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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1119 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2007-11-02 20:25:11 +00:00
parent f12471d507
commit 6de4e59a38
28 changed files with 610 additions and 280 deletions
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139
src/thermo.cpp
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@ -111,14 +111,16 @@ Thermo::Thermo(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
temperature = NULL;
pressure = NULL;
pe = NULL;
rotate_dipole = NULL;
rotate_gran = NULL;
index_temp = index_press = index_drot = index_grot = -1;
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";
@ -131,7 +133,7 @@ Thermo::Thermo(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
parse_fields(line);
// create the requested compute styles
// temperature and pressure always exist b/c Output class created them
// temperature,pressure,pe always exist b/c Output class created them
if (index_drot >= 0) {
create_compute(id_drot,(char *) "rotate/dipole",NULL);
@ -247,6 +249,7 @@ void Thermo::init()
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];
}
@ -593,13 +596,12 @@ void Thermo::deallocate()
/* ----------------------------------------------------------------------
parse list of thermo keywords from str
set compute flags (temp, press, etc)
set compute flags (temp, press, pe, etc)
------------------------------------------------------------------------- */
void Thermo::parse_fields(char *str)
{
nfield = 0;
peflag = 0;
// customize a new keyword by adding to if statement
@ -622,39 +624,50 @@ void Thermo::parse_fields(char *str)
index_press = add_compute(id_press,0);
} else if (strcmp(word,"pe") == 0) {
addfield("PotEng",&Thermo::compute_pe,FLOAT);
peflag = 1;
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);
peflag = 1;
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);
@ -876,34 +889,78 @@ void Thermo::create_compute(char *id, char *cstyle, char *extra)
}
/* ----------------------------------------------------------------------
compute a single thermodyanmic value matching word to custom list
called when a variable is evaluated in input script
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
customize a new keyword by adding to if statement and error tests
------------------------------------------------------------------------- */
int Thermo::evaluate_keyword(char *word, double *answer)
{
// could do tests to insure user does not invoke variable at wrong time
// don't allow use of thermo keyword before first run
// since system is not setup (e.g. no forces have been called for energy)
// all keywords:
// if (domain->box_exist == 0)
// error->all("Variable equal keyword used before simulation box defined");
// keywords except step,atoms,vol,ly,ly,lz
// if (update->first_update == 0)
// error->all("Variable equal keyword used before initial run");
// if (update->ntimestep != output->next_thermo && me == 0)
// error->warning("Variable equal keyword used with non-current thermo");
// keywords that require Compute objects like T,P
// ptrs like temperature will not be set if init() hasn't been called
// Compute objects will not exist if thermo style isn't using them
if (update->first_update == 0)
error->all("Variable equal thermo keyword used before initial run");
// toggle thermoflag off/on so inidividual compute routines don't assume
// they are being called from compute() which pre-calls Compute objects
// check if Compute pointers exist for keywords that need them
// error if thermo style does not use the Compute
// all energy-related keywords require PE, even if they don't call it
// this is b/c Verlet::eflag is triggered by compute_pe invocation schedule
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 unused by thermo");
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 unused by thermo");
if (strcmp(word,"pe") == 0 || strcmp(word,"etotal") == 0 ||
strcmp(word,"enthalpy") == 0 || 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 unused by thermo");
if (strcmp(word,"drot") == 0)
if (!rotate_dipole)
error->all("Variable uses compute via thermo keyword unused by thermo");
if (strcmp(word,"grot") == 0)
if (!rotate_gran)
error->all("Variable uses compute via thermo keyword unused by thermo");
// 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)
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;
@ -914,12 +971,13 @@ int Thermo::evaluate_keyword(char *word, double *answer)
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();
@ -930,7 +988,7 @@ int Thermo::evaluate_keyword(char *word, double *answer)
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();
@ -949,7 +1007,7 @@ int Thermo::evaluate_keyword(char *word, double *answer)
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();
@ -1049,33 +1107,9 @@ void Thermo::compute_press()
void Thermo::compute_pe()
{
double tmp = 0.0;
if (force->pair) tmp += force->pair->eng_vdwl + force->pair->eng_coul;
if (force->bond) tmp += force->bond->eng_vdwl;
if (force->dihedral)
tmp += force->dihedral->eng_vdwl + force->dihedral->eng_coul;
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 (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 (modify->n_thermo_energy) dvalue += modify->thermo_energy();
if (thermoflag) dvalue = pe->scalar;
else dvalue = pe->compute_scalar();
if (normflag) dvalue /= natoms;
// also store PE in potential_energy so other classes can grab it
potential_energy = dvalue;
}
/* ---------------------------------------------------------------------- */
@ -1093,6 +1127,7 @@ void Thermo::compute_ke()
void Thermo::compute_etotal()
{
compute_pe();
double ke;
if (thermoflag) ke = temperature->scalar;
else ke = temperature->compute_scalar();