git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2330 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
385
src/thermo.cpp
385
src/thermo.cpp
@ -60,9 +60,6 @@ enum{INT,FLOAT};
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#define MIN(A,B) ((A) < (B)) ? (A) : (B)
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#define MAX(A,B) ((A) > (B)) ? (A) : (B)
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#define INVOKED_SCALAR 1 // same as in computes
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#define INVOKED_VECTOR 2
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/* ---------------------------------------------------------------------- */
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Thermo::Thermo(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
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@ -73,8 +70,6 @@ Thermo::Thermo(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
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style = new char[n];
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strcpy(style,arg[0]);
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thermoflag = 1;
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// set thermo_modify defaults
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normuserflag = 0;
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@ -261,6 +256,7 @@ void Thermo::compute(int flag)
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int i;
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firststep = flag;
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int ntimestep = update->ntimestep;
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// check for lost atoms
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// turn off normflag if natoms = 0 to avoid divide by 0
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@ -274,12 +270,13 @@ void Thermo::compute(int flag)
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for (i = 0; i < ncompute; i++) {
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if (compute_which[i] == 0) {
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if (!(computes[i]->invoked & INVOKED_SCALAR))
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double tmp = computes[i]->compute_scalar();
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if (computes[i]->invoked_scalar != ntimestep)
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computes[i]->compute_scalar();
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} else {
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if (!(computes[i]->invoked & INVOKED_VECTOR))
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if (computes[i]->invoked_vector != ntimestep)
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computes[i]->compute_vector();
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}
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computes[i]->invoked_flag = 1;
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}
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// if lineflag = MULTILINE, prepend step/cpu header line
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@ -289,7 +286,7 @@ void Thermo::compute(int flag)
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double cpu;
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if (flag) cpu = timer->elapsed(TIME_LOOP);
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else cpu = 0.0;
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loc = sprintf(&line[loc],format_multi,update->ntimestep,cpu);
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loc = sprintf(&line[loc],format_multi,ntimestep,cpu);
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}
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// add each thermo value to line with its specific format
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@ -301,7 +298,7 @@ void Thermo::compute(int flag)
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}
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// kludge for RedStorm timing issue
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// if (update->ntimestep == 100) return;
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// if (ntimestep == 100) return;
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// print line to screen and logfile
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@ -819,89 +816,203 @@ void Thermo::create_compute(char *id, char *cstyle, char *extra)
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}
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/* ----------------------------------------------------------------------
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compute a single thermodyanmic value
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word is any supported keyword in custom list
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compute a single thermodyanmic value, word is any keyword in custom list
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called when a variable is evaluated by Variable class
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return value as double in answer
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return 0 if OK, 1 if str is invalid
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customize a new keyword by adding to if statement and error tests
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return 0 if str is recoginzed keyword, 1 if unrecognized
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customize a new keyword by adding to if statement
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------------------------------------------------------------------------- */
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int Thermo::evaluate_keyword(char *word, double *answer)
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{
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// check if Compute pointers exist for keywords that need them
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// error if thermo style does not use the Compute
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if (strcmp(word,"temp") == 0 || strcmp(word,"press") == 0 ||
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strcmp(word,"ke") == 0 || strcmp(word,"etotal") == 0 ||
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strcmp(word,"pxx") == 0 || strcmp(word,"pyy") == 0 ||
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strcmp(word,"pzz") == 0 || strcmp(word,"pxy") == 0 ||
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strcmp(word,"pxz") == 0 || strcmp(word,"pyz") == 0)
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if (!temperature)
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error->all("Variable uses compute via thermo keyword that thermo does not");
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if (strcmp(word,"press") == 0 ||
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strcmp(word,"pxx") == 0 || strcmp(word,"pyy") == 0 ||
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strcmp(word,"pzz") == 0 || strcmp(word,"pxy") == 0 ||
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strcmp(word,"pxz") == 0 || strcmp(word,"pyz") == 0)
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if (!pressure)
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error->all("Variable uses compute via thermo keyword that thermo does not");
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if (strcmp(word,"pe") == 0 || strcmp(word,"etotal") == 0 ||
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strcmp(word,"enthalpy") == 0)
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if (!pe)
