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lammps/src/USER-GLE/fix_gle.cpp
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fix_gle.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Michele Ceriotti (Oxford), Joe Morrone (Columbia)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "fix_gle.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "domain.h"
#include "region.h"
#include "respa.h"
#include "comm.h"
#include "input.h"
#include "variable.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
#include "group.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{NOBIAS,BIAS};
enum{CONSTANT,EQUAL,ATOM};
//#define GLE_DEBUG 1
/* syntax for fix_gle:
* fix_gle nfix id-group gle ns amatrix [temp|cmatrix] seed
*
* */
/* ---------------------------------------------------------------------- */
namespace GLE {
/*!!MC!! here begins the GLE stuff*/
#define midx(n,i,j) ((i)*(n)+(j))
//"stabilized" cholesky decomposition. does a LDL^t decomposition, then sets to zero the negative diagonal elements and gets MM^t
void StabCholesky(unsigned long n, const double* MMt, double* M)
{
double L[n*n], D[n];
unsigned long i,j,k;
for(i=0; i<n; ++i) D[i]=0.;
for(i=0; i<n*n; ++i) L[i]=0.;
for(i=0; i<n; ++i)
{
L[midx(n,i,i)]=1.;
for (j=0; j<i; j++)
{
printf("%d %d\n", i,j);
L[midx(n,i,j)]=MMt[midx(n,i,j)];
for (k=0; k<j; ++k) L[midx(n,i,j)]-=L[midx(n,i,k)]*L[midx(n,j,k)]*D[k];
if (D[j]!=0.) L[midx(n,i,j)]/=D[j];
else L[midx(n,i,j)]=0.0;
}
D[i]=MMt[midx(n,i,i)];
for (k=0; k<i; ++k) D[i]-=L[midx(n,i,k)]*L[midx(n,i,k)]*D[k];
}
for(i=0; i<n; ++i) D[i]=(D[i]>0.?sqrt(D[i]):0.);
for(i=0; i<n; ++i) for (j=0; j<n; j++) M[midx(n,i,j)]=L[midx(n,i,j)]*D[j];
}
void MyMult(unsigned long n, unsigned long m, unsigned long r, const double* A, const double* B, double* C, double cf=0.0)
{
// !! TODO !! should probably call BLAS (or check if some efficient matrix-matrix multiply is implemented somewhere in LAMMPS)
// (rows x cols) :: A is n x r, B is r x m, C is n x m
unsigned long i,j,k; double *cij;
for (i=0; i<n; ++i)
for (j=0; j<m; ++j)
{
cij=&C[midx(m,i,j)]; *cij *= cf;
for (k=0; k<r; ++k) *cij+=A[midx(r,i,k)]*B[midx(m,k,j)];
}
}
void MyTrans(unsigned long n, const double* A, double* AT)
{
for (unsigned long i=0; i<n; ++i) for (unsigned long j=0; j<n; ++j) AT[j*n+i]=A[i*n+j];
}
void MyPrint(unsigned long n, const double* A)
{
for (unsigned long k=0; k<n*n; ++k) { printf("%10.5e ", A[k]); if ((k+1)%n==0) printf("\n");}
}
//matrix exponential by scaling and squaring.
