ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

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

Browse Source
This commit is contained in:
sjplimp
2007-01-30 00:22:05 +00:00
parent 9cdbeaf9f2
commit 209f169cbc
414 changed files with 6935 additions and 10462 deletions
Download Patch File Download Diff File Expand all files Collapse all files

99
src/velocity.cpp
View File

@ -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
@ -22,23 +22,19 @@
#include "domain.h"
#include "lattice.h"
#include "force.h"
#include "temperature.h"
#include "temp_full.h"
#include "modify.h"
#include "compute.h"
#include "compute_temp.h"
#include "random_park.h"
#include "group.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#define CREATE 1
#define SET 2
#define SCALE 3
#define RAMP 4
#define ZERO 5
using namespace LAMMPS_NS;
#define ALL 1
#define LOCAL 2
#define GEOM 3
enum{CREATE,SET,SCALE,RAMP,ZERO};
enum{ALL,LOCAL,GEOM};
#define WARMUP 100
#define SMALL 0.001
@ -48,6 +44,10 @@
/* ---------------------------------------------------------------------- */
Velocity::Velocity(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void Velocity::command(int narg, char **arg)
{
// require atom masses to all be set
@ -77,7 +77,7 @@ void Velocity::command(int narg, char **arg)
// set defaults
tempwhich = -1;
temperature = NULL;
dist_flag = 0;
sum_flag = 0;
momentum_flag = 1;
@ -126,24 +126,24 @@ void Velocity::create(int narg, char **arg)
double t_desired = atof(arg[0]);
int seed = atoi(arg[1]);
// if tempwhich = -1, create a new temperature full style with the vel group
// else use pre-defined temperature
// if temperature = NULL, create a new ComputeTemp with the velocity group
Temperature *temperature;
if (tempwhich == -1) {
int tflag = 0;
if (temperature == NULL) {
char **arg = new char*[3];
arg[0] = "temp";
arg[0] = "velocity_temp";
arg[1] = group->names[igroup];
arg[2] = "full";
temperature = new TempFull(3,arg);
arg[2] = "temp";
temperature = new ComputeTemp(lmp,3,arg);
tflag = 1;
delete [] arg;
} else temperature = force->templist[tempwhich];
}
// initialize temperature computation
// warn if groups don't match
if (igroup != temperature->igroup && comm->me == 0)
error->warning("Mismatch between velocity and temperature groups");
error->warning("Mismatch between velocity and compute groups");
temperature->init();
// store a copy of current velocities
@ -177,7 +177,6 @@ void Velocity::create(int narg, char **arg)
double *mass = atom->mass;
double *rmass = atom->rmass;
int dimension = force->dimension;
int mass_require = atom->mass_require;
int m;
double vx,vy,vz,factor;
@ -195,7 +194,7 @@ void Velocity::create(int narg, char **arg)
atom->map_set();
}
random = new RanPark(seed);
random = new RanPark(lmp,seed);
if (atom->tag_enable == 0)
error->all("Cannot use velocity create loop all unless atoms have IDs");
@ -237,7 +236,7 @@ void Velocity::create(int narg, char **arg)
m = atom->map(i);
if (m >= 0 && m < nlocal) {
if (mask[m] & groupbit) {
if (mass_require) factor = 1.0/sqrt(mass[type[m]]);
if (mass) factor = 1.0/sqrt(mass[type[m]]);
else factor = 1.0/sqrt(rmass[m]);
v[m][0] = vx * factor;
v[m][1] = vy * factor;
@ -255,7 +254,7 @@ void Velocity::create(int narg, char **arg)
}
} else if (loop_flag == LOCAL) {
random = new RanPark(seed + comm->me);
random = new RanPark(lmp,seed + comm->me);
for (i = 0; i < WARMUP; i++) random->uniform();
for (i = 0; i < nlocal; i++) {
@ -269,7 +268,7 @@ void Velocity::create(int narg, char **arg)
vy = random->gaussian();
vz = random->gaussian();
}
if (mass_require) factor = 1.0/sqrt(mass[type[i]]);
