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thermo.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "mpi.h"
#include "stdlib.h"
#include "string.h"
#include "thermo.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "output.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
// customize a new keyword by adding to this list:
// step, atoms, cpu, temp, press, pe, ke, etotal, enthalpy
// evdwl, ecoul, epair, ebond, eangle, edihed, eimp, emol, elong, etail
// vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi
// pxx, pyy, pzz, pxy, pxz, pyz
// drot, grot (rotational KE for dipole and granular particles)
// customize a new thermo style by adding a DEFINE to this list
#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 ke grot"
#define DIPOLE "step temp epair drot etotal press"
enum{IGNORE,WARN,ERROR}; // same as write_restart.cpp
enum{ONELINE,MULTILINE};
enum{INT,FLOAT};
#define MAXLINE 1024
#define DELTA 8
/* ---------------------------------------------------------------------- */
Thermo::Thermo(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
int n = strlen(arg[0]) + 1;
style = new char[n];
strcpy(style,arg[0]);
thermoflag = 1;
// set thermo_modify defaults
normuserflag = 0;
lineflag = ONELINE;
lostflag = ERROR;
lostbefore = 0;
flushflag = 0;
// set style and corresponding lineflag
// custom style builds its own line of keywords
// customize a new thermo style by adding to if statement
line = new char[MAXLINE];
if (strcmp(style,"one") == 0) {
strcpy(line,ONE);
} else if (strcmp(style,"multi") == 0) {
strcpy(line,MULTI);
lineflag = MULTILINE;
} else if (strcmp(style,"granular") == 0) {
strcpy(line,GRANULAR);
} else if (strcmp(style,"dipole") == 0) {
strcpy(line,DIPOLE);
} else if (strcmp(style,"custom") == 0) {
if (narg == 1) error->all("Illegal thermo style custom command");
line[0] = '\0';
for (int iarg = 1; iarg < narg; iarg++) {
strcat(line,arg[iarg]);
strcat(line," ");
}
line[strlen(line)-1] = '\0';
} else error->all("Illegal thermo style command");
// ptrs, flags, IDs for compute objects thermo may use or create
temperature = NULL;
pressure = NULL;
pe = NULL;
rotate_dipole = NULL;
rotate_gran = NULL;
index_temp = index_press = index_pe = index_drot = index_grot = -1;
internal_drot = internal_grot = 0;
id_temp = (char *) "thermo_temp";
id_press = (char *) "thermo_pressure";
id_pe = (char *) "thermo_pe";
id_drot = (char *) "thermo_rotate_dipole";
id_grot = (char *) "thermo_rotate_gran";
// count fields in line
// allocate per-field memory
// process line of keywords
nfield_initial = atom->count_words(line);
allocate();
parse_fields(line);
// create the requested compute styles
// temperature,pressure,pe always exist b/c Output class created them
if (index_drot >= 0) {
create_compute(id_drot,(char *) "rotate/dipole",NULL);
internal_drot = 1;
}
if (index_grot >= 0) {
create_compute(id_grot,(char *) "rotate/gran",NULL);
internal_grot = 1;
}
// format strings
format_multi = (char *) "---------------- Step %8d ----- "
"CPU = %11.4f (sec) ----------------";
format_int_one_def = (char *) "%8d";
format_int_multi_def = (char *) "%14d";
format_g_def = (char *) "%12.8g";
format_f_def = (char *) "%14.4f";
format_int_user = NULL;
format_float_user = NULL;
}
/* ---------------------------------------------------------------------- */
Thermo::~Thermo()
{
delete [] style;
delete [] line;
// delete Compute classes if thermo created them
if (index_drot >= 0 && internal_drot)
modify->delete_compute(id_compute[index_drot]);
if (index_grot >= 0 && internal_grot)
modify->delete_compute(id_compute[index_grot]);
deallocate();
// format strings
delete [] format_int_user;
delete [] format_float_user;
}
/* ---------------------------------------------------------------------- */
void Thermo::init()
{
int i,n;
// set normvalue to default setting unless user has specified it
if (normuserflag) normvalue = normuser;
else if (strcmp(style,"granular") == 0) normvalue = 0;
else if (strcmp(update->unit_style,"lj") == 0) normvalue = 1;
else normvalue = 0;
// add Volume field if volume changes and not style = custom
// this check must come after domain init, so box_change is set
nfield = nfield_initial;
if (domain->box_change && strcmp(style,"custom") != 0)
addfield("Volume",&Thermo::compute_vol,FLOAT);
// set format string for each field
// include keyword if lineflag = MULTILINE
// add '/n' every 3 values if lineflag = MULTILINE
// add trailing '/n' to last value
char *ptr;
for (i = 0; i < nfield; i++) {
format[i][0] = '\0';
if (lineflag == MULTILINE && i % 3 == 0) strcat(format[i],"\n");
if (format_user[i]) ptr = format_user[i];
else if (vtype[i] == INT && format_int_user) ptr = format_int_user;
else if (vtype[i] == INT && lineflag == ONELINE) ptr = format_int_one_def;
else if (vtype[i] == INT && lineflag == MULTILINE)
ptr = format_int_multi_def;
else if (vtype[i] == FLOAT && format_float_user) ptr = format_float_user;
