,GE,EQ,NEQ};
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enum{INT,DOUBLE};
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@ -38,6 +40,8 @@ enum{INT,DOUBLE};
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DumpCustom::DumpCustom(int narg, char **arg) : Dump(narg, arg)
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{
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int i;
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if (narg == 5) error->all("No dump custom arguments specified");
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nevery = atoi(arg[3]);
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@ -52,13 +56,16 @@ DumpCustom::DumpCustom(int narg, char **arg) : Dump(narg, arg)
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thresh_op = NULL;
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thresh_value = NULL;
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fixflag_epair = 0;
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fixflag_centro = 0;
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fixflag_energy = 0;
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fixflag_stress = 0;
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computeflag_etotal = 0;
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computeflag_ke = 0;
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// process command args
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// customize by adding to if statement
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int i;
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for (int iarg = 5; iarg < narg; iarg++) {
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i = iarg-5;
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if (strcmp(arg[iarg],"tag") == 0) {
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@ -161,14 +168,24 @@ DumpCustom::DumpCustom(int narg, char **arg) : Dump(narg, arg)
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error->all("Dumping an atom quantity that isn't allocated");
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pack_choice[i] = &DumpCustom::pack_tqz;
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vtype[i] = DOUBLE;
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} else if (strcmp(arg[iarg],"etotal") == 0) {
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pack_choice[i] = &DumpCustom::pack_etotal;
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vtype[i] = DOUBLE;
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computeflag_etotal = 1;
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computeflag_ke = 1;
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fixflag_epair = 1;
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} else if (strcmp(arg[iarg],"ke") == 0) {
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pack_choice[i] = &DumpCustom::pack_ke;
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vtype[i] = DOUBLE;
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computeflag_ke = 1;
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} else if (strcmp(arg[iarg],"epair") == 0) {
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pack_choice[i] = &DumpCustom::pack_epair;
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vtype[i] = DOUBLE;
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fixflag_epair = 1;
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} else if (strcmp(arg[iarg],"centro") == 0) {
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pack_choice[i] = &DumpCustom::pack_centro;
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vtype[i] = DOUBLE;
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fixflag_centro = 1;
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} else if (strcmp(arg[iarg],"eng") == 0) {
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pack_choice[i] = &DumpCustom::pack_energy;
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vtype[i] = DOUBLE;
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fixflag_energy = 1;
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} else if (strcmp(arg[iarg],"sxx") == 0) {
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pack_choice[i] = &DumpCustom::pack_sxx;
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vtype[i] = DOUBLE;
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@ -196,10 +213,19 @@ DumpCustom::DumpCustom(int narg, char **arg) : Dump(narg, arg)
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} else error->all("Invalid keyword in dump custom command");
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}
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if (fixflag_epair) fix_create("ENERGY");
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if (fixflag_centro) fix_create("CENTRO");
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if (fixflag_energy) fix_create("ENERGY");
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if (fixflag_stress) fix_create("STRESS");
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maxlocal = 0;
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choose = NULL;
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dchoose = NULL;
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if (computeflag_etotal) etotal = NULL;
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if (computeflag_ke) ke = NULL;
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// setup format strings
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vformat = new char*[size_one];
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format_default = new char[3*size_one+1];
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@ -211,10 +237,6 @@ DumpCustom::DumpCustom(int narg, char **arg) : Dump(narg, arg)
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vformat[i] = NULL;
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}
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maxchoose = 0;
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choose = NULL;
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dchoose = NULL;
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// one-time file open
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if (multifile == 0) openfile();
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@ -226,10 +248,10 @@ DumpCustom::DumpCustom(int narg, char **arg) : Dump(narg, arg)
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DumpCustom::~DumpCustom()
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{
