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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@254 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2007-01-30 00:22:05 +00:00
parent 9cdbeaf9f2
commit 209f169cbc
414 changed files with 6935 additions and 10462 deletions
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213
src/fix_nph.cpp
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@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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
@ -24,20 +24,22 @@
#include "comm.h"
#include "output.h"
#include "modify.h"
#include "compute.h"
#include "kspace.h"
#include "update.h"
#include "respa.h"
#include "temperature.h"
#include "pressure.h"
#include "domain.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
FixNPH::FixNPH(int narg, char **arg) : Fix(narg, arg)
FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 4) error->all("Illegal fix nph command");
@ -125,19 +127,6 @@ FixNPH::FixNPH(int narg, char **arg) : Fix(narg, arg)
if (p_flag[2] && domain->zperiodic == 0)
error->all("Cannot fix nph on a non-periodic dimension");
// create a new temperature full style with fix ID and group all
// pressure is always global (group all) and thus its
// KE/temperature contribution should use group all
char **newarg = new char*[3];
newarg[0] = id;
newarg[1] = "all";
newarg[2] = "full";
force->add_temp(3,newarg,1);
delete [] newarg;
temperature = force->find_temp(id);
// convert input periods to frequencies
if ((p_flag[0] && p_period[0] <= 0.0) ||
@ -149,9 +138,44 @@ FixNPH::FixNPH(int narg, char **arg) : Fix(narg, arg)
if (p_flag[1]) p_freq[1] = 1.0 / p_period[1];
if (p_flag[2]) p_freq[2] = 1.0 / p_period[2];
// pressure init
// create a new compute temp style
// id = fix-ID + temp
// compute group = all since pressure is always global (group all)
// and thus its KE/temperature contribution should use group all
int n = strlen(id) + 6;
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = "all";
newarg[2] = "temp";
modify->add_compute(3,newarg);
delete [] newarg;
tflag = 1;
// create a new compute pressure style
// id = fix-ID + press, compute group = all
// pass id_temp as 4th arg to pressure constructor
n = strlen(id) + 7;
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = "all";
newarg[2] = "pressure";
newarg[3] = id_temp;
modify->add_compute(4,newarg);
delete [] newarg;
pflag = 1;
// Nose/Hoover pressure init
pressure = force->pressure;
omega[0] = omega[1] = omega[2] = 0.0;
omega_dot[0] = omega_dot[1] = omega_dot[2] = 0.0;
@ -164,6 +188,13 @@ FixNPH::FixNPH(int narg, char **arg) : Fix(narg, arg)
FixNPH::~FixNPH()
{
delete [] rfix;
// delete temperature and pressure if fix created them
if (tflag) modify->delete_compute(id_temp);
if (pflag) modify->delete_compute(id_press);
delete [] id_temp;
delete [] id_press;
}
/* ---------------------------------------------------------------------- */
@ -173,7 +204,7 @@ int FixNPH::setmask()
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= THERMO;
mask |= THERMO_ENERGY;
mask |= INITIAL_INTEGRATE_RESPA;
mask |= FINAL_INTEGRATE_RESPA;
return mask;
@ -183,8 +214,27 @@ int FixNPH::setmask()
void FixNPH::init()
{
if (atom->mass_require == 0)
error->all("Cannot use fix nph with no per-type mass defined");
if (atom->mass == NULL)
error->all("Cannot use fix nph without per-type mass defined");
// set temperature and pressure ptrs
// set ptemperature only if pressure's id_pre is not id_temp
int icompute = modify->find_compute(id_temp);
if (icompute < 0) error->all("Temp ID for fix nph does not exist");
temperature = modify->compute[icompute];
icompute = modify->find_compute(id_press);
if (icompute < 0) error->all("Press ID for fix nph does not exist");
pressure = modify->compute[icompute];
if (strcmp(id_temp,pressure->id_pre) == 0) ptemperature = NULL;
else {
icompute = modify->find_compute(pressure->id_pre);
if (icompute < 0)
error->all("Temp ID of press ID for fix nph does not exist");
ptemperature = modify->compute[icompute];
}
// set timesteps and frequencies
// Nkt = initial value for piston mass and energy conservation
@ -202,7 +252,8 @@ void FixNPH::init()
nktv2p = force->nktv2p;
vol0 = domain->xprd * domain->yprd * domain->zprd;
double t_initial = temperature->compute();
temperature->init(); // not yet called by Modify::init()
double t_initial = temperature->compute_scalar();
if (t_initial == 0.0) {
if (strcmp(update->unit_style,"lj") == 0) t_initial = 1.0;
else t_initial = 300.0;
@ -246,12 +297,19 @@ void FixNPH::init()
void FixNPH::setup()
{
p_target[0] = p_start[0]; // used by thermo_compute()