else if (lineflag == ONELINE) ptr = format_g_def;
else if (lineflag == MULTILINE) ptr = format_f_def;
n = strlen(format[i]);
if (lineflag == ONELINE) sprintf(&format[i][n],"%s ",ptr);
else sprintf(&format[i][n],"%-8s = %s ",keyword[i],ptr);
if (i == nfield-1) strcat(format[i],"\n");
}
// find current ptr for each Compute ID
int icompute;
for (i = 0; i < ncompute; i++) {
icompute = modify->find_compute(id_compute[i]);
if (icompute < 0) error->all("Could not find thermo compute ID");
computes[i] = modify->compute[icompute];
}
// find current ptr for each Fix ID
// check that fix frequency is acceptable with thermo output frequency
int ifix;
for (i = 0; i < nfix; i++) {
ifix = modify->find_fix(id_fix[i]);
if (ifix < 0) error->all("Could not find thermo fix ID");
fixes[i] = modify->fix[ifix];
if (output->thermo_every % fixes[i]->scalar_vector_freq)
error->all("Thermo and fix not computed at compatible times");
}
// set ptrs to keyword-specific Compute objects
if (index_temp >= 0) temperature = computes[index_temp];
if (index_press >= 0) pressure = computes[index_press];
if (index_pe >= 0) pe = computes[index_pe];
if (index_drot >= 0) rotate_dipole = computes[index_drot];
if (index_grot >= 0) rotate_gran = computes[index_grot];
}
/* ---------------------------------------------------------------------- */
void Thermo::header()
{
if (lineflag == MULTILINE) return;
int loc = 0;
for (int i = 0; i < nfield; i++)
loc += sprintf(&line[loc],"%s ",keyword[i]);
sprintf(&line[loc],"\n");
if (me == 0) {
if (screen) fprintf(screen,line);
if (logfile) fprintf(logfile,line);
}
}
/* ---------------------------------------------------------------------- */
void Thermo::compute(int flag)
{
int i;
firststep = flag;
// check for lost atoms
// turn off normflag if natoms = 0 to avoid divide by 0
natoms = lost_check();
if (natoms == 0) normflag = 0;
else normflag = normvalue;
// invoke Compute methods needed for thermo keywords
// call compute_scalar() if which = 0, else compute_vector()
for (i = 0; i < ncompute; i++) {
if (compute_which[i] % 2 == 0) double tmp = computes[i]->compute_scalar();
if (compute_which[i] > 0) computes[i]->compute_vector();
}
// if lineflag = MULTILINE, prepend step/cpu header line
int loc = 0;
if (lineflag == MULTILINE) {
double cpu;
if (flag) cpu = timer->elapsed(TIME_LOOP);
else cpu = 0.0;
loc = sprintf(&line[loc],format_multi,update->ntimestep,cpu);
}
// add each thermo value to line with its specific format
for (ifield = 0; ifield < nfield; ifield++) {
(this->*vfunc[ifield])();
if (vtype[ifield] == INT) loc += sprintf(&line[loc],format[ifield],ivalue);
else loc += sprintf(&line[loc],format[ifield],dvalue);
}
// print line to screen and logfile
if (me == 0) {
if (screen) fprintf(screen,line);
if (logfile) {
fprintf(logfile,line);
if (flushflag) fflush(logfile);
}
}
}
/* ----------------------------------------------------------------------
check for lost atoms, return current number of atoms
------------------------------------------------------------------------- */
double Thermo::lost_check()
{
// ntotal = current # of atoms
double ntotal;
double rlocal = atom->nlocal;
MPI_Allreduce(&rlocal,&ntotal,1,MPI_DOUBLE,MPI_SUM,world);
if (ntotal == atom->natoms) return ntotal;
// if not checking or already warned, just return
if (lostflag == IGNORE) return ntotal;
if (lostflag == WARN && lostbefore == 1) return ntotal;
// error message
if (lostflag == ERROR) {
char str[128];
sprintf(str,"Lost atoms: original %.15g current %.15g",
atom->natoms,ntotal);
error->all(str);
}
// warning message
char str[128];
sprintf(str,"Lost atoms: original %.15g current %.15g",atom->natoms,ntotal);
if (me == 0) error->warning(str);
lostbefore = 1;
return ntotal;
}
/* ----------------------------------------------------------------------
modify thermo parameters
------------------------------------------------------------------------- */
void Thermo::modify_params(int narg, char **arg)
{
if (narg == 0) error->all("Illegal thermo_modify command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+2 > narg) error->all("Illegal thermo_modify command");
if (index_temp < 0) error->all("Thermo style does not use temp");
delete [] id_compute[index_temp];
int n = strlen(arg[iarg+1]) + 1;
id_compute[index_temp] = new char[n];
strcpy(id_compute[index_temp],arg[iarg+1]);
int icompute = modify->find_compute(id_compute[index_temp]);
if (icompute < 0) error->all("Could not find thermo_modify temp ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all("Thermo_modify temp ID does not compute temperature");
if (temperature->igroup != 0 && comm->me == 0)
error->warning("Temperature for thermo pressure is not for group all");
// reset id_pre[0] of pressure to new temp ID
// either pressure currently being used by thermo or "thermo_pressure"
if (index_press >= 0) {
icompute = modify->find_compute(id_compute[index_press]);