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error->all("Variable uses compute via thermo keyword that thermo does not");
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// set compute_pe invocation flag for keywords that use energy
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// but don't call compute_pe explicitly
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if (strcmp(word,"evdwl") == 0 || strcmp(word,"ecoul") == 0 ||
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strcmp(word,"epair") == 0 || strcmp(word,"ebond") == 0 ||
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strcmp(word,"eangle") == 0 || strcmp(word,"edihed") == 0 ||
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strcmp(word,"eimp") == 0 || strcmp(word,"emol") == 0 ||
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strcmp(word,"elong") == 0 || strcmp(word,"etail") == 0) {
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if (!pe)
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error->all("Variable uses compute via thermo keyword that thermo does not");
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pe->invoked |= INVOKED_SCALAR;
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}
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// toggle thermoflag off/on
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// so individual compute routines know they are not being called from
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// Thermo::compute() which pre-calls Computes
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thermoflag = 0;
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// invoke the lo-level thermo routine to compute the variable value
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// invoke a lo-level thermo routine to compute the variable value
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// if keyword requires a compute, is error if thermo doesn't use the compute
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// if in middle of run and needed compute is not current, invoke it
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// if inbetween runs and needed compute is not current, error
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// set invoked flag for pe and pressure for keywords that use them
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// this insures tallying on future needed steps via clearstep/addstep
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// for keywords that use pe indirectly (evdwl, ebond, etc):
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// check if energy was tallied on this timestep and set pe->invoked_flag
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if (strcmp(word,"step") == 0) {
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compute_step();
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dvalue = ivalue;
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} else if (strcmp(word,"atoms") == 0) {
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compute_atoms();
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dvalue = ivalue;
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}
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else if (strcmp(word,"cpu") == 0) compute_cpu();
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else if (strcmp(word,"temp") == 0) compute_temp();
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} else if (strcmp(word,"cpu") == 0) {
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if (update->whichflag < 0) firststep = 0;
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compute_cpu();
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else if (strcmp(word,"press") == 0) compute_press();
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else if (strcmp(word,"pe") == 0) compute_pe();
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else if (strcmp(word,"ke") == 0) compute_ke();
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else if (strcmp(word,"etotal") == 0) compute_etotal();
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else if (strcmp(word,"enthalpy") == 0) compute_enthalpy();
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else if (strcmp(word,"evdwl") == 0) compute_evdwl();
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else if (strcmp(word,"ecoul") == 0) compute_ecoul();
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else if (strcmp(word,"epair") == 0) compute_epair();
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else if (strcmp(word,"ebond") == 0) compute_ebond();
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else if (strcmp(word,"eangle") == 0) compute_eangle();
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else if (strcmp(word,"edihed") == 0) compute_edihed();
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else if (strcmp(word,"eimp") == 0) compute_eimp();
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else if (strcmp(word,"emol") == 0) compute_emol();
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else if (strcmp(word,"elong") == 0) compute_elong();
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else if (strcmp(word,"etail") == 0) compute_etail();
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else if (strcmp(word,"vol") == 0) compute_vol();
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} else if (strcmp(word,"temp") == 0) {
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if (!temperature)
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error->all("Thermo keyword in variable requires thermo to use/init temp");
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if (temperature->invoked_scalar != update->ntimestep) {
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if (update->whichflag < 0)
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error->all("Compute used in variable thermo keyword is not current");
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else temperature->compute_scalar();
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}
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compute_temp();
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} else if (strcmp(word,"press") == 0) {
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if (!pressure)
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error->all("Thermo keyword in variable requires thermo to use/init press");
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if (pressure->invoked_scalar != update->ntimestep) {
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if (update->whichflag < 0)
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error->all("Compute used in variable thermo keyword is not current");
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else pressure->compute_scalar();
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}
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pressure->invoked_flag = 1;
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compute_press();
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} else if (strcmp(word,"pe") == 0) {
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if (!pe)
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error->all("Thermo keyword in variable requires thermo to use/init pe");
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if (pe->invoked_scalar != update->ntimestep) {
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if (update->whichflag < 0)
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error->all("Compute used in variable thermo keyword is not current");
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else pe->compute_scalar();
