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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12775 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-11-24 17:23:55 +00:00
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2
src/USER-MISC/README
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@ -36,7 +36,9 @@ dihedral_style quadratic, Loukas Peristeras, loukas.peristeras at scienomics.com
dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12
fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
fix ave/spatial/sphere, Niall Jackson (Imperial College), niall.jackson at gmail.com, 18 Nov 14
fix gle, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014
fix imd, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 2009
fix ipi, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014
fix smd, Axel Kohlmeyer, akohlmey at gmail.com, 19 May 2008
fix ti/rs, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013
fix ti/spring, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013

868
src/USER-MISC/fix_gle.cpp Normal file
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@ -0,0 +1,868 @@
/* ----------------------------------------------------------------------
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 authors: Michele Ceriotti (EPFL), Joe Morrone (Stony Brook)
------------------------------------------------------------------------- */
#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
#define MAXLINE 1024
/* syntax for fix_gle:
* fix nfix id-group gle ns Tstart Tstop seed amatrix [noneq cmatrix] [every nmts]
*
* */
/* ---------------------------------------------------------------------- */
namespace GLE {
/* GLE Utility functions -- might perhaps use standard LAMMPS routines if available */
#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(int n, const double* MMt, double* M)
{
double L[n*n], D[n];
int 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++)
{
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(int n, int m, int 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
int 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)];
}
}
#define MIN(A,B) ((A) < (B) ? (A) : (B))
// BLAS-like version of MyMult(). AK 2014-08-06
inline void AkMult(const int n, const int m, const int r,
const double * const A, const double * const B,
double * const C, const double cf=0.0)
{
// block buffer
const int blk=64;
double buf[blk*blk];
int i,j,k,ib,jb,kb;
for (i = 0; i < (n*m); ++i) C[i] *= cf;
for (kb = 0; kb < r; kb +=blk) {
// fill buffer
const int ke = MIN(kb+blk,r);
for (ib = 0; ib < n; ib += blk) {
const int ie = MIN(ib+blk,n);
for (i = ib; i < ie; ++i) {
for (k = kb; k < ke; ++k) {
buf[midx(blk,k-kb,i-ib)] = A[midx(r,i,k)];
}
}
for (jb = 0; jb < m; jb += blk) {
double tmp;
const int je = MIN(jb+blk,m);
for (j = jb; j < je; ++j) {
for (i = ib; i < ie; ++i) {
tmp = 0.0;
for (k = kb; k < ke; ++k)
tmp += buf[midx(blk,k-kb,i-ib)] * B[midx(m,k,j)];
C[midx(m,i,j)] += tmp;
}
}
}
}
}
}
void MyTrans(int n, const double* A, double* AT)
{
for (int i=0; i<n; ++i) for (int j=0; j<n; ++j) AT[j*n+i]=A[i*n+j];
}
void MyPrint(int n, const double* A)
{
for (int 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(int n, const double* M, double* EM, int j=8, int 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 < 8)
