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lammps/src/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.
------------------------------------------------------------------------- */
// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h
// due to OpenMPI bug which sets INT64_MAX via its mpi.h
// before lmptype.h can set flags to insure it is done correctly
#include "thermo.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include "atom.h"
#include "update.h"
#include "comm.h"
#include "domain.h"
#include "universe.h"
#include "lattice.h"
#include "group.h"
#include "modify.h"
#include "fix.h"
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "neighbor.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"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace MathConst;
// customize a new keyword by adding to this list:
// step, elapsed, elaplong, dt, time, cpu, tpcpu, spcpu, cpuremain,
// part, timeremain
// atoms, temp, press, pe, ke, etotal, enthalpy
// evdwl, ecoul, epair, ebond, eangle, edihed, eimp, emol, elong, etail
// vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi, xy, xz, yz,
// xlat, ylat, zlat
// bonds, angles, dihedrals, impropers,
// pxx, pyy, pzz, pxy, pxz, pyz
// fmax, fnorm, nbuild, ndanger,
// cella, cellb, cellc, cellalpha, cellbeta, cellgamma
// customize a new thermo style by adding a DEFINE to this list
// also insure allocation of line string is correct in constructor
#define ONE "step temp epair emol etotal press"
#define MULTI "etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press"
enum{ONELINE,MULTILINE};
enum{INT,FLOAT,BIGINT};
enum{SCALAR,VECTOR,ARRAY};
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
#define INVOKED_ARRAY 4
#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]);
// set thermo_modify defaults
modified = 0;
normuserflag = 0;
lineflag = ONELINE;
lostflag = lostbond = Thermo::ERROR;
lostbefore = 0;
flushflag = 0;
// set style and corresponding lineflag
// custom style builds its own line of keywords, including wildcard expansion
// customize a new thermo style by adding to if statement
// allocate line string used for 3 tasks
// concat of custom style args
// one-time thermo output of header line
// each line of numeric thermo output
// 256 = extra for ONE or MULTI string or multi formatting
// 64 = max per-arg chars in header or numeric output
if (strcmp(style,"one") == 0) {
line = new char[256+6*64];
memset(line,0,256+6*64);
strcpy(line,ONE);
} else if (strcmp(style,"multi") == 0) {
line = new char[256+12*64];
memset(line,0,256+12*64);
strcpy(line,MULTI);
lineflag = MULTILINE;
} else if (strcmp(style,"custom") == 0) {
if (narg == 1) error->all(FLERR,"Illegal thermo style custom command");
// expand args if any have wildcard character "*"
int expand = 0;
char **earg;
int nvalues = input->expand_args(narg-1,&arg[1],0,earg);
if (earg != &arg[1]) expand = 1;
line = new char[256+nvalues*64];
line[0] = '\0';
for (int iarg = 0; iarg < nvalues; iarg++) {
strcat(line,earg[iarg]);
strcat(line," ");
}
line[strlen(line)-1] = '\0';
// if wildcard expansion occurred, free earg memory from exapnd_args()
if (expand) {
for (int i = 0; i < nvalues; i++) delete [] earg[i];
memory->sfree(earg);
}
} else error->all(FLERR,"Illegal thermo style command");
// ptrs, flags, IDs for compute objects thermo may use or create
temperature = NULL;
pressure = NULL;
pe = NULL;
index_temp = index_press_scalar = index_press_vector = index_pe = -1;
id_temp = (char *) "thermo_temp";
id_press = (char *) "thermo_press";
id_pe = (char *) "thermo_pe";
// count fields in line
// allocate per-field memory
// process line of keywords
nfield_initial = atom->count_words(line);
allocate();
parse_fields(line);
// format strings
char *bigint_format = (char *) BIGINT_FORMAT;
char *fformat_multi = (char *) "---------------- Step %%8%s ----- "
"CPU = %%11.4f (sec) ----------------";
sprintf(format_multi,fformat_multi,&bigint_format[1]);
format_float_one_def = (char *) "%12.8g";
format_float_multi_def = (char *) "%14.4f";
format_int_one_def = (char *) "%8d";
format_int_multi_def = (char *) "%14d";
sprintf(format_bigint_one_def,"%%8%s",&bigint_format[1]);
sprintf(format_bigint_multi_def,"%%14%s",&bigint_format[1]);
format_line_user = NULL;
format_float_user = NULL;
format_int_user = NULL;
format_bigint_user = NULL;
}
/* ---------------------------------------------------------------------- */
Thermo::~Thermo()
{
delete [] style;
delete [] line;
deallocate();
// format strings
delete [] format_line_user;
delete [] format_float_user;
delete [] format_int_user;
delete [] format_bigint_user;
}
/* ---------------------------------------------------------------------- */
void Thermo::init()
{
int i,n;
// set normvalue to default setting unless user has specified it
if (normuserflag) normvalue = normuser;
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 *format_line = NULL;
if (format_line_user) {
int n = strlen(format_line_user) + 1;
format_line = new char[n];
strcpy(format_line,format_line_user);
}
char *ptr,*format_line_ptr;
for (i = 0; i < nfield; i++) {
format[i][0] = '\0';
if (lineflag == MULTILINE && i % 3 == 0) strcat(format[i],"\n");
if (format_line) {
if (i == 0) format_line_ptr = strtok(format_line," \0");
else format_line_ptr = strtok(NULL," \0");
}
if (format_column_user[i]) ptr = format_column_user[i];
else if (vtype[i] == FLOAT) {
if (format_float_user) ptr = format_float_user;
else if (format_line_user) ptr = format_line_ptr;
else if (lineflag == ONELINE) ptr = format_float_one_def;
else if (lineflag == MULTILINE) ptr = format_float_multi_def;
} else if (vtype[i] == INT) {
if (format_int_user) ptr = format_int_user;
else if (format_line_user) ptr = format_line_ptr;
else if (lineflag == ONELINE) ptr = format_int_one_def;
else if (lineflag == MULTILINE) ptr = format_int_multi_def;
} else if (vtype[i] == BIGINT) {
if (format_bigint_user) ptr = format_bigint_user;
else if (format_line_user) ptr = format_line_ptr;
else if (lineflag == ONELINE) ptr = format_bigint_one_def;
else if (lineflag == MULTILINE) ptr = format_bigint_multi_def;
}
n = strlen(format[i]);
if (lineflag == ONELINE) sprintf(&format[i][n],"%s ",ptr);
else sprintf(&format[i][n],"%-8s = %s ",keyword[i],ptr);