if (icompute < 0) error->all("Press ID for thermo does not exist");
} else icompute = modify->find_compute((char *) "thermo_pressure");
delete [] modify->compute[icompute]->id_pre[0];
modify->compute[icompute]->id_pre[0] = new char[n];
strcpy(modify->compute[icompute]->id_pre[0],arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"press") == 0) {
if (iarg+2 > narg) error->all("Illegal thermo_modify command");
if (index_press < 0) error->all("Thermo style does not use press");
delete [] id_compute[index_press];
int n = strlen(arg[iarg+1]) + 1;
id_compute[index_press] = new char[n];
strcpy(id_compute[index_press],arg[iarg+1]);
int icompute = modify->find_compute(id_compute[index_press]);
if (icompute < 0) error->all("Could not find thermo_modify press ID");
pressure = modify->compute[icompute];
if (pressure->pressflag == 0)
error->all("Thermo_modify press ID does not compute pressure");
// if id_pre[0] of new pressure not being computed, add to compute list
// swap it with pressure in list so id_pre[0] will be computed first
// OK to call add_compute with "which" acting as index
int which = compute_which[index_press];
int ncompute_current = ncompute;
icompute = add_compute(pressure->id_pre[0],which);
if (icompute == ncompute_current) {
int iswap = compute_which[index_press];
compute_which[index_press] = compute_which[icompute];
compute_which[icompute] = iswap;
char *cswap = id_compute[index_press];
id_compute[index_press] = id_compute[icompute];
id_compute[icompute] = cswap;
index_press = icompute;
}
iarg += 2;
} else if (strcmp(arg[iarg],"drot") == 0) {
if (iarg+2 > narg) error->all("Illegal thermo_modify command");
if (index_drot < 0) error->all("Thermo style does not use drot");
if (internal_drot) {
modify->delete_compute(id_compute[index_drot]);
internal_drot = 0;
}
delete [] id_compute[index_drot];
int n = strlen(arg[iarg+1]) + 1;
id_compute[index_drot] = new char[n];
strcpy(id_compute[index_drot],arg[iarg+1]);
int icompute = modify->find_compute(id_compute[index_drot]);
if (icompute < 0) error->all("Could not find thermo_modify drot ID");
iarg += 2;
} else if (strcmp(arg[iarg],"grot") == 0) {
if (iarg+2 > narg) error->all("Illegal thermo_modify command");
if (index_grot < 0) error->all("Thermo style does not use grot");
if (internal_grot) {
modify->delete_compute(id_compute[index_grot]);
internal_grot = 0;
}
delete [] id_compute[index_grot];
int n = strlen(arg[iarg+1]) + 1;
id_compute[index_grot] = new char[n];
strcpy(id_compute[index_grot],arg[iarg+1]);
int icompute = modify->find_compute(id_compute[index_grot]);
if (icompute < 0) error->all("Could not find thermo_modify grot ID");
iarg += 2;
} else if (strcmp(arg[iarg],"lost") == 0) {
if (iarg+2 > narg) error->all("Illegal thermo_modify command");
if (strcmp(arg[iarg+1],"ignore") == 0) lostflag = IGNORE;
else if (strcmp(arg[iarg+1],"warn") == 0) lostflag = WARN;
else if (strcmp(arg[iarg+1],"error") == 0) lostflag = ERROR;
else error->all("Illegal thermo_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"norm") == 0) {
if (iarg+2 > narg) error->all("Illegal thermo_modify command");
normuserflag = 1;
if (strcmp(arg[iarg+1],"no") == 0) normuser = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) normuser = 1;
else error->all("Illegal thermo_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"flush") == 0) {
if (iarg+2 > narg) error->all("Illegal thermo_modify command");
if (strcmp(arg[iarg+1],"no") == 0) flushflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) flushflag = 1;
else error->all("Illegal thermo_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"line") == 0) {
if (iarg+2 > narg) error->all("Illegal thermo_modify command");
if (strcmp(arg[iarg+1],"one") == 0) lineflag = ONELINE;
else if (strcmp(arg[iarg+1],"multi") == 0) lineflag = MULTILINE;
else error->all("Illegal thermo_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"format") == 0) {
if (iarg+3 > narg) error->all("Illegal thermo_modify command");
if (strcmp(arg[iarg+1],"int") == 0) {
if (format_int_user) delete [] format_int_user;
int n = strlen(arg[iarg+2]) + 1;
format_int_user = new char[n];
strcpy(format_int_user,arg[iarg+2]);
} else if (strcmp(arg[iarg+1],"float") == 0) {
if (format_float_user) delete [] format_float_user;
int n = strlen(arg[iarg+2]) + 1;
format_float_user = new char[n];
strcpy(format_float_user,arg[iarg+2]);
} else {
int i = atoi(arg[iarg+1]) - 1;
if (i < 0 || i >= nfield_initial)
error->all("Illegal thermo_modify command");
if (format_user[i]) delete [] format_user[i];
int n = strlen(arg[iarg+2]) + 1;
format_user[i] = new char[n];
strcpy(format_user[i],arg[iarg+2]);
}
iarg += 3;
} else error->all("Illegal thermo_modify command");
}
}
/* ----------------------------------------------------------------------
allocate all per-field memory
------------------------------------------------------------------------- */