error->all(FLERR,"Illegal fix gle command. Expecting: fix <fix-ID>"
" <group-ID> gle <ns> <Tstart> <Tstop> <seed> <Amatrix>");
restart_peratom = 1;
time_integrate = 1;
// number of additional momenta
ns = force->inumeric(FLERR,arg[3]);
ns1sq = (ns+1)*(ns+1);
// allocate GLE matrices
A = new double[ns1sq];
C = new double[ns1sq];
T = new double[ns1sq];
S = new double[ns1sq];
TT = new double[ns1sq];
ST = new double[ns1sq];
// start temperature (t ramp)
t_start = force->numeric(FLERR,arg[4]);
// final temperature (t ramp)
t_stop = force->numeric(FLERR,arg[5]);
// PRNG seed
int seed = force->inumeric(FLERR,arg[6]);
// LOADING A matrix
FILE *fgle = NULL;
char *fname = arg[7];
if (comm->me == 0) {
fgle = force->open_potential(fname);
if (fgle == NULL) {
char str[128];
sprintf(str,"Cannot open A-matrix file %s",fname);
error->one(FLERR,str);
}
if (screen) fprintf(screen,"Reading A-matrix from %s\n", fname);
if (logfile) fprintf(logfile,"Reading A-matrix from %s\n", fname);
}
// read each line of the file, skipping blank lines or leading '#'
char line[MAXLINE],*ptr;
int n,nwords,ndone=0,eof=0;
while (1) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fgle);
if (ptr == NULL) {
eof = 1;
fclose(fgle);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
// strip comment, skip line if blank
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = atom->count_words(line);
if (nwords == 0) continue;
ptr = strtok(line," \t\n\r\f");
do {
A[ndone] = atof(ptr);
ptr = strtok(NULL," \t\n\r\f");
ndone++;
} while ((ptr != NULL) && (ndone < ns1sq));
}
fnoneq=0; gle_every=1; gle_step=0;
for (int iarg=8; iarg<narg; iarg+=2) {
if(strcmp(arg[iarg],"noneq") == 0) {
fnoneq = 1;
if (iarg+2>narg)
error->all(FLERR,"Did not specify C matrix for non-equilibrium GLE");
fname = arg[iarg+1];
} else if (strcmp(arg[iarg],"every") == 0) {
if (iarg+2>narg)
error->all(FLERR, "Did not specify interval for applying the GLE");
gle_every=force->inumeric(FLERR,arg[iarg+1]);
}
}
// set C matrix
if (fnoneq == 0) {
t_target=t_start;
const double kT = t_target * force->boltz / force->mvv2e;
memset(C,0,sizeof(double)*ns1sq);
for (int i=0; i<ns1sq; i+=(ns+2))
C[i]=kT;
} else {
if (comm->me == 0) {
fgle = force->open_potential(fname);
if (fgle == NULL) {
char str[128];
sprintf(str,"Cannot open C-matrix file %s",fname);
error->one(FLERR,str);
}
if (screen)
fprintf(screen,"Reading C-matrix from %s\n", fname);
if (logfile)
fprintf(logfile,"Reading C-matrix from %s\n", fname);
}
// read each line of the file, skipping blank lines or leading '#'
ndone = eof = 0;
const double cfac = force->boltz / force->mvv2e;
while (1) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fgle);
if (ptr == NULL) {
eof = 1;
fclose(fgle);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
// strip comment, skip line if blank
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = atom->count_words(line);
if (nwords == 0) continue;
ptr = strtok(line," \t\n\r\f");
do {
C[ndone] = cfac*atof(ptr);
ptr = strtok(NULL," \t\n\r\f");
ndone++;
} while ((ptr != NULL) && (ndone < ns1sq));
}
}
#ifdef GLE_DEBUG
printf("A Matrix\n");
GLE::MyPrint(ns+1,A);
printf("C Matrix\n");
GLE::MyPrint(ns+1,C);
#endif
// initialize Marsaglia RNG with processor-unique seed
// NB: this means runs will not be the same with different numbers of processors
if (seed <= 0) error->all(FLERR,"Illegal fix gle command");