}
strcat(format[nfield-1],"\n");
delete [] format_line;
// 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(FLERR,"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(FLERR,"Could not find thermo fix ID");
fixes[i] = modify->fix[ifix];
if (output->thermo_every % fixes[i]->global_freq)
error->all(FLERR,"Thermo and fix not computed at compatible times");
}
// find current ptr for each Variable ID
int ivariable;
for (i = 0; i < nvariable; i++) {
ivariable = input->variable->find(id_variable[i]);
if (ivariable < 0)
error->all(FLERR,"Could not find thermo variable name");
variables[i] = ivariable;
}
// set ptrs to keyword-specific Compute objects
if (index_temp >= 0) temperature = computes[index_temp];
if (index_press_scalar >= 0) pressure = computes[index_press_scalar];
if (index_press_vector >= 0) pressure = computes[index_press_vector];
if (index_pe >= 0) pe = computes[index_pe];
}
/* ---------------------------------------------------------------------- */
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,"%s",line);
if (logfile) fprintf(logfile,"%s",line);
}
}
/* ---------------------------------------------------------------------- */
void Thermo::compute(int flag)
{
int i;
firststep = flag;
bigint ntimestep = update->ntimestep;
// check for lost atoms
// turn off normflag if natoms = 0 to avoid divide by 0
natoms = atom->natoms = lost_check();
if (natoms == 0) normflag = 0;
else normflag = normvalue;
// invoke Compute methods needed for thermo keywords
for (i = 0; i < ncompute; i++)
if (compute_which[i] == SCALAR) {
if (!(computes[i]->invoked_flag & INVOKED_SCALAR)) {
computes[i]->compute_scalar();
computes[i]->invoked_flag |= INVOKED_SCALAR;
}
} else if (compute_which[i] == VECTOR) {
if (!(computes[i]->invoked_flag & INVOKED_VECTOR)) {
computes[i]->compute_vector();
computes[i]->invoked_flag |= INVOKED_VECTOR;
}
} else if (compute_which[i] == ARRAY) {
if (!(computes[i]->invoked_flag & INVOKED_ARRAY)) {
computes[i]->compute_array();
computes[i]->invoked_flag |= INVOKED_ARRAY;
}
}
// if lineflag = MULTILINE, prepend step/cpu header line
int loc = 0;
if (lineflag == MULTILINE) {
double cpu;
if (flag) cpu = timer->elapsed(Timer::TOTAL);
else cpu = 0.0;
loc = sprintf(&line[loc],format_multi,ntimestep,cpu);
}
// add each thermo value to line with its specific format
for (ifield = 0; ifield < nfield; ifield++) {
(this->*vfunc[ifield])();
if (vtype[ifield] == FLOAT)
loc += sprintf(&line[loc],format[ifield],dvalue);
else if (vtype[ifield] == INT)
loc += sprintf(&line[loc],format[ifield],ivalue);
else if (vtype[ifield] == BIGINT)
loc += sprintf(&line[loc],format[ifield],bivalue);
}
// print line to screen and logfile
if (me == 0) {
if (screen) fprintf(screen,"%s",line);
if (logfile) {
fprintf(logfile,"%s",line);
if (flushflag) fflush(logfile);
}
}
// set to 1, so that subsequent invocations of CPU time will be non-zero
// e.g. via variables in print command
firststep = 1;
}
/* ----------------------------------------------------------------------
call function to compute property
------------------------------------------------------------------------- */
void Thermo::call_vfunc(int ifield_in)
{
ifield = ifield_in;
(this->*vfunc[ifield])();
}
/* ----------------------------------------------------------------------
check for lost atoms, return current number of atoms
------------------------------------------------------------------------- */
bigint Thermo::lost_check()
{
// ntotal = current # of atoms
bigint ntotal;
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&ntotal,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (ntotal < 0)
error->all(FLERR,"Too many total atoms");
if (ntotal == atom->natoms) return ntotal;
// if not checking or already warned, just return
if (lostflag == Thermo::IGNORE) return ntotal;
if (lostflag == Thermo::WARN && lostbefore == 1) {
return ntotal;
}
// error message
if (lostflag == Thermo::ERROR) {
char str[64];
sprintf(str,
"Lost atoms: original " BIGINT_FORMAT " current " BIGINT_FORMAT,
atom->natoms,ntotal);
error->all(FLERR,str);
}
// warning message
char str[64];
sprintf(str,
"Lost atoms: original " BIGINT_FORMAT " current " BIGINT_FORMAT,
atom->natoms,ntotal);
if (me == 0) error->warning(FLERR,str,0);
// reset total atom count
atom->natoms = ntotal;
lostbefore = 1;
return ntotal;
}
/* ----------------------------------------------------------------------
modify thermo parameters
------------------------------------------------------------------------- */
void Thermo::modify_params(int narg, char **arg)
{
if (narg == 0) error->all(FLERR,"Illegal thermo_modify command");
modified = 1;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal thermo_modify command");
if (index_temp < 0) error->all(FLERR,"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(arg[iarg+1]);
if (icompute < 0)
error->all(FLERR,"Could not find thermo_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,"Thermo_modify temperature ID does not "
"compute temperature");
if (temperature->igroup != 0 && comm->me == 0)
error->warning(FLERR,
"Temperature for thermo pressure is not for group all");
// reset id_temp of pressure to new temperature ID
// either pressure currently being used by thermo or "thermo_press"
if (index_press_scalar >= 0) {
icompute = modify->find_compute(id_compute[index_press_scalar]);
if (icompute < 0) error->all(FLERR,
"Pressure ID for thermo does not exist");
} else if (index_press_vector >= 0) {
icompute = modify->find_compute(id_compute[index_press_vector]);
if (icompute < 0) error->all(FLERR,
"Pressure ID for thermo does not exist");
} else icompute = modify->find_compute((char *) "thermo_press");
modify->compute[icompute]->reset_extra_compute_fix(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"press") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal thermo_modify command");
if (index_press_scalar < 0 && index_press_vector < 0)
error->all(FLERR,"Thermo style does not use press");
if (index_press_scalar >= 0) {
delete [] id_compute[index_press_scalar];
int n = strlen(arg[iarg+1]) + 1;
id_compute[index_press_scalar] = new char[n];
strcpy(id_compute[index_press_scalar],arg[iarg+1]);
}
if (index_press_vector >= 0) {