void MatrixExp(unsigned long n, const double* M, double* EM, unsigned long j=8, unsigned long k=8)
{
double tc[j+1], SM[n*n], TMP[n*n];
double onetotwok=pow(0.5,1.0*k);
tc[0]=1;
for (int i=0; i<j; ++i) tc[i+1]=tc[i]/(i+1.0);
for (int i=0; i<n*n; ++i) { SM[i]=M[i]*onetotwok; EM[i]=0.0; TMP[i]=0.0; }
for (int i=0; i<n; ++i) EM[midx(n,i,i)]=tc[j];
//taylor exp of scaled matrix
for (int p=j-1; p>=0; p--)
{
MyMult(n, n, n, SM, EM, TMP); for (int i=0; i<n*n; ++i) EM[i]=TMP[i];
for (int i=0; i<n; ++i) EM[midx(n,i,i)]+=tc[p];
}
for (int p=0; p<k; p++)
{ MyMult(n, n, n, EM, EM, TMP); for (int i=0; i<n*n; ++i) EM[i]=TMP[i]; }
}
}
FixGLE::FixGLE(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 5) error->all(FLERR,"Illegal fix gle command");
ns = atof(arg[3]);
if (ns>atom->ns) error->all(FLERR, "Atom kind has not enough GLE slots");
A = new double[(ns+1)*(ns+1)];
C = new double[(ns+1)*(ns+1)];
T=S=gle_tmp=gle_rnd=NULL; gle_buff=0;
// LOADS A matrix
printf("Reading A from %s\n", arg[4]);
FILE* fgle = fopen(arg[4], "r");
if (fgle==NULL) error->all(FLERR, "Cannot open A matrix GLE input");
for (int i=0; i<(ns+1)*(ns+1); ++i) //ASSUMES A IS IN THE CORRECT INVERSE TIME UNITS
if (!fscanf(fgle,"%lf",&(A[i]))) error->all(FLERR, "Cannot read A matrix GLE input");
fclose(fgle);
temp=atof(arg[5]);
if (temp==0.0)
{
printf("Reading C from %s\n", arg[5]);
fgle = fopen(arg[5], "r");
if (fgle==NULL) error->all(FLERR, "Cannot open C matrix GLE input");
for (int i=0; i<(ns+1)*(ns+1); ++i) //ASSUMES C IS IN THE CORRECT TEMPERATURE UNITS
if (!fscanf(fgle,"%lf",&(C[i]))) error->all(FLERR, "Cannot read C matrix GLE input");
}
else
{
for (int i=0; i<(ns+1)*(ns+1); ++i) C[i]=0.0;
for (int i=0; i<(ns+1)*(ns+1); i+=(ns+2)) C[i]=temp*force->boltz/force->mvv2e;
}
#ifdef GLE_DEBUG
printf("A Matrix\n");
GLE::MyPrint(ns+1,A);
printf("C Matrix\n");
GLE::MyPrint(ns+1,C);
#endif
tau=10;
int seed = atoi(arg[6]);
// initialize Marsaglia RNG with processor-unique seed
// NB: this means runs will not be the same with different numbers of processors
random = new RanMars(lmp,seed + comm->me);
if (seed <= 0) error->all(FLERR,"Illegal fix gle command");
// allocate per-type arrays for mass-scaling
sqrt_m = new double[atom->ntypes+1];
energy = 0.0;
}
/* ---------------------------------------------------------------------- */
FixGLE::~FixGLE()
{
delete random;
delete [] sqrt_m;
delete [] A; delete [] C; delete [] S; delete [] T;
delete [] gle_tmp; delete [] gle_rnd;
}
/* ---------------------------------------------------------------------- */
int FixGLE::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= INITIAL_INTEGRATE_RESPA;
mask |= FINAL_INTEGRATE_RESPA;
mask |= THERMO_ENERGY;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixGLE::init()
{
dogle = 1;
dorattle = 1;
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
// compute Langevin terms
T = new double[(ns+1)*(ns+1)]; S = new double[(ns+1)*(ns+1)];
double *tmp1 = new double[(ns+1)*(ns+1)], *tmp2 = new double[(ns+1)*(ns+1)];
for (int i=0; i<(ns+1)*(ns+1); ++i) { tmp1[i]=-A[i]*update->dt*0.5; tmp2[i]=S[i]=0.0; }
GLE::MatrixExp(ns+1,tmp1,T);
GLE::MyMult(ns+1,ns+1,ns+1,T,C,tmp1);
GLE::MyTrans(ns+1,T,tmp2);
GLE::MyMult(ns+1,ns+1,ns+1,tmp1,tmp2,S);
for (int i=0; i<(ns+1)*(ns+1); ++i) tmp1[i]=C[i]-S[i];
GLE::StabCholesky(ns+1, tmp1, S); //!TODO use symmetric square root, which is more stable.