random = new RanMars(lmp,seed + comm->me);
// allocate per-type arrays for mass-scaling
sqrt_m=NULL;
memory->grow(sqrt_m, atom->ntypes+1,"gle:sqrt_m");
// allocates space for additional degrees of freedom
gle_s=NULL;
// allocates space for temporaries
gle_tmp1=gle_tmp2=NULL;
grow_arrays(atom->nmax);
init_gles();
// add callbacks to enable restarts
atom->add_callback(0);
atom->add_callback(1);
energy = 0.0;
}
/* --- Frees up memory used by temporaries and buffers ------------------ */
FixGLE::~FixGLE()
{
delete random;
delete [] A;
delete [] C;
delete [] S;
delete [] T;
delete [] TT;
delete [] ST;
memory->destroy(sqrt_m);
memory->destroy(gle_s);
memory->destroy(gle_tmp1);
memory->destroy(gle_tmp2);
}
/* ---------------------------------------------------------------------- */
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;
}
/* ------- Initializes one-time quantities for GLE ---------------------- */
void FixGLE::init()
{
dogle = 1;
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
// 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;
}
init_gle();
}
/* ------- Initializes integrator matrices (change with T and dt) ------- */
void FixGLE::init_gle()
{
// compute Langevin terms
double *tmp1 = new double[ns1sq];
double *tmp2 = new double[ns1sq];
for (int i=0; i<ns1sq; ++i) {
tmp1[i]=-A[i]*update->dt*0.5*gle_every;
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<ns1sq; ++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
// transposed evolution matrices to have fast index multiplication in gle_integrate
GLE::MyTrans(ns+1,T,TT);
GLE::MyTrans(ns+1,S,ST);
delete[] tmp1;
delete[] tmp2;
}
/* ------- Sets initial values of additional DOF for free particles ----- */
void FixGLE::init_gles()
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *rootC = new double[ns1sq];
double *rootCT = new double[ns1sq];
double *newg = new double[3*(ns+1)*nlocal];
double *news = new double[3*(ns+1)*nlocal];
GLE::StabCholesky(ns+1, C, rootC);
GLE::MyTrans(ns+1,rootC,rootCT);
memset(news,0,sizeof(double)*3*(ns+1)*nlocal);
for (int i = 0; i < nlocal*3*(ns+1); ++i)
newg[i] = random->gaussian();
GLE::AkMult(nlocal*3,ns+1,ns+1, newg, rootCT, news);
int nk=0; // unpacks temporary into gle_s
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
// first loads velocities
for (int k = 0; k<3; k++) {
for (int j=0; j<ns; ++j)
gle_s[i][k*ns+j]=news[nk++];
}
}
}
delete[] rootC;
delete[] rootCT;
delete[] news;
delete[] newg;
return;
}
/* ---------------------------------------------------------------------- */
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 *rmass = atom->rmass, smi, ismi;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
#ifdef GLE_DEBUG
printf("!MC! GLE THERMO STEP dt=%f\n",update->dt);
#endif
// loads momentum data (mass-scaled) into the temporary vectors for the propagation
int nk=0, ni=0; double deltae=0.0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ni++;
if (rmass) {
smi = sqrt(rmass[i]);
} else {
smi=sqrt_m[type[i]];
}
for (int k = 0; k<3; k++) {
//also zeroes tmp1
gle_tmp1[nk]=0.0;
// first loads velocities and accumulates conserved quantity
gle_tmp2[nk]=v[i][k]*smi; deltae+= gle_tmp2[nk]*gle_tmp2[nk]; ++nk;
// then copies in the additional momenta
for (int j=0; j<ns; ++j)
gle_tmp2[nk++] = gle_s[i][k*ns+j];
}
}
}
// s(t+dt) = T.s ....