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}
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pe->invoked_flag = 1;
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compute_pe();
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} else if (strcmp(word,"ke") == 0) {
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if (!temperature)
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error->all("Thermo keyword in variable requires thermo to use/init temp");
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if (temperature->invoked_scalar != update->ntimestep) {
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if (update->whichflag < 0)
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error->all("Compute used in variable thermo keyword is not current");
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else temperature->compute_scalar();
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}
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compute_ke();
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} else if (strcmp(word,"etotal") == 0) {
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if (!pe)
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error->all("Thermo keyword in variable requires thermo to use/init pe");
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if (pe->invoked_scalar != update->ntimestep) {
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if (update->whichflag < 0)
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error->all("Compute used in variable thermo keyword is not current");
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else pe->compute_scalar();
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}
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if (!temperature)
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error->all("Thermo keyword in variable requires thermo to use/init temp");
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if (temperature->invoked_scalar != update->ntimestep) {
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if (update->whichflag < 0)
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error->all("Compute used in variable thermo keyword is not current");
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else temperature->compute_scalar();
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}
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pe->invoked_flag = 1;
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compute_etotal();
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} else if (strcmp(word,"enthalpy") == 0) {
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if (!pe)
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error->all("Thermo keyword in variable requires thermo to use/init pe");
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if (pe->invoked_scalar != update->ntimestep) {
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if (update->whichflag < 0)
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error->all("Compute used in variable thermo keyword is not current");
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else pe->compute_scalar();
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}
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if (!temperature)
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error->all("Thermo keyword in variable requires thermo to use/init temp");
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if (temperature->invoked_scalar != update->ntimestep) {
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if (update->whichflag < 0)
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error->all("Compute used in variable thermo keyword is not current");
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else temperature->compute_scalar();
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}
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if (!pressure)
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error->all("Thermo keyword in variable requires thermo to use/init press");
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if (pressure->invoked_scalar != update->ntimestep) {
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if (update->whichflag < 0)
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error->all("Compute used in variable thermo keyword is not current");
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else pressure->compute_scalar();
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}
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pe->invoked_flag = 1;
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pressure->invoked_flag = 1;
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compute_enthalpy();
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} else if (strcmp(word,"evdwl") == 0) {
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if (!pe)
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error->all("Thermo keyword in variable requires thermo to use/init pe");
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if (update->eflag_global != update->ntimestep)
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error->all("Energy was not tallied on needed timestep");
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pe->invoked_flag = 1;
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compute_evdwl();
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} else if (strcmp(word,"ecoul") == 0) {
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if (!pe)
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error->all("Thermo keyword in variable requires thermo to use/init pe");
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if (update->eflag_global != update->ntimestep)
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error->all("Energy was not tallied on needed timestep");
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pe->invoked_flag = 1;
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compute_ecoul();
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} else if (strcmp(word,"epair") == 0) {
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if (!pe)
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error->all("Thermo keyword in variable requires thermo to use/init pe");
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if (update->eflag_global != update->ntimestep)
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error->all("Energy was not tallied on needed timestep");
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pe->invoked_flag = 1;
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compute_epair();
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} else if (strcmp(word,"ebond") == 0) {
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if (!pe)
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error->all("Thermo keyword in variable requires thermo to use/init pe");
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if (update->eflag_global != update->ntimestep)
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error->all("Energy was not tallied on needed timestep");
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pe->invoked_flag = 1;
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compute_ebond();
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} else if (strcmp(word,"eangle") == 0) {
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if (!pe)
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error->all("Thermo keyword in variable requires thermo to use/init pe");
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if (update->eflag_global != update->ntimestep)