#ifdef GLE_DEBUG
printf("T Matrix\n");
GLE::MyPrint(ns+1,T);
printf("S Matrix\n");
GLE::MyPrint(ns+1,S);
#endif
delete[] tmp1; delete[] tmp2;
// set force prefactors
if (!atom->rmass) {
for (int i = 1; i <= atom->ntypes; i++) {
sqrt_m[i] = sqrt(atom->mass[i]);
}
}
if (strstr(update->integrate_style,"respa")) {
nlevels_respa = ((Respa *) update->integrate)->nlevels;
step_respa = ((Respa *) update->integrate)->step;
}
}
/* ---------------------------------------------------------------------- */
void FixGLE::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
}
void FixGLE::gle_integrate()
{
double **v = atom->v;
double **s = atom->s;
double *rmass = atom->rmass, smi, ismi;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (nlocal > gle_buff)
{
if (gle_tmp !=NULL) {
delete [] gle_tmp; delete [] gle_rnd;
}
gle_tmp = new double[nlocal*(ns+1)];
gle_rnd = new double[nlocal*(ns+1)];
gle_buff = nlocal;
}
#ifdef GLE_DEBUG
printf("!MC! GLE THERMO STEP dt=%f\n",update->dt);
#endif
// gets kinetic energy before doing anything to the velocities
double deltae=0.0;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ismi=rmass[i];
for (int j = 0; j<3; ++j) { deltae-=ismi*v[i][j]*v[i][j]; }
} }
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ismi=atom->mass[type[i]];
for (int j = 0; j<3; ++j) { deltae-=ismi*v[i][j]*v[i][j]; }
} }
}
// s is just taken to be the mass-scaled velocity!
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
smi=sqrt(rmass[i]);
for (int j = 0; j<3; ++j) { s[i][j] = v[i][j]*smi; }
} }
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
smi=sqrt_m[type[i]];
for (int j = 0; j<3; ++j) { s[i][j] = v[i][j]*smi; }
} }
}
for (int k = 0; k<3; k++) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) for (int j = 0; j<(ns+1); ++j) gle_rnd[j*(nlocal)+i] = s[i][3*j+k];
}
GLE::MyMult(ns+1,nlocal,ns+1,T,gle_rnd,gle_tmp);
for (int i = 0; i < nlocal*(ns+1); i++) gle_rnd[i] = random->gaussian();
GLE::MyMult(ns+1,nlocal,ns+1,S,gle_rnd,gle_tmp,1.0);
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) for (int j = 0; j<(ns+1); ++j) s[i][3*j+k] = gle_tmp[j*(nlocal)+i];
}
}
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ismi=1.0/sqrt(rmass[i]);
for (int j = 0; j<3; ++j) { v[i][j] = s[i][j]*ismi; }
} }
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ismi=1.0/sqrt_m[type[i]];
for (int j = 0; j<3; ++j) { v[i][j] = s[i][j]*ismi; }
} }
}
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ismi=rmass[i];
for (int j = 0; j<3; ++j) { deltae+=ismi*v[i][j]*v[i][j]; }
} }
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ismi=atom->mass[type[i]];
for (int j = 0; j<3; ++j) { deltae+=ismi*v[i][j]*v[i][j]; }
} }
}
energy += deltae*0.5*force->mvv2e;
}
void FixGLE::initial_integrate(int vflag)
{
double dtfm;
// update v and x of atoms in group
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
if (dogle) gle_integrate();
#ifdef GLE_DEBUG
printf("!MC! GLE P1 STEP dt=%f\n",dtv);
printf("!MC! GLE Q STEP\n");
#endif
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
}
void FixGLE::final_integrate()
{
double dtfm;
// update v of atoms in group
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
}
#ifdef GLE_DEBUG
printf("!MC! GLE P2 STEP dt=%f\n",dtv);
#endif
if (dogle) gle_integrate();
}
/* ---------------------------------------------------------------------- */
void FixGLE::initial_integrate_respa(int vflag, int ilevel, int iloop)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
// innermost level - NVE update of v and x
// all other levels - NVE update of v
if (ilevel==nlevels_respa-1) gle_integrate();
dogle=0;
if (ilevel == 0) initial_integrate(vflag);
else { dorattle=1; final_integrate();} // If RATTLE S2 should not be called here, dorattle=0
}
void FixGLE::final_integrate_respa(int ilevel, int iloop)
{
dtv = step_respa[ilevel]; //!MC!
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
dogle=0;
if(0) { // If true turn on stage 2 rattle for final integrate only
if(ilevel==nlevels_respa-1)
dorattle=1;
else
dorattle=0;
} else { dorattle=1; }
final_integrate();
if (ilevel==nlevels_respa-1) gle_integrate();
}
double FixGLE::compute_scalar()
{
double energy_me = energy;
double energy_all;
MPI_Allreduce(&energy_me,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
return -energy_all;
}
/* ----------------------------------------------------------------------
extract thermostat properties
------------------------------------------------------------------------- */
void *FixGLE::extract(const char *str, int &dim)
{
dim = 0;
if (strcmp(str,"t_target") == 0) {
return &temp;
}
return NULL;
}
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