GLE::AkMult(ni*3,ns+1,ns+1,gle_tmp2,TT,gle_tmp1);
//fills up a vector of random numbers
for (int i = 0; i < 3*ni*(ns+1); i++) gle_tmp2[i] = random->gaussian();
// ... + S \xi
GLE::AkMult(ni*3,ns+1,ns+1,gle_tmp2,ST,gle_tmp1,1.0);
// unloads momentum data (mass-scaled) from the temporary vectors
nk=0;
for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) {
if (rmass) ismi = 1.0/sqrt(rmass[i]); else ismi=1.0/sqrt_m[type[i]];
for (int k = 0; k<3; k++)
{
// fetches new velocities and completes computation of the conserved quantity change
v[i][k]=gle_tmp1[nk]*ismi; deltae-= gle_tmp1[nk]*gle_tmp1[nk]; ++nk;
// stores the additional momenta in the gle_s buffer
for (int j=0; j<ns; ++j)
gle_s[i][k*ns+j]=gle_tmp1[nk++];
}
}
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;
gle_step--;
if (dogle && gle_step<1) 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_step<1) { gle_integrate(); gle_step=gle_every; }
// Change the temperature for the next step
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
t_target = t_start + delta * (t_stop - t_start);
if (t_stop != t_start && fnoneq == 0) {
// only updates if it is really necessary
const double kT = t_target * force->boltz / force->mvv2e;
memset(C,0,sizeof(double)*ns1sq);
for (int i=0; i<ns1sq; i+=(ns+2)) C[i]=kT;
init_gle();
}
}
/* ---------------------------------------------------------------------- */
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 { final_integrate();}
}
void FixGLE::final_integrate_respa(int ilevel, int iloop)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
dogle=0;
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 &t_target;
}
return NULL;
}
/* ----------------------------------------------------------------------
Called when a change to the target temperature is requested mid-run
------------------------------------------------------------------------- */
void FixGLE::reset_target(double t_new)
{
t_target = t_start = t_stop = t_new;
if (fnoneq == 0)
{
// only updates if it is really necessary
for (int i=0; i<ns1sq; ++i) C[i]=0.0;
for (int i=0; i<ns1sq; i+=(ns+2)) C[i]=t_target*force->boltz/force->mvv2e;
init_gle();
}
else
{
error->all(FLERR, "Cannot change temperature for a non-equilibrium GLE run");
}
}
/* ----------------------------------------------------------------------
Called when a change to the timestep is requested mid-run
------------------------------------------------------------------------- */
void FixGLE::reset_dt()
{
// set the time integration constants
dtv = update->dt;
dtf = 0.5 * update->dt * (force->ftm2v);
init_gle();
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixGLE::memory_usage()
{
double bytes = atom->nmax*(3*ns+2*3*(ns+1))*sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixGLE::grow_arrays(int nmax)
{
memory->grow(gle_s, nmax, 3*ns,"gle:gle_s");
memory->grow(gle_tmp1, nmax*(ns+1)*3,"gle:tmp1");
memory->grow(gle_tmp2, nmax*(ns+1)*3,"gle:tmp2");
//zeroes out temporary buffers
for (int i=0; i< nmax*(ns+1)*3; ++i) gle_tmp1[i]=0.0;
for (int i=0; i< nmax*(ns+1)*3; ++i) gle_tmp2[i]=0.0;
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixGLE::copy_arrays(int i, int j, int delflag)
{
for (int k = 0; k < 3*ns; k++) gle_s[j][k] = gle_s[i][k];
}
/* ----------------------------------------------------------------------
Pack extended variables assoc. w/ atom i into buffer for exchange
with another processor
------------------------------------------------------------------------- */
int FixGLE::pack_exchange(int i, double *buf)
{
int m = 0;
for (int k = 0; k < 3*ns; k++) buf[m++] = gle_s[i][k];
return m;
}
/* ----------------------------------------------------------------------
Unpack extended variables from exchange with another processor
------------------------------------------------------------------------- */
int FixGLE::unpack_exchange(int nlocal, double *buf)
{
int m = 0;
for (int k = 0; k < 3*ns; k++) gle_s[nlocal][k] = buf[m++];
return m;
}
/* ----------------------------------------------------------------------
Pack extended variables assoc. w/ atom i into buffer for
writing to a restart file
------------------------------------------------------------------------- */
int FixGLE::pack_restart(int i, double *buf)
{
int m = 0;
buf[m++] = 3*ns + 1;
for (int k = 0; k < 3*ns; k=k+3)
{
buf[m++] = gle_s[i][k];
buf[m++] = gle_s[i][k+1];
buf[m++] = gle_s[i][k+2];
}
return m;
}
/* ----------------------------------------------------------------------
Unpack extended variables to restart the fix from a restart file
------------------------------------------------------------------------- */
void FixGLE::unpack_restart(int nlocal, int nth)
{
double **extra = atom->extra;
// skip to the nth set of extended variables
int m = 0;
for (int i = 0; i< nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++;
for (int k = 0; k < 3*ns; k=k+3)
{
gle_s[nlocal][k] = extra[nlocal][m++];
gle_s[nlocal][k+1] = extra[nlocal][m++];
gle_s[nlocal][k+2] = extra[nlocal][m++];
}
}
/* ----------------------------------------------------------------------
Returns the number of items in atomic restart data associated with
local atom nlocal. Used in determining the total extra data stored by
fixes on a given processor.