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delete [] pack_choice;
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delete [] vtype;
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for (int i = 0; i < size_one; i++) delete [] vformat[i];
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delete [] vformat;
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delete [] pack_choice;
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if (nthresh) {
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memory->sfree(thresh_array);
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@ -239,14 +261,17 @@ DumpCustom::~DumpCustom()
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// delete fixes for computing per-atom custom quantities if they exist
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if (fixflag_epair) fix_delete("ENERGY");
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if (fixflag_centro) fix_delete("CENTRO");
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if (fixflag_energy) fix_delete("ENERGY");
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if (fixflag_stress) fix_delete("STRESS");
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if (maxchoose) {
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delete [] choose;
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delete [] dchoose;
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}
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// delete choose arrays and local compute arrys if they exist
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delete [] choose;
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delete [] dchoose;
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if (computeflag_etotal) delete [] etotal;
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if (computeflag_ke) delete [] ke;
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}
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/* ---------------------------------------------------------------------- */
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@ -285,33 +310,32 @@ void DumpCustom::init()
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// set fixflag if dump invokes any fixes
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fixflag = 0;
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if (fixflag_centro || fixflag_energy || fixflag_stress) fixflag = 1;
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if (fixflag_epair || fixflag_centro || fixflag_stress) fixflag = 1;
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// find associated fixes that must exist
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// could have changed locations in fix list since created
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if (fixflag_epair) ifix_epair = fix_match("ENERGY");
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if (fixflag_centro) ifix_centro = fix_match("CENTRO");
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if (fixflag_energy) ifix_energy = fix_match("ENERGY");
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if (fixflag_stress) ifix_stress = fix_match("STRESS");
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// allocate choose arrays if first time
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// set computeflag if dump invokes any local computation
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if (maxchoose == 0) {
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maxchoose = atom->nmax;
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choose = new int[maxchoose];
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dchoose = new double[maxchoose];
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}
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computeflag = 0;
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if (computeflag_etotal || computeflag_ke) computeflag = 1;
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}
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/* ----------------------------------------------------------------------
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return # of bytes of allocated memory in buf and choose arrays
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return # of bytes of allocated memory in buf and choose and local arrays
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------------------------------------------------------------------------- */
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int DumpCustom::memory_usage()
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{
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int bytes = maxbuf * sizeof(double);
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bytes += maxchoose * sizeof(int);
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bytes += maxchoose * sizeof(double);
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bytes += maxlocal * sizeof(int);
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bytes += maxlocal * sizeof(double);
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if (computeflag_etotal) bytes += maxlocal * sizeof(double);
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if (computeflag_ke) bytes += maxlocal * sizeof(double);
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return bytes;
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}
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@ -386,8 +410,10 @@ int DumpCustom::modify_param(int narg, char **arg)
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else if (strcmp(arg[1],"tqx") == 0) thresh_array[nthresh] = TQX;
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else if (strcmp(arg[1],"tqy") == 0) thresh_array[nthresh] = TQY;
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else if (strcmp(arg[1],"tqz") == 0) thresh_array[nthresh] = TQZ;
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else if (strcmp(arg[1],"etotal") == 0) thresh_array[nthresh] = ETOTAL;
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else if (strcmp(arg[1],"ke") == 0) thresh_array[nthresh] = KE;
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else if (strcmp(arg[1],"epair") == 0) thresh_array[nthresh] = EPAIR;
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else if (strcmp(arg[1],"centro") == 0) thresh_array[nthresh] = CENTRO;
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else if (strcmp(arg[1],"eng") == 0) thresh_array[nthresh] = ENG;