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error->all("Energy was not tallied on needed timestep");
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pe->invoked_flag = 1;
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compute_eangle();
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} else if (strcmp(word,"edihed") == 0) {
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if (!pe)
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error->all("Thermo keyword in variable requires thermo to use/init pe");
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if (update->eflag_global != update->ntimestep)
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error->all("Energy was not tallied on needed timestep");
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pe->invoked_flag = 1;
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compute_edihed();
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} else if (strcmp(word,"eimp") == 0) {
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if (!pe)
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error->all("Thermo keyword in variable requires thermo to use/init pe");
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if (update->eflag_global != update->ntimestep)
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error->all("Energy was not tallied on needed timestep");
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pe->invoked_flag = 1;
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compute_eimp();
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} else if (strcmp(word,"emol") == 0) {
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if (!pe)
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error->all("Thermo keyword in variable requires thermo to use/init pe");
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if (update->eflag_global != update->ntimestep)
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error->all("Energy was not tallied on needed timestep");
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pe->invoked_flag = 1;
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compute_emol();
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} else if (strcmp(word,"elong") == 0) {
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if (!pe)
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error->all("Thermo keyword in variable requires thermo to use/init pe");
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if (update->eflag_global != update->ntimestep)
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error->all("Energy was not tallied on needed timestep");
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pe->invoked_flag = 1;
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compute_elong();
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} else if (strcmp(word,"etail") == 0) {
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if (!pe)
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error->all("Thermo keyword in variable requires thermo to use/init pe");
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if (update->eflag_global != update->ntimestep)
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error->all("Energy was not tallied on needed timestep");
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pe->invoked_flag = 1;
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compute_etail();
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} else if (strcmp(word,"vol") == 0) compute_vol();
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else if (strcmp(word,"lx") == 0) compute_lx();
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else if (strcmp(word,"ly") == 0) compute_ly();
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else if (strcmp(word,"lz") == 0) compute_lz();
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@ -917,16 +1028,73 @@ int Thermo::evaluate_keyword(char *word, double *answer)
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else if (strcmp(word,"xz") == 0) compute_xz();
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else if (strcmp(word,"yz") == 0) compute_yz();
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else if (strcmp(word,"pxx") == 0) compute_pxx();
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else if (strcmp(word,"pyy") == 0) compute_pyy();
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else if (strcmp(word,"pzz") == 0) compute_pzz();
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else if (strcmp(word,"pxy") == 0) compute_pxy();
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else if (strcmp(word,"pxz") == 0) compute_pxz();
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else if (strcmp(word,"pyz") == 0) compute_pyz();
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else if (strcmp(word,"pxx") == 0) {
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if (!pressure)
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error->all("Thermo keyword in variable requires thermo to use/init press");
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if (pressure->invoked_vector != update->ntimestep) {
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if (update->whichflag < 0)
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error->all("Compute used in variable thermo keyword is not current");
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else pressure->compute_vector();
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}
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pressure->invoked_flag = 1;
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compute_pxx();
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else return 1;
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} else if (strcmp(word,"pyy") == 0) {
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if (!pressure)
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error->all("Thermo keyword in variable requires thermo to use/init press");
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if (pressure->invoked_vector != update->ntimestep) {
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if (update->whichflag < 0)
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error->all("Compute used in variable thermo keyword is not current");
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else pressure->compute_vector();
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}
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pressure->invoked_flag = 1;
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compute_pyy();
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thermoflag = 1;
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} else if (strcmp(word,"pzz") == 0) {
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if (!pressure)
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error->all("Thermo keyword in variable requires thermo to use/init press");
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if (pressure->invoked_vector != update->ntimestep) {
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if (update->whichflag < 0)
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error->all("Compute used in variable thermo keyword is not current");
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else pressure->compute_vector();
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}
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pressure->invoked_flag = 1;
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compute_pzz();
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} else if (strcmp(word,"pxy") == 0) {
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if (!pressure)