delete [] id_compute[index_press_vector];
int n = strlen(arg[iarg+1]) + 1;
id_compute[index_press_vector] = new char[n];
strcpy(id_compute[index_press_vector],arg[iarg+1]);
}
int icompute = modify->find_compute(arg[iarg+1]);
if (icompute < 0) error->all(FLERR,
"Could not find thermo_modify pressure ID");
pressure = modify->compute[icompute];
if (pressure->pressflag == 0)
error->all(FLERR,"Thermo_modify pressure ID does not compute pressure");
iarg += 2;
} else if (strcmp(arg[iarg],"lost") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal thermo_modify command");
if (strcmp(arg[iarg+1],"ignore") == 0) lostflag = Thermo::IGNORE;
else if (strcmp(arg[iarg+1],"warn") == 0) lostflag = Thermo::WARN;
else if (strcmp(arg[iarg+1],"error") == 0) lostflag = Thermo::ERROR;
else error->all(FLERR,"Illegal thermo_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"lost/bond") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal thermo_modify command");
if (strcmp(arg[iarg+1],"ignore") == 0) lostbond = Thermo::IGNORE;
else if (strcmp(arg[iarg+1],"warn") == 0) lostbond = Thermo::WARN;
else if (strcmp(arg[iarg+1],"error") == 0) lostbond = Thermo::ERROR;
else error->all(FLERR,"Illegal thermo_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"norm") == 0) {
if (iarg+2 > narg) error->all(FLERR,"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(FLERR,"Illegal thermo_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"flush") == 0) {
if (iarg+2 > narg) error->all(FLERR,"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(FLERR,"Illegal thermo_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"line") == 0) {
if (iarg+2 > narg) error->all(FLERR,"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(FLERR,"Illegal thermo_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"format") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal thermo_modify command");
if (strcmp(arg[iarg+1],"none") == 0) {
delete [] format_line_user;
delete [] format_int_user;
delete [] format_bigint_user;
delete [] format_float_user;
format_line_user = NULL;
format_int_user = NULL;
format_bigint_user = NULL;
format_float_user = NULL;
for (int i = 0; i < nfield_initial+1; i++) {
delete [] format_column_user[i];
format_column_user[i] = NULL;
}
iarg += 2;
continue;
}
if (iarg+3 > narg) error->all(FLERR,"Illegal thermo_modify command");
if (strcmp(arg[iarg+1],"line") == 0) {
delete [] format_line_user;
int n = strlen(arg[iarg+2]) + 1;
format_line_user = new char[n];
strcpy(format_line_user,arg[iarg+2]);
} else 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]);
if (format_bigint_user) delete [] format_bigint_user;
n = strlen(format_int_user) + 8;
format_bigint_user = new char[n];
// replace "d" in format_int_user with bigint format specifier
// use of &str[1] removes leading '%' from BIGINT_FORMAT string
char *ptr = strchr(format_int_user,'d');
if (ptr == NULL)
error->all(FLERR,
"Thermo_modify int format does not contain d character");
char str[8];
sprintf(str,"%s",BIGINT_FORMAT);
*ptr = '\0';
sprintf(format_bigint_user,"%s%s%s",format_int_user,&str[1],ptr+1);
*ptr = 'd';
} 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 = force->inumeric(FLERR,arg[iarg+1]) - 1;
if (i < 0 || i >= nfield_initial+1)
error->all(FLERR,"Illegal thermo_modify command");
if (format_column_user[i]) delete [] format_column_user[i];
int n = strlen(arg[iarg+2]) + 1;
format_column_user[i] = new char[n];
strcpy(format_column_user[i],arg[iarg+2]);
}
iarg += 3;
} else error->all(FLERR,"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] = NULL;
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_column_user = new char*[n];
for (int i = 0; i < n; i++) format_column_user[i] = NULL;
field2index = new int[n];
argindex1 = new int[n];
argindex2 = new int[n];
// factor of 3 is max number of computes a single field can add
ncompute = 0;
id_compute = new char*[3*n];
compute_which = new int[3*n];
computes = new Compute*[3*n];
nfix = 0;
id_fix = new char*[n];
fixes = new Fix*[n];
nvariable = 0;
id_variable = new char*[n];
variables = new int[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_column_user[i];
delete [] format_column_user;
delete [] field2index;
delete [] argindex1;
delete [] argindex2;
for (int i = 0; i < ncompute; i++) delete [] id_compute[i];
delete [] id_compute;
delete [] compute_which;
delete [] 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;
delete [] variables;
}
/* ----------------------------------------------------------------------
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,BIGINT);
} else if (strcmp(word,"elapsed") == 0) {
addfield("Elapsed",&Thermo::compute_elapsed,BIGINT);
} else if (strcmp(word,"elaplong") == 0) {
addfield("Elaplong",&Thermo::compute_elapsed_long,BIGINT);
} else if (strcmp(word,"dt") == 0) {
addfield("Dt",&Thermo::compute_dt,FLOAT);
} else if (strcmp(word,"time") == 0) {
addfield("Time",&Thermo::compute_time,FLOAT);
} else if (strcmp(word,"cpu") == 0) {
addfield("CPU",&Thermo::compute_cpu,FLOAT);
} else if (strcmp(word,"tpcpu") == 0) {
addfield("T/CPU",&Thermo::compute_tpcpu,FLOAT);
} else if (strcmp(word,"spcpu") == 0) {
addfield("S/CPU",&Thermo::compute_spcpu,FLOAT);
} else if (strcmp(word,"cpuremain") == 0) {
addfield("CPULeft",&Thermo::compute_cpuremain,FLOAT);
} else if (strcmp(word,"part") == 0) {
addfield("Part",&Thermo::compute_part,INT);
} else if (strcmp(word,"timeremain") == 0) {
addfield("TimeoutLeft",&Thermo::compute_timeremain,FLOAT);
} else if (strcmp(word,"atoms") == 0) {
addfield("Atoms",&Thermo::compute_atoms,BIGINT);
} else if (strcmp(word,"temp") == 0) {
addfield("Temp",&Thermo::compute_temp,FLOAT);
index_temp = add_compute(id_temp,SCALAR);
} else if (strcmp(word,"press") == 0) {
addfield("Press",&Thermo::compute_press,FLOAT);
index_press_scalar = add_compute(id_press,SCALAR);
} else if (strcmp(word,"pe") == 0) {
addfield("PotEng",&Thermo::compute_pe,FLOAT);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"ke") == 0) {
addfield("KinEng",&Thermo::compute_ke,FLOAT);
index_temp = add_compute(id_temp,SCALAR);
} else if (strcmp(word,"etotal") == 0) {
addfield("TotEng",&Thermo::compute_etotal,FLOAT);
index_temp = add_compute(id_temp,SCALAR);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"enthalpy") == 0) {