------------------------------------------------------------------------- */
int FixGLE::size_restart(int nlocal)
{
return 3*ns+1;
}
/* ----------------------------------------------------------------------
Returns the maximum number of items in atomic restart data
Called in Modify::restart for peratom restart.
------------------------------------------------------------------------- */
int FixGLE::maxsize_restart()
{
return 3*ns+1;
}

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/* -*- c++ -*- ----------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(gle,FixGLE)
#else
#ifndef LMP_FIX_GLE_H
#define LMP_FIX_GLE_H
#include "fix.h"
namespace LAMMPS_NS {
class FixGLE : public Fix {
public:
FixGLE(class LAMMPS *, int, char **);
virtual ~FixGLE();
int setmask();
void init();
void setup(int);
void gle_integrate();
void initial_integrate_respa(int vflag, int ilevel, int iloop);
void final_integrate_respa(int ilevel, int iloop);
void initial_integrate(int vflag);
void final_integrate();
double compute_scalar();
void reset_target(double);
virtual void reset_dt();
double memory_usage();
void grow_arrays(int);
void copy_arrays(int, int, int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
int pack_restart(int, double *);
void unpack_restart(int, int);
int size_restart(int);
int maxsize_restart();
virtual void *extract(const char *, int &);
void init_gle(); void init_gles();
protected:
int ns, ns1sq;
double *A, *C, *S, *T, *ST, *TT;
double *gle_tmp1, *gle_tmp2;
double t_start, t_stop, t_target;
double dtv, dtf;
int dogle, fnoneq, gle_every, gle_step;
class RanMars *random;
double *sqrt_m;
double *step_respa;
double energy;
int nlevels_respa;
double **gle_s;
double **vaux;
};
}
#endif
#endif

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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.
------------------------------------------------------------------------- */
#include "mpi.h"
#include "stdio.h"
#include "string.h"
#include "fix_ipi.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "error.h"
#include "kspace.h"
#include "modify.h"
#include "compute.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "compute_pressure.h"
#include "errno.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/******************************************************************************************
* A fix to interface LAMMPS with i-PI - A Python interface for path integral molecular dynamics
* Michele Ceriotti, EPFL (2014)
* Please cite:
* Ceriotti, M., More, J., & Manolopoulos, D. E. (2014).
* i-PI: A Python interface for ab initio path integral molecular dynamics simulations.
* Computer Physics Communications, 185, 1019–1026. doi:10.1016/j.cpc.2013.10.027
* And see [http://github.com/i-pi/i-pi] to download a version of i-PI
******************************************************************************************/
// socket interface
#ifndef _WIN32
#include <stdlib.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/socket.h>
#include <netinet/in.h>
#include <sys/un.h>
#include <netdb.h>
#endif
#define MSGLEN 12
/* Utility functions to simplify the interface with POSIX sockets */
static void open_socket(int &sockfd, int inet, int port, char* host,
Error *error)
/* Opens a socket.