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else if (strcmp(arg[1],"sxx") == 0) thresh_array[nthresh] = SXX;
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else if (strcmp(arg[1],"syy") == 0) thresh_array[nthresh] = SYY;
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else if (strcmp(arg[1],"szz") == 0) thresh_array[nthresh] = SZZ;
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@ -408,14 +434,14 @@ int DumpCustom::modify_param(int narg, char **arg)
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// add new fix if necessary
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if (thresh_array[nthresh] == EPAIR && fixflag_epair == 0) {
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fix_create("ENERGY");
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fixflag_epair = 1;
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}
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if (thresh_array[nthresh] == CENTRO && fixflag_centro == 0) {
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fix_create("CENTRO");
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fixflag_centro = 1;
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}
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if (thresh_array[nthresh] == ENG && fixflag_energy == 0) {
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fix_create("ENERGY");
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fixflag_energy = 1;
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}
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if ((thresh_array[nthresh] == SXX || thresh_array[nthresh] == SYY ||
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thresh_array[nthresh] == SZZ || thresh_array[nthresh] == SXY ||
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thresh_array[nthresh] == SXZ || thresh_array[nthresh] == SYZ) &&
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@ -443,23 +469,35 @@ int DumpCustom::count()
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{
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int i;
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// grow choose and local-computation arrays if needed
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int nlocal = atom->nlocal;
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if (nlocal > maxlocal) {
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delete [] choose;
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delete [] dchoose;
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if (computeflag_etotal) delete [] etotal;
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if (computeflag_ke) delete [] ke;
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maxlocal = atom->nmax;
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choose = new int[maxlocal];
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dchoose = new double[maxlocal];
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if (computeflag_etotal) etotal = new double[maxlocal];
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if (computeflag_ke) ke = new double[maxlocal];
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}
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// invoke any fixes that compute dump quantities
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if (fixflag) {
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if (fixflag_epair) modify->fix[ifix_epair]->dump();
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if (fixflag_centro) modify->fix[ifix_centro]->dump();
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if (fixflag_energy) modify->fix[ifix_energy]->dump();
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if (fixflag_stress) modify->fix[ifix_stress]->dump();
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}
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// grow choose and dchoose arrays if needed
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// invoke any local computation of dump quantities
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// etotal must come after ke and fix_epair since uses their results
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int nlocal = atom->nlocal;
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if (nlocal > maxchoose) {
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delete [] choose;
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delete [] dchoose;
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maxchoose = atom->nmax;
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choose = new int[maxchoose];
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dchoose = new double[maxchoose];
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if (computeflag) {
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if (computeflag_ke) compute_ke();
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if (computeflag_etotal) compute_etotal();
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}
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// choose all local atoms for output
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@ -631,12 +669,18 @@ int DumpCustom::count()
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} else if (thresh_array[ithresh] == TQZ) {
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ptr = &atom->torque[0][2];
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nstride = 3;
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} else if (thresh_array[ithresh] == ETOTAL) {
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ptr = etotal;
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nstride = 1;
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} else if (thresh_array[ithresh] == KE) {
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ptr = ke;
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nstride = 1;
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} else if (thresh_array[ithresh] == EPAIR) {
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ptr = ((FixEnergy *) modify->fix[ifix_epair])->energy;
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nstride = 3;
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} else if (thresh_array[ithresh] == CENTRO) {
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ptr = ((FixCentro *) modify->fix[ifix_centro])->centro;
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nstride = 3;
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} else if (thresh_array[ithresh] == ENG) {
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ptr = ((FixEnergy *) modify->fix[ifix_energy])->energy;
