complete moving packages and styles around
This commit is contained in:
Axel Kohlmeyer
879
src/EXTRA-FIX/fix_gle.cpp
Normal file
879
src/EXTRA-FIX/fix_gle.cpp
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@ -0,0 +1,879 @@
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing authors: Michele Ceriotti (EPFL), Joe Morrone (Stony Brook),
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Axel Kohylmeyer (Temple U)
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------------------------------------------------------------------------- */
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#include "fix_gle.h"
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#include <cmath>
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#include <cstring>
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#include "atom.h"
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#include "force.h"
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#include "update.h"
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#include "respa.h"
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#include "comm.h"
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#include "random_mars.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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enum{NOBIAS,BIAS};
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enum{CONSTANT,EQUAL,ATOM};
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//#define GLE_DEBUG 1
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#define MAXLINE 1024
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/* syntax for fix_gle:
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* fix nfix id-group gle ns Tstart Tstop seed amatrix [noneq cmatrix] [every nmts]
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*
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* */
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/* ---------------------------------------------------------------------- */
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namespace GLE {
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/* GLE Utility functions -- might perhaps use standard LAMMPS routines if available */
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#define midx(n,i,j) ((i)*(n)+(j))
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//"stabilized" cholesky decomposition. does a LDL^t decomposition, then sets to zero the negative diagonal elements and gets MM^t
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void StabCholesky(int n, const double* MMt, double* M)
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{
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double *L = new double[n*n];
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double *D = new double[n];
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int i,j,k;
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for (i=0; i<n; ++i) D[i]=0.0;
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for (i=0; i<n*n; ++i) L[i]=0.0;
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for (i=0; i<n; ++i) {
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L[midx(n,i,i)]=1.0;
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for (j=0; j<i; j++) {
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L[midx(n,i,j)]=MMt[midx(n,i,j)];
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for (k=0; k<j; ++k) L[midx(n,i,j)]-=L[midx(n,i,k)]*L[midx(n,j,k)]*D[k];
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if (D[j]!=0.) L[midx(n,i,j)]/=D[j];
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else L[midx(n,i,j)]=0.0;
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}
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D[i]=MMt[midx(n,i,i)];
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for (k=0; k<i; ++k) D[i]-=L[midx(n,i,k)]*L[midx(n,i,k)]*D[k];
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}
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for (i=0; i<n; ++i) {
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#ifdef GLE_DEBUG
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if (D[i]<0) fprintf(stderr,"GLE Cholesky: Negative diagonal term %le, has been set to zero.\n", D[i]);
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#endif
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D[i]=(D[i]>0.0) ? sqrt(D[i]):0.0;
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}
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for (i=0; i<n; ++i)
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for (j=0; j<n; j++) M[midx(n,i,j)]=L[midx(n,i,j)]*D[j];
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delete[] D;
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delete[] L;
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}
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void MyMult(int n, int m, int r, const double* A, const double* B, double* C, double cf=0.0)
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{
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// !! TODO !! should probably call BLAS (or check if some efficient matrix-matrix multiply is implemented somewhere in LAMMPS)
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// (rows x cols) :: A is n x r, B is r x m, C is n x m
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int i,j,k; double *cij;
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for (i=0; i<n; ++i)
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for (j=0; j<m; ++j)
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{
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cij=&C[midx(m,i,j)]; *cij *= cf;
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for (k=0; k<r; ++k) *cij+=A[midx(r,i,k)]*B[midx(m,k,j)];
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}
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}
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#define MIN(A,B) ((A) < (B) ? (A) : (B))
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// BLAS-like version of MyMult(). AK 2014-08-06
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inline void AkMult(const int n, const int m, const int r,
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const double * const A, const double * const B,
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double * const C, const double cf=0.0)
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{
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// block buffer
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const int blk=64;
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double buf[blk*blk];
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int i,j,k,ib,jb,kb;
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for (i = 0; i < (n*m); ++i) C[i] *= cf;
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for (kb = 0; kb < r; kb +=blk) {
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// fill buffer
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const int ke = MIN(kb+blk,r);
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for (ib = 0; ib < n; ib += blk) {
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const int ie = MIN(ib+blk,n);
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for (i = ib; i < ie; ++i) {
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for (k = kb; k < ke; ++k) {
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buf[midx(blk,k-kb,i-ib)] = A[midx(r,i,k)];
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}
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}
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for (jb = 0; jb < m; jb += blk) {
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double tmp;
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const int je = MIN(jb+blk,m);
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for (j = jb; j < je; ++j) {
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for (i = ib; i < ie; ++i) {
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tmp = 0.0;
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for (k = kb; k < ke; ++k)
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tmp += buf[midx(blk,k-kb,i-ib)] * B[midx(m,k,j)];
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C[midx(m,i,j)] += tmp;
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}
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}
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}
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}
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}
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}
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void MyTrans(int n, const double* A, double* AT)
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{
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for (int i=0; i<n; ++i) for (int j=0; j<n; ++j) AT[j*n+i]=A[i*n+j];
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}
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void MyPrint(int n, const double* A)
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{
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for (int k=0; k<n*n; ++k) { printf("%10.5e ", A[k]); if ((k+1)%n==0) printf("\n");}
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}
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//matrix exponential by scaling and squaring.