addfield("Enthalpy",&Thermo::compute_enthalpy,FLOAT);
index_temp = add_compute(id_temp,SCALAR);
index_press_scalar = add_compute(id_press,SCALAR);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"evdwl") == 0) {
addfield("E_vdwl",&Thermo::compute_evdwl,FLOAT);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"ecoul") == 0) {
addfield("E_coul",&Thermo::compute_ecoul,FLOAT);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"epair") == 0) {
addfield("E_pair",&Thermo::compute_epair,FLOAT);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"ebond") == 0) {
addfield("E_bond",&Thermo::compute_ebond,FLOAT);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"eangle") == 0) {
addfield("E_angle",&Thermo::compute_eangle,FLOAT);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"edihed") == 0) {
addfield("E_dihed",&Thermo::compute_edihed,FLOAT);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"eimp") == 0) {
addfield("E_impro",&Thermo::compute_eimp,FLOAT);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"emol") == 0) {
addfield("E_mol",&Thermo::compute_emol,FLOAT);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"elong") == 0) {
addfield("E_long",&Thermo::compute_elong,FLOAT);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"etail") == 0) {
addfield("E_tail",&Thermo::compute_etail,FLOAT);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"vol") == 0) {
addfield("Volume",&Thermo::compute_vol,FLOAT);
} else if (strcmp(word,"density") == 0) {
addfield("Density",&Thermo::compute_density,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,"xy") == 0) {
addfield("Xy",&Thermo::compute_xy,FLOAT);
} else if (strcmp(word,"xz") == 0) {
addfield("Xz",&Thermo::compute_xz,FLOAT);
} else if (strcmp(word,"yz") == 0) {
addfield("Yz",&Thermo::compute_yz,FLOAT);
} else if (strcmp(word,"xlat") == 0) {
addfield("Xlat",&Thermo::compute_xlat,FLOAT);
} else if (strcmp(word,"ylat") == 0) {
addfield("Ylat",&Thermo::compute_ylat,FLOAT);
} else if (strcmp(word,"zlat") == 0) {
addfield("Zlat",&Thermo::compute_zlat,FLOAT);
} else if (strcmp(word,"bonds") == 0) {
addfield("Bonds",&Thermo::compute_bonds,BIGINT);
} else if (strcmp(word,"angles") == 0) {
addfield("Angles",&Thermo::compute_angles,BIGINT);
} else if (strcmp(word,"dihedrals") == 0) {
addfield("Diheds",&Thermo::compute_dihedrals,BIGINT);
} else if (strcmp(word,"impropers") == 0) {
addfield("Impros",&Thermo::compute_impropers,BIGINT);
} else if (strcmp(word,"pxx") == 0) {
addfield("Pxx",&Thermo::compute_pxx,FLOAT);
index_press_vector = add_compute(id_press,VECTOR);
} else if (strcmp(word,"pyy") == 0) {
addfield("Pyy",&Thermo::compute_pyy,FLOAT);
index_press_vector = add_compute(id_press,VECTOR);
} else if (strcmp(word,"pzz") == 0) {
addfield("Pzz",&Thermo::compute_pzz,FLOAT);
index_press_vector = add_compute(id_press,VECTOR);
} else if (strcmp(word,"pxy") == 0) {
addfield("Pxy",&Thermo::compute_pxy,FLOAT);
index_press_vector = add_compute(id_press,VECTOR);
} else if (strcmp(word,"pxz") == 0) {
addfield("Pxz",&Thermo::compute_pxz,FLOAT);
index_press_vector = add_compute(id_press,VECTOR);
} else if (strcmp(word,"pyz") == 0) {
addfield("Pyz",&Thermo::compute_pyz,FLOAT);
index_press_vector = add_compute(id_press,VECTOR);
} else if (strcmp(word,"fmax") == 0) {
addfield("Fmax",&Thermo::compute_fmax,FLOAT);
} else if (strcmp(word,"fnorm") == 0) {
addfield("Fnorm",&Thermo::compute_fnorm,FLOAT);
} else if (strcmp(word,"nbuild") == 0) {
addfield("Nbuild",&Thermo::compute_nbuild,BIGINT);
} else if (strcmp(word,"ndanger") == 0) {
addfield("Ndanger",&Thermo::compute_ndanger,BIGINT);
} else if (strcmp(word,"cella") == 0) {
addfield("Cella",&Thermo::compute_cella,FLOAT);
} else if (strcmp(word,"cellb") == 0) {
addfield("Cellb",&Thermo::compute_cellb,FLOAT);
} else if (strcmp(word,"cellc") == 0) {
addfield("Cellc",&Thermo::compute_cellc,FLOAT);
} else if (strcmp(word,"cellalpha") == 0) {
addfield("CellAlpha",&Thermo::compute_cellalpha,FLOAT);
} else if (strcmp(word,"cellbeta") == 0) {
addfield("CellBeta",&Thermo::compute_cellbeta,FLOAT);
} else if (strcmp(word,"cellgamma") == 0) {
addfield("CellGamma",&Thermo::compute_cellgamma,FLOAT);
// compute value = c_ID, fix value = f_ID, variable value = v_ID
// count trailing [] and store int arguments
} 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]);
// parse zero or one or two trailing brackets from ID
// argindex1,argindex2 = int inside each bracket pair, 0 if no bracket
char *ptr = strchr(id,'[');
if (ptr == NULL) argindex1[nfield] = argindex2[nfield] = 0;
else {
*ptr = '\0';
argindex1[nfield] =
(int) input->variable->int_between_brackets(ptr,0);
ptr++;
if (*ptr == '[') {
argindex2[nfield] =
(int) input->variable->int_between_brackets(ptr,0);
ptr++;
} else argindex2[nfield] = 0;
}
if (word[0] == 'c') {
n = modify->find_compute(id);
if (n < 0) error->all(FLERR,"Could not find thermo custom compute ID");
if (argindex1[nfield] == 0 && modify->compute[n]->scalar_flag == 0)
error->all(FLERR,"Thermo compute does not compute scalar");
if (argindex1[nfield] > 0 && argindex2[nfield] == 0) {
if (modify->compute[n]->vector_flag == 0)
error->all(FLERR,"Thermo compute does not compute vector");
if (argindex1[nfield] > modify->compute[n]->size_vector &&
modify->compute[n]->size_vector_variable == 0)
error->all(FLERR,"Thermo compute vector is accessed out-of-range");
}
if (argindex1[nfield] > 0 && argindex2[nfield] > 0) {
if (modify->compute[n]->array_flag == 0)
error->all(FLERR,"Thermo compute does not compute array");
if (argindex1[nfield] > modify->compute[n]->size_array_rows &&
modify->compute[n]->size_array_rows_variable == 0)
error->all(FLERR,"Thermo compute array is accessed out-of-range");
if (argindex2[nfield] > modify->compute[n]->size_array_cols)
error->all(FLERR,"Thermo compute array is accessed out-of-range");
}
if (argindex1[nfield] == 0)
field2index[nfield] = add_compute(id,SCALAR);
else if (argindex2[nfield] == 0)
field2index[nfield] = add_compute(id,VECTOR);
else
field2index[nfield] = add_compute(id,ARRAY);
addfield(word,&Thermo::compute_compute,FLOAT);
} else if (word[0] == 'f') {
n = modify->find_fix(id);
if (n < 0) error->all(FLERR,"Could not find thermo custom fix ID");