void Thermo::allocate()
{
// n = specified fields + Volume field (added at run time)
int n = nfield_initial + 1;
keyword = new char*[n];
for (int i = 0; i < n; i++) keyword[i] = new char[32];
vfunc = new FnPtr[n];
vtype = new int[n];
format = new char*[n];
for (int i = 0; i < n; i++) format[i] = new char[32];
format_user = new char*[n];
for (int i = 0; i < n; i++) format_user[i] = NULL;
field2object = new int[n];
arg_object = new int[n];
ncompute = 0;
id_compute = NULL;
compute_which = NULL;
computes = NULL;
nfix = 0;
id_fix = new char*[n];
fixes = new Fix*[n];
nvariable = 0;
id_variable = new char*[n];
}
/* ----------------------------------------------------------------------
deallocate all per-field memory
------------------------------------------------------------------------- */
void Thermo::deallocate()
{
int n = nfield_initial + 1;
for (int i = 0; i < n; i++) delete [] keyword[i];
delete [] keyword;
delete [] vfunc;
delete [] vtype;
for (int i = 0; i < n; i++) delete [] format[i];
delete [] format;
for (int i = 0; i < n; i++) delete [] format_user[i];
delete [] format_user;
delete [] field2object;
delete [] arg_object;
for (int i = 0; i < ncompute; i++) delete [] id_compute[i];
memory->sfree(id_compute);
memory->sfree(compute_which);
memory->sfree(computes);
for (int i = 0; i < nfix; i++) delete [] id_fix[i];
delete [] id_fix;
delete [] fixes;
for (int i = 0; i < nvariable; i++) delete [] id_variable[i];
delete [] id_variable;
}
/* ----------------------------------------------------------------------
parse list of thermo keywords from str
set compute flags (temp, press, pe, etc)
------------------------------------------------------------------------- */
void Thermo::parse_fields(char *str)
{
nfield = 0;
// customize a new keyword by adding to if statement
char *word = strtok(str," \0");
while (word) {
if (strcmp(word,"step") == 0) {
addfield("Step",&Thermo::compute_step,INT);
} else if (strcmp(word,"atoms") == 0) {
addfield("Atoms",&Thermo::compute_atoms,INT);
} else if (strcmp(word,"cpu") == 0) {
addfield("CPU",&Thermo::compute_cpu,FLOAT);
} else if (strcmp(word,"temp") == 0) {
addfield("Temp",&Thermo::compute_temp,FLOAT);
index_temp = add_compute(id_temp,0);
} else if (strcmp(word,"press") == 0) {
addfield("Press",&Thermo::compute_press,FLOAT);
index_temp = add_compute(id_temp,0);
index_press = add_compute(id_press,0);
} else if (strcmp(word,"pe") == 0) {
addfield("PotEng",&Thermo::compute_pe,FLOAT);
index_pe = add_compute(id_pe,0);
} else if (strcmp(word,"ke") == 0) {
addfield("KinEng",&Thermo::compute_ke,FLOAT);
index_temp = add_compute(id_temp,0);
} else if (strcmp(word,"etotal") == 0) {
addfield("TotEng",&Thermo::compute_etotal,FLOAT);
index_temp = add_compute(id_temp,0);
index_pe = add_compute(id_pe,0);
} else if (strcmp(word,"enthalpy") == 0) {
addfield("Enthalpy",&Thermo::compute_enthalpy,FLOAT);
index_temp = add_compute(id_temp,0);
index_press = add_compute(id_press,0);
index_pe = add_compute(id_pe,0);
} else if (strcmp(word,"evdwl") == 0) {
addfield("E_vdwl",&Thermo::compute_evdwl,FLOAT);
index_pe = add_compute(id_pe,0);
} else if (strcmp(word,"ecoul") == 0) {
addfield("E_coul",&Thermo::compute_ecoul,FLOAT);
index_pe = add_compute(id_pe,0);
} else if (strcmp(word,"epair") == 0) {
addfield("E_pair",&Thermo::compute_epair,FLOAT);
index_pe = add_compute(id_pe,0);
} else if (strcmp(word,"ebond") == 0) {
addfield("E_bond",&Thermo::compute_ebond,FLOAT);
index_pe = add_compute(id_pe,0);
} else if (strcmp(word,"eangle") == 0) {
addfield("E_angle",&Thermo::compute_eangle,FLOAT);
index_pe = add_compute(id_pe,0);
} else if (strcmp(word,"edihed") == 0) {
addfield("E_dihed",&Thermo::compute_edihed,FLOAT);
index_pe = add_compute(id_pe,0);
} else if (strcmp(word,"eimp") == 0) {
addfield("E_impro",&Thermo::compute_eimp,FLOAT);
index_pe = add_compute(id_pe,0);
} else if (strcmp(word,"emol") == 0) {
addfield("E_mol",&Thermo::compute_emol,FLOAT);
index_pe = add_compute(id_pe,0);
} else if (strcmp(word,"elong") == 0) {
addfield("E_long",&Thermo::compute_elong,FLOAT);
index_pe = add_compute(id_pe,0);
} else if (strcmp(word,"etail") == 0) {
addfield("E_tail",&Thermo::compute_etail,FLOAT);
index_pe = add_compute(id_pe,0);
} else if (strcmp(word,"vol") == 0) {
addfield("Volume",&Thermo::compute_vol,FLOAT);
} else if (strcmp(word,"lx") == 0) {
addfield("Lx",&Thermo::compute_lx,FLOAT);
} else if (strcmp(word,"ly") == 0) {
addfield("Ly",&Thermo::compute_ly,FLOAT);
} else if (strcmp(word,"lz") == 0) {
addfield("Lz",&Thermo::compute_lz,FLOAT);
} else if (strcmp(word,"xlo") == 0) {
addfield("Xlo",&Thermo::compute_xlo,FLOAT);
} else if (strcmp(word,"xhi") == 0) {
addfield("Xhi",&Thermo::compute_xhi,FLOAT);
} else if (strcmp(word,"ylo") == 0) {
addfield("Ylo",&Thermo::compute_ylo,FLOAT);
} else if (strcmp(word,"yhi") == 0) {
addfield("Yhi",&Thermo::compute_yhi,FLOAT);
} else if (strcmp(word,"zlo") == 0) {
