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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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101
src/fix_nvt.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
@ -25,12 +25,16 @@
#include "group.h"
#include "update.h"
#include "respa.h"
#include "temperature.h"
#include "modify.h"
#include "compute.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixNVT::FixNVT(int narg, char **arg) : Fix(narg, arg)
FixNVT::FixNVT(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 6) error->all("Illegal fix nvt command");
@ -52,18 +56,33 @@ FixNVT::FixNVT(int narg, char **arg) : Fix(narg, arg)
if (t_period <= 0.0) error->all("Fix nvt period must be > 0.0");
t_freq = 1.0 / t_period;
// create a new temperature full style with fix ID and fix group
eta = eta_dot = 0.0;
char **newarg = new char*[3];
newarg[0] = id;
newarg[1] = group->names[igroup];
newarg[2] = "full";
force->add_temp(3,newarg,1);
delete [] newarg;
// create a new compute temp style
// id = fix-ID + temp, compute group = fix group
temperature = force->find_temp(id);
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] = group->names[igroup];
newarg[2] = "temp";
modify->add_compute(3,newarg);
delete [] newarg;
tflag = 1;
}
/* ---------------------------------------------------------------------- */
FixNVT::~FixNVT()
{
// delete temperature if fix created it
if (tflag) modify->delete_compute(id_temp);
delete [] id_temp;
}
/* ---------------------------------------------------------------------- */
@ -73,7 +92,7 @@ int FixNVT::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;
@ -83,8 +102,14 @@ int FixNVT::setmask()
void FixNVT::init()
{
if (atom->mass_require == 0)
error->all("Cannot use fix nvt with no per-type mass defined");
if (atom->mass == NULL)
error->all("Cannot use fix nvt without per-type mass defined");
int icompute = modify->find_compute(id_temp);
if (icompute < 0) error->all("Temp ID for fix nvt does not exist");
temperature = modify->compute[icompute];
// set timesteps and frequencies
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
@ -102,8 +127,8 @@ void FixNVT::init()
void FixNVT::setup()
{
t_target = t_start; // used by thermo_compute()
t_current = temperature->compute();
t_target = t_start; // used by thermo()
t_current = temperature->compute_scalar();
}
/* ---------------------------------------------------------------------- */
@ -173,7 +198,7 @@ void FixNVT::final_integrate()
// compute current T
t_current = temperature->compute();
t_current = temperature->compute_scalar();
// update eta_dot
@ -332,13 +357,23 @@ int FixNVT::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 != igroup && comm->me == 0)
error->warning("Group for fix_modify temp != fix group");
if (strcmp(temperature->style,"region") == 0 && comm->me == 0)
error->warning("Temperature for NVT is style region");
return 2;
}
return 0;
@ -353,19 +388,11 @@ void FixNVT::reset_target(double t_new)
/* ---------------------------------------------------------------------- */
int FixNVT::thermo_fields(int n, int *flags, char **keywords)
{
if (n == 0) return 1;
flags[0] = 3;
strcpy(keywords[0],"EngNVT");
return 1;
}
/* ---------------------------------------------------------------------- */
int FixNVT::thermo_compute(double *values)
double FixNVT::thermo(int n)
{
double ke = temperature->dof * force->boltz * t_target;
values[0] = ke * (eta + 0.5*eta_dot*eta_dot/(t_freq*t_freq));
return 1;
double energy = ke * (eta + 0.5*eta_dot*eta_dot/(t_freq*t_freq));
if (n == 0) return energy;
else return 0.0;
}