Args:
sockfd: The id of the socket that will be created.
inet: An integer that determines whether the socket will be an inet or unix
domain socket. Gives unix if 0, inet otherwise.
port: The port number for the socket to be created. Low numbers are often
reserved for important channels, so use of numbers of 4 or more digits is
recommended.
host: The name of the host server.
error: pointer to a LAMMPS Error object
*/
{
int ai_err;
#ifdef _WIN32
error->one(FLERR,"i-PI socket implementation requires UNIX environment");
#else
if (inet>0) { // creates an internet socket
// fetches information on the host
struct addrinfo hints, *res;
char service[256];
memset(&hints, 0, sizeof(hints));
hints.ai_socktype = SOCK_STREAM;
hints.ai_family = AF_UNSPEC;
hints.ai_flags = AI_PASSIVE;
sprintf(service,"%d",port); // convert the port number to a string
ai_err = getaddrinfo(host, service, &hints, &res);
if (ai_err!=0)
error->one(FLERR,"Error fetching host data. Wrong host name?");
// creates socket
sockfd = socket(res->ai_family, res->ai_socktype, res->ai_protocol);
if (sockfd < 0)
error->one(FLERR,"Error opening socket");
// makes connection
if (connect(sockfd, res->ai_addr, res->ai_addrlen) < 0)
error->one(FLERR,"Error opening INET socket: wrong port or server unreachable");
freeaddrinfo(res);
} else { // creates a unix socket
struct sockaddr_un serv_addr;
// fills up details of the socket addres
memset(&serv_addr, 0, sizeof(serv_addr));
serv_addr.sun_family = AF_UNIX;
strcpy(serv_addr.sun_path, "/tmp/ipi_");
strcpy(serv_addr.sun_path+9, host);
// creates the socket
sockfd = socket(AF_UNIX, SOCK_STREAM, 0);
// connects
if (connect(sockfd, (struct sockaddr *) &serv_addr, sizeof(serv_addr)) < 0)
error->one(FLERR,"Error opening UNIX socket: server may not be running "
"or the path to the socket unavailable");
}
#endif
}
static void writebuffer(int sockfd, const char *data, int len, Error* error)
/* Writes to a socket.
Args:
sockfd: The id of the socket that will be written to.
data: The data to be written to the socket.
len: The length of the data in bytes.
*/
{
int n;
n = write(sockfd,data,len);
if (n < 0)
error->one(FLERR,"Error writing to socket: broken connection");
}
static void readbuffer(int sockfd, char *data, int len, Error* error)
/* Reads from a socket.
Args:
sockfd: The id of the socket that will be read from.
data: The storage array for data read from the socket.
len: The length of the data in bytes.
*/
{
int n, nr;
n = nr = read(sockfd,data,len);
while (nr>0 && n<len ) {
nr=read(sockfd,&data[n],len-n);
n+=nr;
}
if (n == 0)
error->one(FLERR,"Error reading from socket: broken connection");
}
/* ---------------------------------------------------------------------- */
FixIPI::FixIPI(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
/* format for fix:
* fix num group_id ipi host port [unix]
*/
if (strcmp(style,"ipi") != 0 && narg < 5)
error->all(FLERR,"Illegal fix ipi command");
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use fix ipi without atom IDs");
if (atom->tag_consecutive() == 0)
error->all(FLERR,"Fix ipi requires consecutive atom IDs");
if (strcmp(arg[1],"all"))
error->warning(FLERR,"Fix ipi always uses group all");
strcpy(host, arg[3]);
port=force->inumeric(FLERR,arg[4]);
inet = ((narg > 5) && (strcmp(arg[5],"unix") ==0) ) ? 0 : 1;
master = (comm->me==0) ? 1 : 0;
hasdata = bsize = 0;
// creates a temperature compute for all atoms
char** newarg = new char*[3];
newarg[0] = (char *) "IPI_TEMP";
newarg[1] = (char *) "all";
newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
delete [] newarg;
// creates a pressure compute to extract the virial
newarg = new char*[5];
newarg[0] = (char *) "IPI_PRESS";
newarg[1] = (char *) "all";
newarg[2] = (char *) "pressure";
newarg[3] = (char *) "IPI_TEMP";
newarg[4] = (char *) "virial";
modify->add_compute(5,newarg);
delete [] newarg;
}
/* ---------------------------------------------------------------------- */
FixIPI::~FixIPI()
{
if (bsize) delete[] buffer;
modify->delete_compute("IPI_TEMP");
modify->delete_compute("IPI_PRESS");
}
/* ---------------------------------------------------------------------- */
int FixIPI::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixIPI::init()
{
//only opens socket on master process
if (master) open_socket(ipisock, inet, port, host, error);
else ipisock=0;
//! should check for success in socket opening -- but the current open_socket routine dies brutally if unsuccessful
// asks for evaluation of PE at first step
modify->compute[modify->find_compute("thermo_pe")]->invoked_scalar = -1;
modify->addstep_compute_all(update->ntimestep + 1);
kspace_flag = (force->kspace) ? 1 : 0;
// makes sure that neighbor lists are re-built at each step (cannot make assumptions when cycling over beads!)
