From 11bd1a45ed40e2bc942a5766392aa16e624c0ba1 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Mon, 24 Nov 2014 17:23:55 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12775
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/USER-MISC/README | 2 +
src/USER-MISC/fix_gle.cpp | 868 ++++++++++++++++++++++++++++++++++++++
src/USER-MISC/fix_gle.h | 77 ++++
src/USER-MISC/fix_ipi.cpp | 437 +++++++++++++++++++
src/USER-MISC/fix_ipi.h | 45 ++
5 files changed, 1429 insertions(+)
create mode 100644 src/USER-MISC/fix_gle.cpp
create mode 100644 src/USER-MISC/fix_gle.h
create mode 100644 src/USER-MISC/fix_ipi.cpp
create mode 100644 src/USER-MISC/fix_ipi.h
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index 8b94144059..19ed6c3756 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -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
diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp
new file mode 100644
index 0000000000..1f80e19cfe
--- /dev/null
+++ b/src/USER-MISC/fix_gle.cpp
@@ -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;
+}
diff --git a/src/USER-MISC/fix_gle.h b/src/USER-MISC/fix_gle.h
new file mode 100644
index 0000000000..01f50f8925
--- /dev/null
+++ b/src/USER-MISC/fix_gle.h
@@ -0,0 +1,77 @@
+/* -*- 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
diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp
new file mode 100644
index 0000000000..6e02bdd747
--- /dev/null
+++ b/src/USER-MISC/fix_ipi.cpp
@@ -0,0 +1,437 @@
+/* ----------------------------------------------------------------------
+ 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;
+}
+
+
diff --git a/src/USER-MISC/fix_ipi.h b/src/USER-MISC/fix_ipi.h
new file mode 100644
index 0000000000..d6b8a6413e
--- /dev/null
+++ b/src/USER-MISC/fix_ipi.h
@@ -0,0 +1,45 @@
+/* ----------------------------------------------------------------------
+ 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
--
GitLab