if (argindex1[nfield] == 0 && modify->fix[n]->scalar_flag == 0)
error->all(FLERR,"Thermo fix does not compute scalar");
if (argindex1[nfield] > 0 && argindex2[nfield] == 0) {
if (modify->fix[n]->vector_flag == 0)
error->all(FLERR,"Thermo fix does not compute vector");
if (argindex1[nfield] > modify->fix[n]->size_vector &&
modify->fix[n]->size_vector_variable == 0)
error->all(FLERR,"Thermo fix vector is accessed out-of-range");
}
if (argindex1[nfield] > 0 && argindex2[nfield] > 0) {
if (modify->fix[n]->array_flag == 0)
error->all(FLERR,"Thermo fix does not compute array");
if (argindex1[nfield] > modify->fix[n]->size_array_rows &&
modify->fix[n]->size_array_rows_variable == 0)
error->all(FLERR,"Thermo fix array is accessed out-of-range");
if (argindex2[nfield] > modify->fix[n]->size_array_cols)
error->all(FLERR,"Thermo fix array is accessed out-of-range");
}
field2index[nfield] = add_fix(id);
addfield(word,&Thermo::compute_fix,FLOAT);
} else if (word[0] == 'v') {
n = input->variable->find(id);
if (n < 0)
error->all(FLERR,"Could not find thermo custom variable name");
if (argindex1[nfield] == 0 && input->variable->equalstyle(n) == 0)
error->all(FLERR,
"Thermo custom variable is not equal-style variable");
if (argindex1[nfield] && input->variable->vectorstyle(n) == 0)
error->all(FLERR,
"Thermo custom variable is not vector-style variable");
if (argindex2[nfield])
error->all(FLERR,"Thermo custom variable cannot have two indices");
field2index[nfield] = add_variable(id);
addfield(word,&Thermo::compute_variable,FLOAT);
}
delete [] id;
} else error->all(FLERR,"Unknown 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)
{
int n = strlen(key) + 1;
delete[] keyword[nfield];
keyword[nfield] = new char[n];
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 with same which, do not add, just return index
------------------------------------------------------------------------- */
int Thermo::add_compute(const char *id, int which)
{
int icompute;
for (icompute = 0; icompute < ncompute; icompute++)
if ((strcmp(id,id_compute[icompute]) == 0) &&
which == compute_which[icompute]) break;
if (icompute < ncompute) return icompute;
int n = strlen(id) + 1;
id_compute[ncompute] = new char[n];
strcpy(id_compute[ncompute],id);
compute_which[ncompute] = which;
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;
}
/* ----------------------------------------------------------------------
compute a single thermodynamic value, word is any keyword in custom list
called when a variable is evaluated by Variable class
return value as double in answer
return 0 if str is recognized keyword, 1 if unrecognized
customize a new keyword by adding to if statement
------------------------------------------------------------------------- */
int Thermo::evaluate_keyword(char *word, double *answer)
{
// turn off normflag if natoms = 0 to avoid divide by 0
// normflag must be set for lo-level thermo routines that may be invoked
natoms = atom->natoms;
if (natoms == 0) normflag = 0;
else normflag = normvalue;
// invoke a lo-level thermo routine to compute the variable value
// if keyword requires a compute, error if thermo doesn't use the compute
// if inbetween runs and needed compute is not current, error
// if in middle of run and needed compute is not current, invoke it
// for keywords that use energy (evdwl, ebond, etc):
// check if energy was tallied on this timestep and set pe->invoked_flag
// this will trigger next timestep for energy tallying via addstep()
// this means keywords that use pe (pe, etotal, enthalpy)
// need to always invoke it even if invoked_flag is set,
// because evdwl/etc may have set invoked_flag w/out
// actually invoking pe->compute_scalar()
if (strcmp(word,"step") == 0) {
compute_step();
dvalue = bivalue;
} else if (strcmp(word,"elapsed") == 0) {
if (update->whichflag == 0)
error->all(FLERR,
"This variable thermo keyword cannot be used between runs");
compute_elapsed();
dvalue = bivalue;
} else if (strcmp(word,"elaplong") == 0) {
if (update->whichflag == 0)
error->all(FLERR,
"This variable thermo keyword cannot be used between runs");
compute_elapsed_long();
dvalue = bivalue;
} else if (strcmp(word,"dt") == 0) {
compute_dt();
} else if (strcmp(word,"time") == 0) {
compute_time();
} else if (strcmp(word,"cpu") == 0) {
if (update->whichflag == 0)
error->all(FLERR,
"This variable thermo keyword cannot be used between runs");
compute_cpu();
} else if (strcmp(word,"tpcpu") == 0) {
if (update->whichflag == 0)
error->all(FLERR,
"This variable thermo keyword cannot be used between runs");
compute_tpcpu();
} else if (strcmp(word,"spcpu") == 0) {
if (update->whichflag == 0)
error->all(FLERR,
"This variable thermo keyword cannot be used between runs");
compute_spcpu();
} else if (strcmp(word,"cpuremain") == 0) {
if (update->whichflag == 0)
error->all(FLERR,
"This variable thermo keyword cannot be used between runs");
compute_cpuremain();
} else if (strcmp(word,"part") == 0) {
compute_part();
dvalue = ivalue;
} else if (strcmp(word,"timeremain") == 0) {
compute_timeremain();
} else if (strcmp(word,"atoms") == 0) {
compute_atoms();
dvalue = bivalue;
} else if (strcmp(word,"bonds") == 0) {
compute_bonds();
dvalue = bivalue;
} else if (strcmp(word,"angles") == 0) {
compute_angles();
dvalue = bivalue;
} else if (strcmp(word,"dihedrals") == 0) {
compute_dihedrals();
dvalue = bivalue;
} else if (strcmp(word,"impropers") == 0) {
compute_impropers();
dvalue = bivalue;
} else if (strcmp(word,"temp") == 0) {
if (!temperature)
error->all(FLERR,"Thermo keyword in variable requires "
"thermo to use/init temp");
if (update->whichflag == 0) {
if (temperature->invoked_scalar != update->ntimestep)
error->all(FLERR,"Compute used in variable thermo keyword between runs "
"is not current");
} else if (!(temperature->invoked_flag & INVOKED_SCALAR)) {
temperature->compute_scalar();
temperature->invoked_flag |= INVOKED_SCALAR;
}
compute_temp();
} else if (strcmp(word,"press") == 0) {
if (!pressure)
error->all(FLERR,"Thermo keyword in variable requires "
"thermo to use/init press");
if (update->whichflag == 0) {
if (pressure->invoked_scalar != update->ntimestep)
error->all(FLERR,"Compute used in variable thermo keyword between runs "