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nstride = 3;
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} else if (thresh_array[ithresh] == SXX) {
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ptr = &((FixStress *) modify->fix[ifix_stress])->stress[0][0];
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nstride = 6;
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@ -839,7 +883,7 @@ int DumpCustom::fix_match(char *keyword)
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}
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// ----------------------------------------------------------------------
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// one routine for every kind of quantity dump custom can output
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// one method for every kind of quantity dump custom can output
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// the atom quantity is packed into buf starting at n with stride size_one
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// customize by adding a method
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// ----------------------------------------------------------------------
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@ -1253,6 +1297,47 @@ void DumpCustom::pack_tqz(int n)
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/* ---------------------------------------------------------------------- */
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void DumpCustom::pack_etotal(int n)
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{
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double *epair = ((FixEnergy *) modify->fix[ifix_epair])->energy;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (choose[i]) {
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buf[n] = ke[i] + epair[i];
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n += size_one;
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpCustom::pack_ke(int n)
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{
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (choose[i]) {
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buf[n] = ke[i];
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n += size_one;
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpCustom::pack_epair(int n)
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{
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double *epair = ((FixEnergy *) modify->fix[ifix_epair])->energy;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (choose[i]) {
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buf[n] = epair[i];
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n += size_one;
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpCustom::pack_centro(int n)
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{
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double *centro = ((FixCentro *) modify->fix[ifix_centro])->centro;
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@ -1267,20 +1352,6 @@ void DumpCustom::pack_centro(int n)
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/* ---------------------------------------------------------------------- */
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void DumpCustom::pack_energy(int n)
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{
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double *energy = ((FixEnergy *) modify->fix[ifix_energy])->energy;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (choose[i]) {
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buf[n] = energy[i];
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n += size_one;
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpCustom::pack_sxx(int n)
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{
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double **stress = ((FixStress *) modify->fix[ifix_stress])->stress;
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@ -1362,3 +1433,39 @@ void DumpCustom::pack_syz(int n)
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n += size_one;
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}
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}
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// ----------------------------------------------------------------------
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// one method for each locally-computed dump quantity
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// ----------------------------------------------------------------------
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/* ---------------------------------------------------------------------- */
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void DumpCustom::compute_etotal()
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{
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double *epair = ((FixEnergy *) modify->fix[ifix_epair])->energy;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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etotal[i] = ke[i] + epair[i];
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}
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/* ---------------------------------------------------------------------- */
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void DumpCustom::compute_ke()
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{
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double mvv2e = force->mvv2e;
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double **v = atom->v;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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if (atom->mass_require)
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for (int i = 0; i < nlocal; i++)
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ke[i] = 0.5 * mvv2e * mass[type[i]] *
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(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
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else
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for (int i = 0; i < nlocal; i++)
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ke[i] = 0.5 * mvv2e * rmass[i] *
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(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
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}
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@ -34,20 +34,31 @@ class DumpCustom : public Dump {