if (mass) factor = 1.0/sqrt(mass[type[i]]);
else factor = 1.0/sqrt(rmass[i]);
v[i][0] = vx * factor;
v[i][1] = vy * factor;
@ -279,13 +278,13 @@ void Velocity::create(int narg, char **arg)
}
} else if (loop_flag == GEOM) {
random = new RanPark(seed);
random = new RanPark(lmp,seed);
double **x = atom->x;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
triple(x[i][0],x[i][1],x[i][2],&vx,&vy,&vz,seed,random);
if (mass_require) factor = 1.0/sqrt(mass[type[i]]);
if (mass) factor = 1.0/sqrt(mass[type[i]]);
else factor = 1.0/sqrt(rmass[i]);
v[i][0] = vx * factor;
v[i][1] = vy * factor;
@ -302,7 +301,7 @@ void Velocity::create(int narg, char **arg)
// scale temp to desired value
double t = temperature->compute();
double t = temperature->compute_scalar();
rescale(t,t_desired);
// if sum_flag set, add back in previous velocities
@ -322,7 +321,7 @@ void Velocity::create(int narg, char **arg)
memory->destroy_2d_double_array(vhold);
delete random;
if (tempwhich == -1) delete temperature;
if (tflag) delete temperature;
}
/* ---------------------------------------------------------------------- */
@ -376,34 +375,34 @@ void Velocity::scale(int narg, char **arg)
{
double t_desired = atof(arg[0]);
// if tempwhich = -1, create a new temperature full style with the vel group
// else use pre-defined temperature
// if temperature = NULL, create a new ComputeTemp with the velocity group
Temperature *temperature;
if (tempwhich == -1) {
int tflag = 0;
if (temperature == NULL) {
char **arg = new char*[3];
arg[0] = "temp";
arg[0] = "velocity_temp";
arg[1] = group->names[igroup];
arg[2] = "full";
temperature = new TempFull(3,arg);
arg[2] = "temp";
temperature = new ComputeTemp(lmp,3,arg);
tflag = 1;
delete [] arg;
} else temperature = force->templist[tempwhich];
}
// initialize temperature computation
// warn if groups don't match
if (igroup != temperature->igroup && comm->me == 0)
error->warning("Mismatch between velocity and temperature groups");
error->warning("Mismatch between velocity and compute groups");
temperature->init();
// scale temp to desired value
double t = temperature->compute();
double t = temperature->compute_scalar();
rescale(t,t_desired);
// if temperature was created, delete it
if (tempwhich == -1) delete temperature;
if (tflag) delete temperature;
}
/* ----------------------------------------------------------------------
@ -542,7 +541,7 @@ void Velocity::zero_momentum()
void Velocity::zero_rotation()
{
int i,j;
int i;
// cannot have 0 atoms in group
@ -556,7 +555,7 @@ void Velocity::zero_rotation()
group->xcm(igroup,masstotal,xcm);
group->angmom(igroup,xcm,angmom);
group->inertia(igroup,xcm,inertia);
group->omega(igroup,angmom,inertia,omega);
group->omega(angmom,inertia,omega);
// adjust velocities to zero omega
// vnew_i = v_i - w x r_i
@ -624,10 +623,14 @@ void Velocity::options(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+2 > narg) error->all("Illegal velocity command");
for (tempwhich = 0; tempwhich < force->ntemp; tempwhich++)
if (strcmp(arg[iarg+1],force->templist[tempwhich]->id) == 0) break;
if (tempwhich == force->ntemp)
error->all("Could not find velocity temperature ID");
int icompute;
for (icompute = 0; icompute < modify->ncompute; icompute++)
if (strcmp(arg[iarg+1],modify->compute[icompute]->id) == 0) break;
if (icompute == modify->ncompute)
error->all("Could not find velocity temp ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all("Velocity temp ID does not compute temperature");
iarg += 2;
} else if (strcmp(arg[iarg],"loop") == 0) {
if (iarg+2 > narg) error->all("Illegal velocity command");