"is not current");
} else if (!(pressure->invoked_flag & INVOKED_SCALAR)) {
pressure->compute_scalar();
pressure->invoked_flag |= INVOKED_SCALAR;
}
compute_press();
} else if (strcmp(word,"pe") == 0) {
if (!pe)
error->all(FLERR,
"Thermo keyword in variable requires thermo to use/init pe");
if (update->whichflag == 0) {
if (pe->invoked_scalar != update->ntimestep)
error->all(FLERR,"Compute used in variable thermo keyword between runs "
"is not current");
} else {
pe->compute_scalar();
pe->invoked_flag |= INVOKED_SCALAR;
}
compute_pe();
} else if (strcmp(word,"ke") == 0) {
if (!temperature)
error->all(FLERR,"Thermo keyword in variable requires "
"thermo to use/init temp");
if (update->whichflag == 0) {
if (temperature->invoked_scalar != update->ntimestep)
error->all(FLERR,"Compute used in variable thermo keyword between runs "
"is not current");
} else if (!(temperature->invoked_flag & INVOKED_SCALAR)) {
temperature->compute_scalar();
temperature->invoked_flag |= INVOKED_SCALAR;
}
compute_ke();
} else if (strcmp(word,"etotal") == 0) {
if (!pe)
error->all(FLERR,
"Thermo keyword in variable requires thermo to use/init pe");
if (update->whichflag == 0) {
if (pe->invoked_scalar != update->ntimestep)
error->all(FLERR,"Compute used in variable thermo keyword between runs "
"is not current");
} else {
pe->compute_scalar();
pe->invoked_flag |= INVOKED_SCALAR;
}
if (!temperature)
error->all(FLERR,"Thermo keyword in variable requires "
"thermo to use/init temp");
if (update->whichflag == 0) {
if (temperature->invoked_scalar != update->ntimestep)
error->all(FLERR,"Compute used in variable thermo keyword between runs "
"is not current");
} else if (!(temperature->invoked_flag & INVOKED_SCALAR)) {
temperature->compute_scalar();
temperature->invoked_flag |= INVOKED_SCALAR;
}
compute_etotal();
} else if (strcmp(word,"enthalpy") == 0) {
if (!pe)
error->all(FLERR,
"Thermo keyword in variable requires thermo to use/init pe");
if (update->whichflag == 0) {
if (pe->invoked_scalar != update->ntimestep)
error->all(FLERR,"Compute used in variable thermo keyword between runs "
"is not current");
} else {
pe->compute_scalar();
pe->invoked_flag |= INVOKED_SCALAR;
}
if (!temperature)
error->all(FLERR,"Thermo keyword in variable requires "
"thermo to use/init temp");
if (update->whichflag == 0) {
if (temperature->invoked_scalar != update->ntimestep)
error->all(FLERR,"Compute used in variable thermo keyword between runs "
"is not current");
} else if (!(temperature->invoked_flag & INVOKED_SCALAR)) {
temperature->compute_scalar();
temperature->invoked_flag |= INVOKED_SCALAR;
}
if (!pressure)
error->all(FLERR,"Thermo keyword in variable requires "
"thermo to use/init press");
if (update->whichflag == 0) {
if (pressure->invoked_scalar != update->ntimestep)
error->all(FLERR,"Compute used in variable thermo keyword between runs "
"is not current");
} else if (!(pressure->invoked_flag & INVOKED_SCALAR)) {
pressure->compute_scalar();
pressure->invoked_flag |= INVOKED_SCALAR;
}
compute_enthalpy();
} else if (strcmp(word,"evdwl") == 0) {
if (update->eflag_global != update->ntimestep)
error->all(FLERR,"Energy was not tallied on needed timestep");
if (!pe)
error->all(FLERR,
"Thermo keyword in variable requires thermo to use/init pe");
pe->invoked_flag |= INVOKED_SCALAR;
compute_evdwl();
} else if (strcmp(word,"ecoul") == 0) {
if (update->eflag_global != update->ntimestep)
error->all(FLERR,"Energy was not tallied on needed timestep");
if (!pe)
error->all(FLERR,
"Thermo keyword in variable requires thermo to use/init pe");
pe->invoked_flag |= INVOKED_SCALAR;
compute_ecoul();
} else if (strcmp(word,"epair") == 0) {
if (update->eflag_global != update->ntimestep)
error->all(FLERR,"Energy was not tallied on needed timestep");
if (!pe)
error->all(FLERR,
"Thermo keyword in variable requires thermo to use/init pe");
pe->invoked_flag |= INVOKED_SCALAR;
compute_epair();
} else if (strcmp(word,"ebond") == 0) {
if (update->eflag_global != update->ntimestep)
error->all(FLERR,"Energy was not tallied on needed timestep");
if (!pe)
error->all(FLERR,
"Thermo keyword in variable requires thermo to use/init pe");
pe->invoked_flag |= INVOKED_SCALAR;
compute_ebond();
} else if (strcmp(word,"eangle") == 0) {
if (update->eflag_global != update->ntimestep)
error->all(FLERR,"Energy was not tallied on needed timestep");
if (!pe)
error->all(FLERR,
"Thermo keyword in variable requires thermo to use/init pe");
pe->invoked_flag |= INVOKED_SCALAR;
compute_eangle();
} else if (strcmp(word,"edihed") == 0) {
if (update->eflag_global != update->ntimestep)
error->all(FLERR,"Energy was not tallied on needed timestep");
if (!pe)
error->all(FLERR,
"Thermo keyword in variable requires thermo to use/init pe");
pe->invoked_flag |= INVOKED_SCALAR;
compute_edihed();
} else if (strcmp(word,"eimp") == 0) {
if (update->eflag_global != update->ntimestep)
error->all(FLERR,"Energy was not tallied on needed timestep");
if (!pe)
error->all(FLERR,
"Thermo keyword in variable requires thermo to use/init pe");
pe->invoked_flag |= INVOKED_SCALAR;
compute_eimp();
} else if (strcmp(word,"emol") == 0) {
if (update->eflag_global != update->ntimestep)
error->all(FLERR,"Energy was not tallied on needed timestep");
if (!pe)
error->all(FLERR,
"Thermo keyword in variable requires thermo to use/init pe");
pe->invoked_flag |= INVOKED_SCALAR;
compute_emol();
} else if (strcmp(word,"elong") == 0) {
if (update->eflag_global != update->ntimestep)
error->all(FLERR,"Energy was not tallied on needed timestep");
if (!pe)
error->all(FLERR,
"Thermo keyword in variable requires thermo to use/init pe");
pe->invoked_flag |= INVOKED_SCALAR;
compute_elong();
} else if (strcmp(word,"etail") == 0) {
if (update->eflag_global != update->ntimestep)
error->all(FLERR,"Energy was not tallied on needed timestep");
compute_etail();
} else if (strcmp(word,"vol") == 0) compute_vol();
else if (strcmp(word,"density") == 0) compute_density();
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,"xy") == 0) compute_xy();
else if (strcmp(word,"xz") == 0) compute_xz();
else if (strcmp(word,"yz") == 0) compute_yz();
else if (strcmp(word,"xlat") == 0) compute_xlat();
else if (strcmp(word,"ylat") == 0) compute_ylat();