addfield("Zlo",&Thermo::compute_zlo,FLOAT);
} else if (strcmp(word,"zhi") == 0) {
addfield("Zhi",&Thermo::compute_zhi,FLOAT);
} else if (strcmp(word,"pxx") == 0) {
addfield("Pxx",&Thermo::compute_pxx,FLOAT);
index_temp = add_compute(id_temp,1);
index_press = add_compute(id_press,1);
} else if (strcmp(word,"pyy") == 0) {
addfield("Pyy",&Thermo::compute_pyy,FLOAT);
index_temp = add_compute(id_temp,1);
index_press = add_compute(id_press,1);
} else if (strcmp(word,"pzz") == 0) {
addfield("Pzz",&Thermo::compute_pzz,FLOAT);
index_temp = add_compute(id_temp,1);
index_press = add_compute(id_press,1);
} else if (strcmp(word,"pxy") == 0) {
addfield("Pxy",&Thermo::compute_pxy,FLOAT);
index_temp = add_compute(id_temp,1);
index_press = add_compute(id_press,1);
} else if (strcmp(word,"pxz") == 0) {
addfield("Pxz",&Thermo::compute_pxz,FLOAT);
index_temp = add_compute(id_temp,1);
index_press = add_compute(id_press,1);
} else if (strcmp(word,"pyz") == 0) {
addfield("Pyz",&Thermo::compute_pyz,FLOAT);
index_temp = add_compute(id_temp,1);
index_press = add_compute(id_press,1);
} else if (strcmp(word,"drot") == 0) {
addfield("RotKEdip",&Thermo::compute_drot,FLOAT);
index_drot = add_compute(id_drot,0);
} else if (strcmp(word,"grot") == 0) {
addfield("RotKEgrn",&Thermo::compute_grot,FLOAT);
index_grot = add_compute(id_grot,0);
// compute value = c_ID, fix value = f_ID, variable value = v_ID
// if no trailing [], then arg is set to 0, else arg is between []
// copy = at most 8 chars of ID to pass to addfield
// if Compute has pre-computes, first add them to list
} else if ((strncmp(word,"c_",2) == 0) || (strncmp(word,"f_",2) == 0) ||
(strncmp(word,"v_",2) == 0)) {
int n = strlen(word);
char *id = new char[n];
strcpy(id,&word[2]);
char copy[9];
strncpy(copy,id,8);
copy[8] = '\0';
char *ptr = strchr(id,'[');
if (ptr) {
if (id[strlen(id)-1] != ']')
error->all("Invalid keyword in thermo_style custom command");
arg_object[nfield] = atoi(ptr+1);
*ptr = '\0';
} else arg_object[nfield] = 0;
if (word[0] == 'c') {
n = modify->find_compute(id);
if (n < 0) error->all("Could not find thermo custom compute ID");
if (arg_object[nfield] == 0 && modify->compute[n]->scalar_flag == 0)
error->all("Thermo compute ID does not compute scalar info");
if (arg_object[nfield] > 0 && modify->compute[n]->vector_flag == 0)
error->all("Thermo compute ID does not compute vector info");
if (arg_object[nfield] > 0 &&
arg_object[nfield] > modify->compute[n]->size_vector)
error->all("Thermo compute ID vector is not large enough");
if (modify->compute[n]->npre)
for (int ic = 0; ic < modify->compute[n]->npre; ic++)
int tmp = add_compute(modify->compute[n]->id_pre[ic],
arg_object[nfield]);
field2object[nfield] = add_compute(id,arg_object[nfield]);
addfield(copy,&Thermo::compute_compute,FLOAT);
} else if (word[0] == 'f') {
n = modify->find_fix(id);
if (n < 0) error->all("Could not find thermo custom fix ID");
if (arg_object[nfield] == 0 && modify->fix[n]->scalar_flag == 0)
error->all("Thermo fix ID does not compute scalar info");
if (arg_object[nfield] > 0 && modify->fix[n]->vector_flag == 0)
error->all("Thermo fix ID does not compute vector info");
if (arg_object[nfield] > 0 &&
arg_object[nfield] > modify->fix[n]->size_vector)
error->all("Thermo fix ID vector is not large enough");
field2object[nfield] = add_fix(id);
addfield(copy,&Thermo::compute_fix,FLOAT);
} else {
n = input->variable->find(id);
if (n < 0) error->all("Could not find thermo custom variable ID");
field2object[nfield] = add_variable(id);
addfield(copy,&Thermo::compute_variable,FLOAT);
}
delete [] id;
} else error->all("Invalid keyword in thermo_style custom command");
word = strtok(NULL," \0");
}
}
/* ----------------------------------------------------------------------
add field to list of quantities to print
------------------------------------------------------------------------- */
void Thermo::addfield(const char *key, FnPtr func, int typeflag)
{
strcpy(keyword[nfield],key);
vfunc[nfield] = func;
vtype[nfield] = typeflag;
nfield++;
}
/* ----------------------------------------------------------------------
add compute ID to list of Compute objects to call
return location of where this Compute is in list
if already in list, do not add, just return index, else add to list
convert index into which param
index = 0 -> scalar, index >= 1 -> vector
which = 1 -> scalar only, which = 2 -> vector only, which = 3 -> both
change which param if Compute is in list with different which param
------------------------------------------------------------------------- */
int Thermo::add_compute(const char *id, int index)
{
int icompute;
for (icompute = 0; icompute < ncompute; icompute++)
if (strcmp(id,id_compute[icompute]) == 0) {
if (index == 0 && compute_which[icompute] == 1)
compute_which[icompute] = 2;
if (index > 0 && compute_which[icompute] == 0)
compute_which[icompute] = 2;
break;
}