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void MatrixExp(int n, const double* M, double* EM, int j=8, int k=8)
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{
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double *tc = new double[j+1];
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double *SM = new double[n*n];
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double *TMP = new double[n*n];
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double onetotwok=pow(0.5,1.0*k);
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tc[0]=1;
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for (int i=0; i<j; ++i) tc[i+1]=tc[i]/(i+1.0);
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for (int i=0; i<n*n; ++i) { SM[i]=M[i]*onetotwok; EM[i]=0.0; TMP[i]=0.0; }
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for (int i=0; i<n; ++i) EM[midx(n,i,i)]=tc[j];
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//taylor exp of scaled matrix
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for (int p=j-1; p>=0; p--) {
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MyMult(n, n, n, SM, EM, TMP); for (int i=0; i<n*n; ++i) EM[i]=TMP[i];
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for (int i=0; i<n; ++i) EM[midx(n,i,i)]+=tc[p];
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}
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for (int p=0; p<k; p++) {
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MyMult(n, n, n, EM, EM, TMP);
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for (int i=0; i<n*n; ++i) EM[i]=TMP[i];
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}
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delete[] tc;
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delete[] SM;
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delete[] TMP;
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}
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}
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/* ---------------------------------------------------------------------- */
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FixGLE::FixGLE(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg < 8)
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error->all(FLERR,"Illegal fix gle command. Expecting: fix <fix-ID>"
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" <group-ID> gle <ns> <Tstart> <Tstop> <seed> <Amatrix>");
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ecouple_flag = 1;
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restart_peratom = 1;
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time_integrate = 1;
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// number of additional momenta
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ns = utils::inumeric(FLERR,arg[3],false,lmp);
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ns1sq = (ns+1)*(ns+1);
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// allocate GLE matrices
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A = new double[ns1sq];
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C = new double[ns1sq];
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T = new double[ns1sq];
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S = new double[ns1sq];
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TT = new double[ns1sq];
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ST = new double[ns1sq];
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// start temperature (t ramp)
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t_start = utils::numeric(FLERR,arg[4],false,lmp);
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// final temperature (t ramp)
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t_stop = utils::numeric(FLERR,arg[5],false,lmp);
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// PRNG seed
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int seed = utils::inumeric(FLERR,arg[6],false,lmp);
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// LOADING A matrix
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FILE *fgle = nullptr;
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char *fname = arg[7];
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if (comm->me == 0) {
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fgle = utils::open_potential(fname,lmp,nullptr);
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if (fgle == nullptr) {
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char str[128];
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snprintf(str,128,"Cannot open A-matrix file %s",fname);
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error->one(FLERR,str);
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}
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if (screen) fprintf(screen,"Reading A-matrix from %s\n", fname);
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if (logfile) fprintf(logfile,"Reading A-matrix from %s\n", fname);
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}
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// read each line of the file, skipping blank lines or leading '#'
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char line[MAXLINE],*ptr;
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int n,nwords,ndone=0,eof=0;
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while (1) {
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if (comm->me == 0) {
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ptr = fgets(line,MAXLINE,fgle);
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if (ptr == nullptr) {
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eof = 1;
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fclose(fgle);
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} else n = strlen(line) + 1;
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}
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MPI_Bcast(&eof,1,MPI_INT,0,world);
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if (eof) break;
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MPI_Bcast(&n,1,MPI_INT,0,world);
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MPI_Bcast(line,n,MPI_CHAR,0,world);
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// strip comment, skip line if blank
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if ((ptr = strchr(line,'#'))) *ptr = '\0';
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nwords = utils::count_words(line);
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if (nwords == 0) continue;
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ptr = strtok(line," \t\n\r\f");
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do {
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A[ndone] = atof(ptr);
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ptr = strtok(nullptr," \t\n\r\f");
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ndone++;
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} while ((ptr != nullptr) && (ndone < ns1sq));
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}
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fnoneq=0; gle_every=1; gle_step=0;
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for (int iarg=8; iarg<narg; iarg+=2) {
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if (strcmp(arg[iarg],"noneq") == 0) {