else if (strcmp(word,"zlat") == 0) compute_zlat();
else if (strcmp(word,"pxx") == 0) {
if (!pressure)
error->all(FLERR,"Thermo keyword in variable requires "
"thermo to use/init press");
if (update->whichflag == 0) {
if (pressure->invoked_vector != update->ntimestep)
error->all(FLERR,"Compute used in variable thermo keyword between runs "
"is not current");
} else if (!(pressure->invoked_flag & INVOKED_VECTOR)) {
pressure->compute_vector();
pressure->invoked_flag |= INVOKED_VECTOR;
}
compute_pxx();
} else if (strcmp(word,"pyy") == 0) {
if (!pressure)
error->all(FLERR,"Thermo keyword in variable requires "
"thermo to use/init press");
if (update->whichflag == 0) {
if (pressure->invoked_vector != update->ntimestep)
error->all(FLERR,"Compute used in variable thermo keyword between runs "
"is not current");
} else if (!(pressure->invoked_flag & INVOKED_VECTOR)) {
pressure->compute_vector();
pressure->invoked_flag |= INVOKED_VECTOR;
}
compute_pyy();
} else if (strcmp(word,"pzz") == 0) {
if (!pressure)
error->all(FLERR,"Thermo keyword in variable requires "
"thermo to use/init press");
if (update->whichflag == 0) {
if (pressure->invoked_vector != update->ntimestep)
error->all(FLERR,"Compute used in variable thermo keyword between runs "
"is not current");
} else if (!(pressure->invoked_flag & INVOKED_VECTOR)) {
pressure->compute_vector();
pressure->invoked_flag |= INVOKED_VECTOR;
}
compute_pzz();
} else if (strcmp(word,"pxy") == 0) {
if (!pressure)
error->all(FLERR,"Thermo keyword in variable requires "
"thermo to use/init press");
if (update->whichflag == 0) {
if (pressure->invoked_vector != update->ntimestep)
error->all(FLERR,"Compute used in variable thermo keyword between runs "
"is not current");
} else if (!(pressure->invoked_flag & INVOKED_VECTOR)) {
pressure->compute_vector();
pressure->invoked_flag |= INVOKED_VECTOR;
}
compute_pxy();
} else if (strcmp(word,"pxz") == 0) {
if (!pressure)
error->all(FLERR,"Thermo keyword in variable requires "
"thermo to use/init press");
if (update->whichflag == 0) {
if (pressure->invoked_vector != update->ntimestep)
error->all(FLERR,"Compute used in variable thermo keyword between runs "
"is not current");
} else if (!(pressure->invoked_flag & INVOKED_VECTOR)) {
pressure->compute_vector();
pressure->invoked_flag |= INVOKED_VECTOR;
}
compute_pxz();
} else if (strcmp(word,"pyz") == 0) {
if (!pressure)
error->all(FLERR,"Thermo keyword in variable requires "
"thermo to use/init press");
if (update->whichflag == 0) {
if (pressure->invoked_vector != update->ntimestep)
error->all(FLERR,"Compute used in variable thermo keyword between runs "
"is not current");
} else if (!(pressure->invoked_flag & INVOKED_VECTOR)) {
pressure->compute_vector();
pressure->invoked_flag |= INVOKED_VECTOR;
}
compute_pyz();
}
else if (strcmp(word,"fmax") == 0) compute_fmax();
else if (strcmp(word,"fnorm") == 0) compute_fnorm();
else if (strcmp(word,"nbuild") == 0) {
compute_nbuild();
dvalue = bivalue;
} else if (strcmp(word,"ndanger") == 0) {
compute_ndanger();
dvalue = bivalue;
}
else if (strcmp(word,"cella") == 0) compute_cella();
else if (strcmp(word,"cellb") == 0) compute_cellb();
else if (strcmp(word,"cellc") == 0) compute_cellc();
else if (strcmp(word,"cellalpha") == 0) compute_cellalpha();
else if (strcmp(word,"cellbeta") == 0) compute_cellbeta();
else if (strcmp(word,"cellgamma") == 0) compute_cellgamma();
else return 1;
*answer = dvalue;
return 0;
}
/* ----------------------------------------------------------------------
extraction of Compute, Fix, Variable results
compute/fix are normalized by atoms if returning extensive value
variable value is not normalized (formula should normalize if desired)
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void Thermo::compute_compute()
{
int m = field2index[ifield];
Compute *compute = computes[m];
// check for out-of-range access if vector/array is variable length
if (compute_which[m] == SCALAR) {
dvalue = compute->scalar;
if (normflag && compute->extscalar) dvalue /= natoms;
} else if (compute_which[m] == VECTOR) {
if (compute->size_vector_variable && argindex1[ifield] >
compute->size_vector) dvalue = 0.0;
else dvalue = compute->vector[argindex1[ifield]-1];
if (normflag) {
if (compute->extvector == 0) return;
else if (compute->extvector == 1) dvalue /= natoms;
else if (compute->extlist[argindex1[ifield]-1]) dvalue /= natoms;
}
} else {
if (compute->size_array_rows_variable && argindex1[ifield] >
compute->size_array_rows) dvalue = 0.0;
else dvalue = compute->array[argindex1[ifield]-1][argindex2[ifield]-1];
if (normflag && compute->extarray) dvalue /= natoms;
}
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_fix()
{
int m = field2index[ifield];
Fix *fix = fixes[m];
if (argindex1[ifield] == 0) {
dvalue = fix->compute_scalar();
if (normflag && fix->extscalar) dvalue /= natoms;
} else if (argindex2[ifield] == 0) {
dvalue = fix->compute_vector(argindex1[ifield]-1);
if (normflag) {
if (fix->extvector == 0) return;
else if (fix->extvector == 1) dvalue /= natoms;
else if (fix->extlist[argindex1[ifield]-1]) dvalue /= natoms;
}
} else {
dvalue = fix->compute_array(argindex1[ifield]-1,argindex2[ifield]-1);
if (normflag && fix->extarray) dvalue /= natoms;
}
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_variable()
{
int iarg = argindex1[ifield];
if (iarg == 0)
dvalue = input->variable->compute_equal(variables[field2index[ifield]]);
else {
double *varvec;
int nvec =
input->variable->compute_vector(variables[field2index[ifield]],&varvec);
if (nvec < iarg) dvalue = 0.0;
else dvalue = varvec[iarg-1];
}
}
/* ----------------------------------------------------------------------
one method for every keyword thermo can output
called by compute() or evaluate_keyword()
compute will have already been called
set ivalue/dvalue/bivalue if value is int/double/bigint
customize a new keyword by adding a method
------------------------------------------------------------------------- */
void Thermo::compute_step()
{
bivalue = update->ntimestep;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_elapsed()
{
bivalue = update->ntimestep - update->firststep;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_elapsed_long()
{