if (icompute < ncompute) return icompute;
id_compute = (char **)
memory->srealloc(id_compute,(ncompute+1)*sizeof(char *),
"thermo:id_compute");
compute_which = (int *)
memory->srealloc(compute_which,(ncompute+1)*sizeof(int),
"thermo:compute_which");
computes = (Compute **)
memory->srealloc(computes,(ncompute+1)*sizeof(Compute *),
"thermo:computes");
int n = strlen(id) + 1;
id_compute[ncompute] = new char[n];
strcpy(id_compute[ncompute],id);
if (index == 0) compute_which[ncompute] = 0;
else compute_which[ncompute] = 1;
ncompute++;
return ncompute-1;
}
/* ----------------------------------------------------------------------
add fix ID to list of Fix objects to call
------------------------------------------------------------------------- */
int Thermo::add_fix(const char *id)
{
int n = strlen(id) + 1;
id_fix[nfix] = new char[n];
strcpy(id_fix[nfix],id);
nfix++;
return nfix-1;
}
/* ----------------------------------------------------------------------
add variable ID to list of Variables to evaluate
------------------------------------------------------------------------- */
int Thermo::add_variable(const char *id)
{
int n = strlen(id) + 1;
id_variable[nvariable] = new char[n];
strcpy(id_variable[nvariable],id);
nvariable++;
return nvariable-1;
}
/* ----------------------------------------------------------------------
create a Compute object for group all
------------------------------------------------------------------------- */
void Thermo::create_compute(char *id, char *cstyle, char *extra)
{
char **newarg = new char*[4];
newarg[0] = id;
newarg[1] = (char *) "all";
newarg[2] = cstyle;
if (extra) newarg[3] = extra;
if (extra) modify->add_compute(4,newarg);
else modify->add_compute(3,newarg);
delete [] newarg;
}
/* ----------------------------------------------------------------------
compute a single thermodyanmic value
word is any supported keyword in custom list
called when a variable is evaluated by Variable class
return value as double in answer
return 0 if OK, 1 if str is invalid
customize a new keyword by adding to if statement and error tests
------------------------------------------------------------------------- */
int Thermo::evaluate_keyword(char *word, double *answer)
{
// don't allow use of thermo keyword before first run
// since system is not setup (e.g. no forces have been called for energy)
if (update->first_update == 0)
error->all("Variable equal thermo keyword used before initial run");
// check if Compute pointers exist for keywords that need them
// error if thermo style does not use the Compute
if (strcmp(word,"temp") == 0 || strcmp(word,"press") == 0 ||
strcmp(word,"ke") == 0 || strcmp(word,"etotal") == 0 ||
strcmp(word,"pxx") == 0 || strcmp(word,"pyy") == 0 ||
strcmp(word,"pzz") == 0 || strcmp(word,"pxy") == 0 ||
strcmp(word,"pxz") == 0 || strcmp(word,"pyz") == 0)
if (!temperature)
error->all("Variable uses compute via thermo keyword that thermo does not");
if (strcmp(word,"press") == 0 ||
strcmp(word,"pxx") == 0 || strcmp(word,"pyy") == 0 ||
strcmp(word,"pzz") == 0 || strcmp(word,"pxy") == 0 ||
strcmp(word,"pxz") == 0 || strcmp(word,"pyz") == 0)
if (!pressure)
error->all("Variable uses compute via thermo keyword that thermo does not");
if (strcmp(word,"pe") == 0 || strcmp(word,"etotal") == 0 ||
strcmp(word,"enthalpy") == 0)
if (!pe)
error->all("Variable uses compute via thermo keyword that thermo does not");
if (strcmp(word,"drot") == 0)
if (!rotate_dipole)
error->all("Variable uses compute via thermo keyword that thermo does not");
if (strcmp(word,"grot") == 0)
if (!rotate_gran)
error->all("Variable uses compute via thermo keyword that thermo does not");
// set compute_pe invocation flag for keywords that use energy
// but don't call compute_pe explicitly
if (strcmp(word,"evdwl") == 0 || strcmp(word,"ecoul") == 0 ||
strcmp(word,"epair") == 0 || strcmp(word,"ebond") == 0 ||
strcmp(word,"eangle") == 0 || strcmp(word,"edihed") == 0 ||
strcmp(word,"eimp") == 0 || strcmp(word,"emol") == 0 ||
strcmp(word,"elong") == 0 || strcmp(word,"etail") == 0) {
if (!pe)
error->all("Variable uses compute via thermo keyword that thermo does not");
pe->invoked = 1;
}
// toggle thermoflag off/on
// so individual compute routines know they are not being called from
// Thermo::compute() which pre-calls Computes
thermoflag = 0;
// invoke the lo-level thermo routine to compute the variable value
if (strcmp(word,"step") == 0) {
compute_step();
dvalue = ivalue;
} else if (strcmp(word,"atoms") == 0) {
compute_atoms();
dvalue = ivalue;
}
else if (strcmp(word,"cpu") == 0) compute_cpu();
else if (strcmp(word,"temp") == 0) compute_temp();
else if (strcmp(word,"press") == 0) compute_press();
else if (strcmp(word,"pe") == 0) compute_pe();
else if (strcmp(word,"ke") == 0) compute_ke();
else if (strcmp(word,"etotal") == 0) compute_etotal();
else if (strcmp(word,"enthalpy") == 0) compute_enthalpy();