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error->all("Thermo keyword in variable requires thermo to use/init press");
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if (pressure->invoked_vector != update->ntimestep) {
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if (update->whichflag < 0)
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error->all("Compute used in variable thermo keyword is not current");
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else pressure->compute_vector();
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}
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pressure->invoked_flag = 1;
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compute_pxy();
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} else if (strcmp(word,"pxz") == 0) {
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if (!pressure)
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error->all("Thermo keyword in variable requires thermo to use/init press");
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if (pressure->invoked_vector != update->ntimestep) {
|
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if (update->whichflag < 0)
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error->all("Compute used in variable thermo keyword is not current");
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else pressure->compute_vector();
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}
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pressure->invoked_flag = 1;
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compute_pxz();
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} else if (strcmp(word,"pyz") == 0) {
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if (!pressure)
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error->all("Thermo keyword in variable requires thermo to use/init press");
|
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if (pressure->invoked_vector != update->ntimestep) {
|
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if (update->whichflag < 0)
|
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error->all("Compute used in variable thermo keyword is not current");
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else pressure->compute_vector();
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}
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pressure->invoked_flag = 1;
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compute_pyz();
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} else return 1;
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*answer = dvalue;
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return 0;
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@ -934,8 +1102,6 @@ int Thermo::evaluate_keyword(char *word, double *answer)
|
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|
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/* ----------------------------------------------------------------------
|
||||
extraction of Compute, Fix, Variable results
|
||||
ignore thermoflag:
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3 methods only called by Thermo::compute(), not by variable evaluation
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compute/fix are normalized by atoms if returning extensive value
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variable value is not normalized (formula should normalize if desired)
|
||||
------------------------------------------------------------------------- */
|
||||
@ -986,8 +1152,8 @@ void Thermo::compute_variable()
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
one method for every keyword thermo can output
|
||||
thermoflag = 1 if called by Thermo::compute()
|
||||
thermoflag = 0 if called by evaluate_keyword() via Variable
|
||||
called by compute() or evaluate_keyword()
|
||||
compute will have already been called
|
||||
set ivalue/dvalue if value is integer/double
|
||||
customize a new keyword by adding a method
|
||||
------------------------------------------------------------------------- */
|
||||
@ -1001,8 +1167,7 @@ void Thermo::compute_step()
|
||||
|
||||
void Thermo::compute_atoms()
|
||||
{
|
||||
if (thermoflag) ivalue = static_cast<int> (natoms);
|
||||
else ivalue = static_cast<int> (atom->natoms);
|
||||
ivalue = static_cast<int> (natoms);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -1017,27 +1182,21 @@ void Thermo::compute_cpu()
|
||||
|
||||
void Thermo::compute_temp()
|
||||
{
|
||||
if (thermoflag || temperature->invoked & INVOKED_SCALAR)
|
||||
dvalue = temperature->scalar;
|
||||
else dvalue = temperature->compute_scalar();
|
||||
dvalue = temperature->scalar;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void Thermo::compute_press()
|
||||
{
|
||||
if (thermoflag || pressure->invoked & INVOKED_SCALAR)
|
||||
dvalue = pressure->scalar;
|
||||
else dvalue = pressure->compute_scalar();
|
||||
dvalue = pressure->scalar;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void Thermo::compute_pe()
|
||||
{
|
||||
if (thermoflag || pe->invoked & INVOKED_SCALAR)
|
||||
dvalue = pe->scalar;
|
||||
else dvalue = pe->compute_scalar();
|
||||
dvalue = pe->scalar;
|
||||
if (normflag) dvalue /= natoms;
|
||||
}
|
||||
|
||||
@ -1045,10 +1204,7 @@ void Thermo::compute_pe()
|
||||
|
||||
void Thermo::compute_ke()
|
||||
{
|
||||
if (thermoflag || temperature->invoked & INVOKED_SCALAR)
|
||||
dvalue = temperature->scalar;
|
||||
else dvalue = temperature->compute_scalar();
|
||||
|
||||
dvalue = temperature->scalar;
|
||||
dvalue *= 0.5 * temperature->dof * force->boltz;
|
||||
if (normflag) dvalue /= natoms;
|
||||
}
|
||||
@ -1058,12 +1214,7 @@ void Thermo::compute_ke()
|
||||
void Thermo::compute_etotal()
|
||||
{
|
||||
compute_pe();
|
||||
|
||||
double ke;
|
||||
if (thermoflag || temperature->invoked & INVOKED_SCALAR)
|
||||
ke = temperature->scalar;
|
||||
else ke = temperature->compute_scalar();
|
||||
|
||||
double ke = temperature->scalar;
|
||||
ke *= 0.5 * temperature->dof * force->boltz;
|
||||
if (normflag) ke /= natoms;
|
||||
dvalue += ke;
|
||||
@ -1307,8 +1458,6 @@ void Thermo::compute_yz()
|
||||
|
||||
void Thermo::compute_pxx()
|
||||
{
|
||||
if (thermoflag == 0 && !(pressure->invoked & INVOKED_VECTOR))
|
||||
pressure->compute_vector();
|
||||
dvalue = pressure->vector[0];
|
||||
}
|
||||
|
||||
@ -1316,8 +1465,6 @@ void Thermo::compute_pxx()
|
||||
|
||||
void Thermo::compute_pyy()
|
||||
{
|
||||
if (thermoflag == 0 && !(pressure->invoked & INVOKED_VECTOR))
|
||||
pressure->compute_vector();
|
||||
dvalue = pressure->vector[1];
|
||||
}
|
||||
|
||||
@ -1325,8 +1472,6 @@ void Thermo::compute_pyy()
|
||||
|
||||
void Thermo::compute_pzz()
|
||||
{
|
||||
if (thermoflag == 0 && !(pressure->invoked & INVOKED_VECTOR))
|
||||
pressure->compute_vector();
|
||||
dvalue = pressure->vector[2];
|
||||
}
|
||||
|
||||
@ -1334,8 +1479,6 @@ void Thermo::compute_pzz()
|
||||
|
||||
void Thermo::compute_pxy()
|
||||
{
|
||||
if (thermoflag == 0 && !(pressure->invoked & INVOKED_VECTOR))
|
||||
pressure->compute_vector();
|
||||
dvalue = pressure->vector[3];
|
||||
}
|
||||
|
||||
@ -1343,8 +1486,6 @@ void Thermo::compute_pxy()
|
||||
|
||||
void Thermo::compute_pxz()
|
||||
{
|
||||
if (thermoflag == 0 && !(pressure->invoked & INVOKED_VECTOR))
|
||||
pressure->compute_vector();
|
||||
dvalue = pressure->vector[4];
|
||||
}
|
||||
|
||||
@ -1352,7 +1493,5 @@ void Thermo::compute_pxz()
|
||||
|
||||
void Thermo::compute_pyz()
|
||||
{
|
||||
if (thermoflag == 0 && !(pressure->invoked & INVOKED_VECTOR))
|
||||
pressure->compute_vector();
|
||||
dvalue = pressure->vector[5];
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user