bivalue = update->ntimestep - update->beginstep;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_dt()
{
dvalue = update->dt;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_time()
{
dvalue = update->atime + (update->ntimestep-update->atimestep)*update->dt;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_cpu()
{
if (firststep == 0) dvalue = 0.0;
else dvalue = timer->elapsed(Timer::TOTAL);
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_tpcpu()
{
double new_cpu;
double new_time = update->ntimestep * update->dt;
if (firststep == 0) {
new_cpu = 0.0;
dvalue = 0.0;
} else {
new_cpu = timer->elapsed(Timer::TOTAL);
double cpu_diff = new_cpu - last_tpcpu;
double time_diff = new_time - last_time;
if (time_diff > 0.0 && cpu_diff > 0.0) dvalue = time_diff/cpu_diff;
else dvalue = 0.0;
}
last_time = new_time;
last_tpcpu = new_cpu;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_spcpu()
{
double new_cpu;
int new_step = update->ntimestep;
if (firststep == 0) {
new_cpu = 0.0;
dvalue = 0.0;
} else {
new_cpu = timer->elapsed(Timer::TOTAL);
double cpu_diff = new_cpu - last_spcpu;
int step_diff = new_step - last_step;
if (cpu_diff > 0.0) dvalue = step_diff/cpu_diff;
else dvalue = 0.0;
}
last_step = new_step;
last_spcpu = new_cpu;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_cpuremain()
{
if (firststep == 0) dvalue = 0.0;
else dvalue = timer->elapsed(Timer::TOTAL) *
(update->laststep - update->ntimestep) /
(update->ntimestep - update->firststep);
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_part()
{
ivalue = universe->iworld;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_timeremain()
{
dvalue = timer->get_timeout_remain();
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_atoms()
{
bivalue = group->count_all();
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_temp()
{
dvalue = temperature->scalar;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_press()
{
dvalue = pressure->scalar;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_pe()
{
dvalue = pe->scalar;
if (normflag) dvalue /= natoms;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_ke()
{
dvalue = temperature->scalar;
dvalue *= 0.5 * temperature->dof * force->boltz;
if (normflag) dvalue /= natoms;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_etotal()
{
compute_pe();
double ke = temperature->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_density()
{
double mass = group->mass(0);
compute_vol();
dvalue = force->mv2d * mass/dvalue;
}
/* ---------------------------------------------------------------------- */
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_xy()
{
dvalue = domain->xy;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_xz()
{
dvalue = domain->xz;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_yz()
{
dvalue = domain->yz;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_xlat()
{
dvalue = domain->lattice->xlattice;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_ylat()
{
dvalue = domain->lattice->ylattice;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_zlat()
{
dvalue = domain->lattice->zlattice;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_bonds()
{
bivalue = atom->nbonds;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_angles()
{
bivalue = atom->nangles;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_dihedrals()
{
bivalue = atom->ndihedrals;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_impropers()
{
bivalue = atom->nimpropers;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_pxx()
{
dvalue = pressure->vector[0];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_pyy()
{
dvalue = pressure->vector[1];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_pzz()
{
dvalue = pressure->vector[2];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_pxy()
{
dvalue = pressure->vector[3];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_pxz()
{
dvalue = pressure->vector[4];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_pyz()
{
dvalue = pressure->vector[5];
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_fmax()
{
double **f = atom->f;
int nlocal = atom->nlocal;
double max = 0.0;
for (int i = 0; i < nlocal; i++) {
max = MAX(max,fabs(f[i][0]));
max = MAX(max,fabs(f[i][1]));
max = MAX(max,fabs(f[i][2]));
}
double maxall;
MPI_Allreduce(&max,&maxall,1,MPI_DOUBLE,MPI_MAX,world);
dvalue = maxall;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_fnorm()
{
double **f = atom->f;
int nlocal = atom->nlocal;
double dot = 0.0;
for (int i = 0; i < nlocal; i++)
dot += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
double dotall;
MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
dvalue = sqrt(dotall);
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_nbuild()
{
bivalue = neighbor->ncalls;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_ndanger()
{
bivalue = neighbor->ndanger;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_cella()
{
dvalue = domain->xprd;
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_cellb()
{
if (!domain->triclinic)
dvalue = domain->yprd;
else {
double* h = domain->h;
dvalue = sqrt(h[1]*h[1]+h[5]*h[5]);
}
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_cellc()
{
if (!domain->triclinic)
dvalue = domain->zprd;
else {
double* h = domain->h;
dvalue = sqrt(h[2]*h[2]+h[3]*h[3]+h[4]*h[4]);
}
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_cellalpha()
{
if (!domain->triclinic)
dvalue = 90.0;
else {
// Cos(alpha) = (xy.xz + ly.yz)/(b.c)
double* h = domain->h;
double cosalpha = (h[5]*h[4]+h[1]*h[3])/
sqrt((h[1]*h[1]+h[5]*h[5])*(h[2]*h[2]+h[3]*h[3]+h[4]*h[4]));
dvalue = acos(cosalpha)*180.0/MY_PI;
}
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_cellbeta()
{
if (!domain->triclinic)
dvalue = 90.0;
else {
// Cos(beta) = xz/c
double* h = domain->h;
double cosbeta = h[4]/sqrt(h[2]*h[2]+h[3]*h[3]+h[4]*h[4]);
dvalue = acos(cosbeta)*180.0/MY_PI;
}
}
/* ---------------------------------------------------------------------- */
void Thermo::compute_cellgamma()
{
if (!domain->triclinic)
dvalue = 90.0;
else {
// Cos(gamma) = xy/b
double* h = domain->h;
double cosgamma = h[5]/sqrt(h[1]*h[1]+h[5]*h[5]);
dvalue = acos(cosgamma)*180.0/MY_PI;
}
}
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