else if (strcmp(word,"evdwl") == 0) compute_evdwl();
else if (strcmp(word,"ecoul") == 0) compute_ecoul();
else if (strcmp(word,"epair") == 0) compute_epair();
else if (strcmp(word,"ebond") == 0) compute_ebond();
else if (strcmp(word,"eangle") == 0) compute_eangle();
else if (strcmp(word,"edihed") == 0) compute_edihed();
else if (strcmp(word,"eimp") == 0) compute_eimp();
else if (strcmp(word,"emol") == 0) compute_emol();
else if (strcmp(word,"elong") == 0) compute_elong();
else if (strcmp(word,"etail") == 0) compute_etail();
else if (strcmp(word,"vol") == 0) compute_vol();
else if (strcmp(word,"lx") == 0) compute_lx();
else if (strcmp(word,"ly") == 0) compute_ly();
else if (strcmp(word,"lz") == 0) compute_lz();
else if (strcmp(word,"xlo") == 0) compute_xlo();
else if (strcmp(word,"xhi") == 0) compute_xhi();
else if (strcmp(word,"ylo") == 0) compute_ylo();
else if (strcmp(word,"yhi") == 0) compute_yhi();
else if (strcmp(word,"zlo") == 0) compute_zlo();
else if (strcmp(word,"zhi") == 0) compute_zhi();
else if (strcmp(word,"pxx") == 0) compute_pxx();
else if (strcmp(word,"pyy") == 0) compute_pyy();
else if (strcmp(word,"pzz") == 0) compute_pzz();
else if (strcmp(word,"pxy") == 0) compute_pxy();
else if (strcmp(word,"pxz") == 0) compute_pxz();
else if (strcmp(word,"pyz") == 0) compute_pyz();
else if (strcmp(word,"drot") == 0) compute_drot();
else if (strcmp(word,"grot") == 0) compute_grot();
else return 1;
thermoflag = 1;
*answer = dvalue;
return 0;
}
/* ----------------------------------------------------------------------
extraction of Compute, Fix, Variable results
ignore thermoflag, since these 3 routines only called by Thermo::compute(),
not by variable evaluation
compute/fix are normalized by atoms if returning extensive value(s)
variable value is not normalized (so formula should normalize if desired)
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void Thermo::compute_compute()
{
int index = field2object[ifield];
if (arg_object[ifield] == 0) dvalue = computes[index]->scalar;
else dvalue = computes[index]->vector[arg_object[ifield]-1];
if (normflag && computes[index]->extensive) dvalue /= natoms;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_fix()
{
int index = field2object[ifield];
if (arg_object[ifield] == 0) dvalue = fixes[index]->compute_scalar();
else dvalue = fixes[index]->compute_vector(arg_object[ifield]-1);
if (normflag && fixes[index]->extensive) dvalue /= natoms;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_variable()
{
int index = field2object[ifield];
dvalue = atof(input->variable->retrieve(id_variable[index]));
}
/* ----------------------------------------------------------------------
one routine for every thermo keyword can output
thermoflag = 1 if called by Thermo::compute()
thermoflag = 0 if called by evaluate_keyword() via Variable
set ivalue/dvalue if value is integer/double
customize a new keyword by adding a method
------------------------------------------------------------------------- */
void Thermo::compute_step()
{
ivalue = update->ntimestep;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_atoms()
{
if (thermoflag) ivalue = static_cast<int> (natoms);
else ivalue = static_cast<int> (atom->natoms);
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_cpu()
{
if (firststep == 0) dvalue = 0.0;
else dvalue = timer->elapsed(TIME_LOOP);
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_temp()
{
if (thermoflag) dvalue = temperature->scalar;
else dvalue = temperature->compute_scalar();
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_press()
{
if (thermoflag) dvalue = pressure->scalar;
else {
dvalue = temperature->compute_scalar();
dvalue = pressure->compute_scalar();
}
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_pe()
{
if (thermoflag) dvalue = pe->scalar;
else dvalue = pe->compute_scalar();
if (normflag) dvalue /= natoms;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_ke()
{
if (thermoflag) dvalue = temperature->scalar;
else dvalue = temperature->compute_scalar();
dvalue *= 0.5 * temperature->dof * force->boltz;
if (normflag) dvalue /= natoms;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_etotal()
{
compute_pe();
double ke;
if (thermoflag) ke = temperature->scalar;
else ke = temperature->compute_scalar();
ke *= 0.5 * temperature->dof * force->boltz;
if (normflag) ke /= natoms;
dvalue += ke;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_enthalpy()
{
compute_etotal();
double etmp = dvalue;
compute_vol();
double vtmp = dvalue;
if (normflag) vtmp /= natoms;
compute_press();
double ptmp = dvalue;
dvalue = etmp + ptmp*vtmp/(force->nktv2p);
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_evdwl()
{
double tmp = 0.0;
if (force->pair) tmp += force->pair->eng_vdwl;
MPI_Allreduce(&tmp,&dvalue,1,MPI_DOUBLE,MPI_SUM,world);
if (force->pair && force->pair->tail_flag) {
double volume = domain->xprd * domain->yprd * domain->zprd;