p_target[0] = p_start[0]; // used by thermo()
p_target[1] = p_start[1];
p_target[2] = p_start[2];
double t_current = temperature->compute();
pressure->compute(temperature);
double tmp = temperature->compute_scalar();
if (press_couple == 0) {
if (ptemperature) tmp = ptemperature->compute_scalar();
tmp = pressure->compute_scalar();
} else {
temperature->compute_vector();
if (ptemperature) ptemperature->compute_vector();
pressure->compute_vector();
}
couple();
}
@ -352,8 +410,15 @@ void FixNPH::final_integrate()
// compute new pressure
double t_current = temperature->compute();
pressure->compute(temperature);
double tmp = temperature->compute_scalar();
if (press_couple == 0) {
if (ptemperature) tmp = ptemperature->compute_scalar();
tmp = pressure->compute_scalar();
} else {
temperature->compute_vector();
if (ptemperature) ptemperature->compute_vector();
pressure->compute_vector();
}
couple();
// update omega_dot
@ -509,26 +574,26 @@ void FixNPH::final_integrate_respa(int ilevel)
void FixNPH::couple()
{
double *p_tensor = pressure->p_tensor;
double *tensor = pressure->vector;
if (press_couple == 0)
p_current[0] = p_current[1] = p_current[2] = pressure->p_total;
p_current[0] = p_current[1] = p_current[2] = pressure->scalar;
else if (press_couple == 1) {
double ave = 0.5 * (p_tensor[0] + p_tensor[1]);
double ave = 0.5 * (tensor[0] + tensor[1]);
p_current[0] = p_current[1] = ave;
p_current[2] = p_tensor[2];
p_current[2] = tensor[2];
} else if (press_couple == 2) {
double ave = 0.5 * (p_tensor[1] + p_tensor[2]);
double ave = 0.5 * (tensor[1] + tensor[2]);
p_current[1] = p_current[2] = ave;
p_current[0] = p_tensor[0];
p_current[0] = tensor[0];
} else if (press_couple == 3) {
double ave = 0.5 * (p_tensor[0] + p_tensor[2]);
double ave = 0.5 * (tensor[0] + tensor[2]);
p_current[0] = p_current[2] = ave;
p_current[1] = p_tensor[1];
p_current[1] = tensor[1];
} if (press_couple == 4) {
p_current[0] = p_tensor[0];
p_current[1] = p_tensor[1];
p_current[2] = p_tensor[2];
p_current[0] = tensor[0];
p_current[1] = tensor[1];
p_current[2] = tensor[2];
}
}
@ -662,13 +727,51 @@ int FixNPH::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"temp") == 0) {
if (narg < 2) error->all("Illegal fix_modify command");
temperature = force->find_temp(arg[1]);
if (temperature == NULL)
error->all("Could not find fix_modify temperature ID");
if (tflag) {
modify->delete_compute(id_temp);
tflag = 0;
}
delete [] id_temp;
int n = strlen(arg[1]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0) error->all("Could not find fix_modify temp ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all("Fix_modify temp ID does not compute temperature");
if (temperature->igroup != 0 && comm->me == 0)
error->warning("Temperature for NPH is not for group all");
if (strcmp(temperature->style,"region") == 0 && comm->me == 0)
error->warning("Temperature for NPH is style region");
// reset id_pre of pressure to new temp ID
icompute = modify->find_compute(id_press);
if (icompute < 0) error->all("Press ID for fix npt does not exist");
delete [] modify->compute[icompute]->id_pre;
modify->compute[icompute]->id_pre = new char[n];
strcpy(modify->compute[icompute]->id_pre,id_temp);
return 2;
} else if (strcmp(arg[0],"press") == 0) {
if (narg < 2) error->all("Illegal fix_modify command");
if (pflag) {
modify->delete_compute(id_press);
pflag = 0;
}
delete [] id_press;
int n = strlen(arg[1]) + 1;
id_press = new char[n];
strcpy(id_press,arg[1]);
int icompute = modify->find_compute(id_press);
if (icompute < 0) error->all("Could not find fix_modify press ID");
pressure = modify->compute[icompute];
if (pressure->pressflag == 0)
error->all("Fix_modify press ID does not compute pressure");
return 2;
}
return 0;
@ -676,25 +779,17 @@ int FixNPH::modify_param(int narg, char **arg)
/* ---------------------------------------------------------------------- */
int FixNPH::thermo_fields(int n, int *flags, char **keywords)
{
if (n == 0) return 1;
flags[0] = 3;
strcpy(keywords[0],"EngNPH");
return 1;
}
/* ---------------------------------------------------------------------- */
int FixNPH::thermo_compute(double *values)
double FixNPH::thermo(int n)
{
double volume = domain->xprd * domain->yprd * domain->zprd;
int pdim = p_flag[0] + p_flag[1] + p_flag[2];
values[0] = 0.0;
double energy = 0.0;
for (int i = 0; i < 3; i++)
if (p_freq[i] > 0.0)
values[0] += 0.5*nkt*omega_dot[i]*omega_dot[i] /
energy += 0.5*nkt*omega_dot[i]*omega_dot[i] /
(p_freq[i]*p_freq[i]) + p_target[i]*(volume-vol0) / (pdim*nktv2p);
return 1;
if (n == 0) return energy;
else return 0.0;
}