neighbor->delay = 0;
neighbor->every = 1;
}
void FixIPI::initial_integrate(int vflag)
{
/* This is called at the beginning of the integration loop,
* and will be used to read positions from the socket. Then,
* everything should be updated, since there is no guarantee
* that successive snapshots will be close together (think
* of parallel tempering for instance) */
char header[MSGLEN+1];
if (hasdata)
error->all(FLERR, "i-PI got out of sync in initial_integrate and will die!");
double cellh[9], cellih[9];
int nat;
if (master) { // only read positions on master
// wait until something happens
while (true) {
// while i-PI just asks for status, signal we are ready and wait
readbuffer(ipisock, header, MSGLEN, error); header[MSGLEN]=0;
if (strcmp(header,"STATUS ") == 0 )
writebuffer(ipisock,"READY ",MSGLEN, error);
else break;
}
if (strcmp(header,"EXIT ") == 0 )
error->one(FLERR, "Got EXIT message from i-PI. Now leaving!");
// when i-PI signals it has positions to evaluate new forces,
// read positions and cell data
if (strcmp(header,"POSDATA ") == 0 ) {
readbuffer(ipisock, (char*) cellh, 9*8, error);
readbuffer(ipisock, (char*) cellih, 9*8, error);
readbuffer(ipisock, (char*) &nat, 4, error);
// allocate buffer, but only do this once.
if (bsize==0) {
bsize=3*nat;
buffer = new double[bsize];
} else if (bsize != 3*nat)
error->one(FLERR, "Number of atoms changed along the way.");
// finally read position data into buffer
readbuffer(ipisock, (char*) buffer, 8*bsize, error);
} else
error->one(FLERR, "Wrapper did not send positions, I will now die!");
}
// shares the atomic coordinates with everyone
MPI_Bcast(&nat,1,MPI_INT,0,world);
// must also allocate the buffer on the non-head nodes
if (bsize==0) {
bsize=3*nat;
buffer = new double[bsize];
}
MPI_Bcast(cellh,9,MPI_DOUBLE,0,world);
MPI_Bcast(cellih,9,MPI_DOUBLE,0,world);
MPI_Bcast(buffer,bsize,MPI_DOUBLE,0,world);
//updates atomic coordinates and cell based on the data received
double *boxhi = domain->boxhi;
double *boxlo = domain->boxlo;
double posconv;
posconv=0.52917721*force->angstrom;
boxlo[0] = 0;
boxlo[1] = 0;
boxlo[2] = 0;
boxhi[0] = cellh[0]*posconv;
boxhi[1] = cellh[4]*posconv;
boxhi[2] = cellh[8]*posconv;
domain->xy = cellh[1]*posconv;
domain->xz = cellh[2]*posconv;
domain->yz = cellh[5]*posconv;
// signal that the box has (or may have) changed
domain->reset_box();
domain->box_change = 1;
if (kspace_flag) force->kspace->setup();
// picks local atoms from the buffer
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
x[i][0]=buffer[3*(atom->tag[i]-1)+0]*posconv;
x[i][1]=buffer[3*(atom->tag[i]-1)+1]*posconv;
x[i][2]=buffer[3*(atom->tag[i]-1)+2]*posconv;
}
}
// compute PE. makes sure that it will be evaluated at next step
modify->compute[modify->find_compute("thermo_pe")]->invoked_scalar = -1;
modify->addstep_compute_all(update->ntimestep+1);
hasdata=1;
}
void FixIPI::final_integrate()
{
/* This is called after forces and energy have been computed. Now we only need to