dvalue += force->pair->etail / volume;
}
if (normflag) dvalue /= natoms;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_ecoul()
{
double tmp = 0.0;
if (force->pair) tmp += force->pair->eng_coul;
MPI_Allreduce(&tmp,&dvalue,1,MPI_DOUBLE,MPI_SUM,world);
if (normflag) dvalue /= natoms;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_epair()
{
double tmp = 0.0;
if (force->pair) tmp += force->pair->eng_vdwl + force->pair->eng_coul;
MPI_Allreduce(&tmp,&dvalue,1,MPI_DOUBLE,MPI_SUM,world);
if (force->kspace) dvalue += force->kspace->energy;
if (force->pair && force->pair->tail_flag) {
double volume = domain->xprd * domain->yprd * domain->zprd;
dvalue += force->pair->etail / volume;
}
if (normflag) dvalue /= natoms;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_ebond()
{
if (force->bond) {
double tmp = force->bond->energy;
MPI_Allreduce(&tmp,&dvalue,1,MPI_DOUBLE,MPI_SUM,world);
if (normflag) dvalue /= natoms;
} else dvalue = 0.0;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_eangle()
{
if (force->angle) {
double tmp = force->angle->energy;
MPI_Allreduce(&tmp,&dvalue,1,MPI_DOUBLE,MPI_SUM,world);
if (normflag) dvalue /= natoms;
} else dvalue = 0.0;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_edihed()
{
if (force->dihedral) {
double tmp = force->dihedral->energy;
MPI_Allreduce(&tmp,&dvalue,1,MPI_DOUBLE,MPI_SUM,world);
if (normflag) dvalue /= natoms;
} else dvalue = 0.0;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_eimp()
{
if (force->improper) {
double tmp = force->improper->energy;
MPI_Allreduce(&tmp,&dvalue,1,MPI_DOUBLE,MPI_SUM,world);
if (normflag) dvalue /= natoms;
} else dvalue = 0.0;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_emol()
{
double tmp = 0.0;
if (atom->molecular) {
if (force->bond) tmp += force->bond->energy;
if (force->angle) tmp += force->angle->energy;
if (force->dihedral) tmp += force->dihedral->energy;
if (force->improper) tmp += force->improper->energy;
MPI_Allreduce(&tmp,&dvalue,1,MPI_DOUBLE,MPI_SUM,world);
if (normflag) dvalue /= natoms;
} else dvalue = 0.0;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_elong()
{
if (force->kspace) {
dvalue = force->kspace->energy;
if (normflag) dvalue /= natoms;
} else dvalue = 0.0;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_etail()
{
if (force->pair && force->pair->tail_flag) {
double volume = domain->xprd * domain->yprd * domain->zprd;
dvalue = force->pair->etail / volume;
if (normflag) dvalue /= natoms;
} else dvalue = 0.0;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_vol()
{
if (domain->dimension == 3)
dvalue = domain->xprd * domain->yprd * domain->zprd;
else
dvalue = domain->xprd * domain->yprd;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_lx()
{
dvalue = domain->xprd;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_ly()
{
dvalue = domain->yprd;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_lz()
{
dvalue = domain->zprd;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_xlo()
{
dvalue = domain->boxlo[0];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_xhi()
{
dvalue = domain->boxhi[0];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_ylo()
{
dvalue = domain->boxlo[1];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_yhi()
{
dvalue = domain->boxhi[1];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_zlo()
{
dvalue = domain->boxlo[2];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_zhi()
{
dvalue = domain->boxhi[2];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_pxx()
{
if (!thermoflag) {
temperature->compute_vector();
pressure->compute_vector();
}
dvalue = pressure->vector[0];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_pyy()
{
if (!thermoflag) {
temperature->compute_vector();
pressure->compute_vector();
}
dvalue = pressure->vector[1];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_pzz()
{
if (!thermoflag) {
temperature->compute_vector();
pressure->compute_vector();
}
dvalue = pressure->vector[2];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_pxy()
{
if (!thermoflag) {
temperature->compute_vector();
pressure->compute_vector();
}
dvalue = pressure->vector[3];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_pxz()
{
if (!thermoflag) {
temperature->compute_vector();
pressure->compute_vector();
}
dvalue = pressure->vector[4];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_pyz()
{
if (!thermoflag) {
temperature->compute_vector();
pressure->compute_vector();
}
dvalue = pressure->vector[5];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_drot()
{
if (thermoflag) dvalue = rotate_dipole->scalar;
else dvalue = rotate_dipole->compute_scalar();
if (normflag) dvalue /= natoms;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_grot()
{
if (thermoflag) dvalue = rotate_gran->scalar;
else dvalue = rotate_gran->compute_scalar();
if (normflag) dvalue /= natoms;
}
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