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int *vtype; // type of each vector (INT, DOUBLE)
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char **vformat; // format string for each vector element
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int maxchoose; // size of choose arrays
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int maxlocal; // size of choose and local-compute arrays
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int *choose; // 1 if output this atom, 0 if no
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double *dchoose; // value for each atom to threshhold against
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int nevery;
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int fixflag; // 1 if this dump invokes any fixes, 0 if not
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int fixflag_centro; // 1 if this fix is invoked, 0 if not
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int fixflag_energy;
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int fixflag_epair; // 1 if this fix is invoked, 0 if not
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int fixflag_centro;
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int fixflag_stress;
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int ifix_centro; // which fix it is (0 to nfixes-1)
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int ifix_energy;
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int ifix_epair; // which fix it is (0 to nfixes-1)
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int ifix_centro;
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int ifix_stress;
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int computeflag; // 1 if this dump invokes any local comp, 0 if not
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int computeflag_etotal; // 1 if this local comp is invoked, 0 if not
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int computeflag_ke;
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// local computation arrays
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||||
double *etotal;
|
||||
double *ke;
|
||||
|
||||
// private methods
|
||||
|
||||
int modify_param(int, char **);
|
||||
void write_header(int);
|
||||
int count();
|
||||
|
|
@ -63,6 +74,11 @@ class DumpCustom : public Dump {
|
|||
void header_binary(int);
|
||||
void header_item(int);
|
||||
|
||||
typedef void (DumpCustom::*FnPtrData)(int, double *);
|
||||
FnPtrData write_choice; // ptr to write data functions
|
||||
void write_binary(int, double *);
|
||||
void write_text(int, double *);
|
||||
|
||||
// customize by adding a method prototype
|
||||
|
||||
typedef void (DumpCustom::*FnPtrPack)(int);
|
||||
|
|
@ -95,8 +111,10 @@ class DumpCustom : public Dump {
|
|||
void pack_tqx(int);
|
||||
void pack_tqy(int);
|
||||
void pack_tqz(int);
|
||||
void pack_etotal(int);
|
||||
void pack_ke(int);
|
||||
void pack_epair(int);
|
||||
void pack_centro(int);
|
||||
void pack_energy(int);
|
||||
void pack_sxx(int);
|
||||
void pack_syy(int);
|
||||
void pack_szz(int);
|
||||
|
|
@ -104,10 +122,10 @@ class DumpCustom : public Dump {
|
|||
void pack_sxz(int);
|
||||
void pack_syz(int);
|
||||
|
||||
typedef void (DumpCustom::*FnPtrData)(int, double *);
|
||||
FnPtrData write_choice; // ptr to write data functions
|
||||
void write_binary(int, double *);
|
||||
void write_text(int, double *);
|
||||
// local computation methods
|
||||
|
||||
void compute_etotal();
|
||||
void compute_ke();
|
||||
};
|
||||
|
||||
#endif
|
||||
|
|
|
|||
|
|
@ -39,7 +39,7 @@
|
|||
|
||||
// customize by adding a keyword to this list:
|
||||
|
||||
// step, atoms, cpu, temp, press, pe, ke, eng,
|
||||
// step, atoms, cpu, temp, press, pe, ke, etotal,
|
||||
// evdwl, ecoul, epair, ebond, eangle, edihed, eimp, emol, elong, etail, erot
|
||||
// vol, lx, ly, lz, pxx, pyy, pzz, pxy, pxz, pyz
|
||||
// gke, grot (granular trans-ke and rotational-ke)
|
||||
|
|
@ -48,10 +48,10 @@
|
|||
|
||||
// customize by adding a DEFINE to this list
|
||||
|
||||
#define ONE "step temp epair emol eng press"
|
||||
#define MULTI "eng ke temp pe ebond eangle edihed eimp evdwl ecoul elong press"
|
||||
#define ONE "step temp epair emol etotal press"
|
||||
#define MULTI "etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press"
|
||||
#define GRANULAR "step atoms gke grot"
|
||||
#define DIPOLE "step temp epair erot eng press"
|
||||
#define DIPOLE "step temp epair erot etotal press"
|
||||
|
||||
enum {IGNORE,WARN,ERROR}; // same as write_restart.cpp
|
||||
enum {ONELINE,MULTILINE};
|
||||
|
|
@ -596,8 +596,8 @@ void Thermo::parse_fields(char *str)
|
|||
} else if (strcmp(word,"ke") == 0) {
|
||||
addfield("KinEng",&Thermo::compute_ke,FLOAT);
|
||||
tempflag = 1;
|
||||
} else if (strcmp(word,"eng") == 0) {
|
||||
addfield("TotEng",&Thermo::compute_eng,FLOAT);
|
||||
} else if (strcmp(word,"etotal") == 0) {
|
||||
addfield("TotEng",&Thermo::compute_etotal,FLOAT);
|
||||
tempflag = 1;
|
||||
} else if (strcmp(word,"evdwl") == 0) {
|
||||
addfield("E_vdwl",&Thermo::compute_evdwl,FLOAT);
|
||||
|
|
@ -737,10 +737,10 @@ int Thermo::compute_value(char *word, double *answer)
|
|||
} else if (strcmp(word,"ke") == 0) {
|
||||
tempvalue = temperature->compute();
|
||||
compute_ke();
|
||||
} else if (strcmp(word,"eng") == 0) {
|
||||
} else if (strcmp(word,"etotal") == 0) {
|
||||
tempvalue = temperature->compute();
|
||||
fix_compute_pe();
|
||||
compute_eng();
|
||||
compute_etotal();
|
||||
} else if (strcmp(word,"evdwl") == 0) compute_evdwl();
|
||||
else if (strcmp(word,"ecoul") == 0) compute_ecoul();
|
||||
else if (strcmp(word,"epair") == 0) compute_epair();
|
||||
|
|
@ -862,7 +862,7 @@ void Thermo::compute_ke()
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void Thermo::compute_eng()
|
||||
void Thermo::compute_etotal()
|
||||
{
|
||||
compute_pe();
|
||||
double ke = 0.5 * temperature->dof * force->boltz * tempvalue;
|
||||
|
|
@ -1195,7 +1195,7 @@ void Thermo::compute_pave()
|
|||
|
||||
void Thermo::compute_eave()
|
||||
{
|
||||
compute_eng();
|
||||
compute_etotal();
|
||||
|
||||
if (firststep == 0) {
|
||||
if (npartial_e == 0) {
|
||||
|
|
|
|||
|
|
@ -98,7 +98,7 @@ class Thermo : public LAMMPS {
|
|||
void compute_press();
|
||||
void compute_pe();
|
||||
void compute_ke();
|
||||
void compute_eng();
|
||||
void compute_etotal();
|
||||
void compute_evdwl();
|
||||
void compute_ecoul();
|
||||
void compute_epair();
|
||||
|
|
|
|||
Loading…
Reference in New Issue