* communicate them back to i-PI so that the integration can continue. */
char header[MSGLEN+1];
double vir[9], pot=0.0;
double forceconv, potconv, posconv, pressconv, posconv3;
char retstr[1024];
// conversions from LAMMPS units to atomic units, which are used by i-PI
potconv=3.1668152e-06/force->boltz;
posconv=0.52917721*force->angstrom;
posconv3=posconv*posconv*posconv;
forceconv=potconv*posconv;
pressconv=1/force->nktv2p*potconv*posconv3;
// compute for potential energy
pot=modify->compute[modify->find_compute("thermo_pe")]->compute_scalar();
pot*=potconv;
// probably useless check
if (!hasdata)
error->all(FLERR, "i-PI got out of sync in final_integrate and will die!");
int nat=bsize/3;
double **f= atom->f;
double lbuf[bsize];
// reassembles the force vector from the local arrays
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < bsize; ++i) lbuf[i]=0.0;
for (int i = 0; i < nlocal; i++) {
lbuf[3*(atom->tag[i]-1)+0]=f[i][0]*forceconv;
lbuf[3*(atom->tag[i]-1)+1]=f[i][1]*forceconv;
lbuf[3*(atom->tag[i]-1)+2]=f[i][2]*forceconv;
}
MPI_Allreduce(lbuf,buffer,bsize,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < 9; ++i) vir[i]=0.0;
int press_id = modify->find_compute("IPI_PRESS");
Compute* comp_p = modify->compute[press_id];
comp_p->compute_vector();
double myvol = domain->xprd*domain->yprd*domain->zprd/posconv3;
vir[0] = comp_p->vector[0]*pressconv*myvol;
vir[4] = comp_p->vector[1]*pressconv*myvol;
vir[8] = comp_p->vector[2]*pressconv*myvol;
vir[1] = comp_p->vector[3]*pressconv*myvol;
vir[2] = comp_p->vector[4]*pressconv*myvol;
vir[5] = comp_p->vector[5]*pressconv*myvol;
retstr[0]=0;
if (master) {
while (true) {
readbuffer(ipisock, header, MSGLEN, error); header[MSGLEN]=0;
if (strcmp(header,"STATUS ") == 0 )
writebuffer(ipisock,"HAVEDATA ",MSGLEN, error);
else break;
}
if (strcmp(header,"EXIT ") == 0 )
error->one(FLERR, "Got EXIT message from i-PI. Now leaving!");
if (strcmp(header,"GETFORCE ") == 0 ) {
writebuffer(ipisock,"FORCEREADY ",MSGLEN, error);
writebuffer(ipisock,(char*) &pot,8, error);
writebuffer(ipisock,(char*) &nat,4, error);
writebuffer(ipisock,(char*) buffer, bsize*8, error);
writebuffer(ipisock,(char*) vir,9*8, error);
nat=strlen(retstr); writebuffer(ipisock,(char*) &nat,4, error);
writebuffer(ipisock,(char*) retstr, nat, error);
}
else
error->one(FLERR, "Wrapper did not ask for forces, I will now die!");
}
hasdata=0;
}

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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.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(ipi,FixIPI)
#else
#ifndef LMP_FIX_IPI_H
#define LMP_FIX_IPI_H
#include "fix.h"
namespace LAMMPS_NS {
class FixIPI : public Fix {
public:
FixIPI(class LAMMPS *, int, char **);
virtual ~FixIPI();
int setmask();
virtual void init();
virtual void initial_integrate(int);
virtual void final_integrate();
protected:
char host[1024]; int port; int inet, master, hasdata;
int ipisock, me; double *buffer; long bsize;
int kspace_flag;
};
}
#endif
#endif