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fnoneq = 1;
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if (iarg+2>narg)
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error->all(FLERR,"Did not specify C matrix for non-equilibrium GLE");
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fname = arg[iarg+1];
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} else if (strcmp(arg[iarg],"every") == 0) {
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if (iarg+2>narg)
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error->all(FLERR, "Did not specify interval for applying the GLE");
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gle_every=utils::inumeric(FLERR,arg[iarg+1],false,lmp);
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}
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}
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// set C matrix
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if (fnoneq == 0) {
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t_target=t_start;
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const double kT = t_target * force->boltz / force->mvv2e;
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memset(C,0,sizeof(double)*ns1sq);
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for (int i=0; i<ns1sq; i+=(ns+2))
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C[i]=kT;
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} else {
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if (comm->me == 0) {
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fgle = utils::open_potential(fname,lmp,nullptr);
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if (fgle == nullptr) {
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char str[128];
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snprintf(str,128,"Cannot open C-matrix file %s",fname);
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error->one(FLERR,str);
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}
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if (screen)
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fprintf(screen,"Reading C-matrix from %s\n", fname);
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if (logfile)
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fprintf(logfile,"Reading C-matrix from %s\n", fname);
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}
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// read each line of the file, skipping blank lines or leading '#'
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ndone = eof = 0;
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const double cfac = force->boltz / force->mvv2e;
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while (1) {
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if (comm->me == 0) {
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ptr = fgets(line,MAXLINE,fgle);
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if (ptr == nullptr) {
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eof = 1;
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fclose(fgle);
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} else n = strlen(line) + 1;
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}
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MPI_Bcast(&eof,1,MPI_INT,0,world);
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if (eof) break;
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MPI_Bcast(&n,1,MPI_INT,0,world);
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MPI_Bcast(line,n,MPI_CHAR,0,world);
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// strip comment, skip line if blank
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if ((ptr = strchr(line,'#'))) *ptr = '\0';
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nwords = utils::count_words(line);
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if (nwords == 0) continue;
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ptr = strtok(line," \t\n\r\f");
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do {
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C[ndone] = cfac*atof(ptr);
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ptr = strtok(nullptr," \t\n\r\f");
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ndone++;
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} while ((ptr != nullptr) && (ndone < ns1sq));
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}
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}
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#ifdef GLE_DEBUG
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printf("A Matrix\n");
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GLE::MyPrint(ns+1,A);
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printf("C Matrix\n");
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GLE::MyPrint(ns+1,C);
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#endif
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// initialize Marsaglia RNG with processor-unique seed
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// NB: this means runs will not be the same with different numbers of processors
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if (seed <= 0) error->all(FLERR,"Illegal fix gle command");
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random = new RanMars(lmp,seed + comm->me);
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// allocate per-type arrays for mass-scaling
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sqrt_m=nullptr;
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memory->grow(sqrt_m, atom->ntypes+1,"gle:sqrt_m");
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// allocates space for additional degrees of freedom
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gle_s=nullptr;
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// allocates space for temporaries
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gle_tmp1=gle_tmp2=nullptr;
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grow_arrays(atom->nmax);
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init_gles();
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// add callbacks to enable restarts
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atom->add_callback(Atom::GROW);
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atom->add_callback(Atom::RESTART);
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energy = 0.0;
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}
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/* --- Frees up memory used by temporaries and buffers ------------------ */
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FixGLE::~FixGLE()
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{
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delete random;
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delete [] A;
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delete [] C;
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delete [] S;
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delete [] T;
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delete [] TT;
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delete [] ST;
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memory->destroy(sqrt_m);
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memory->destroy(gle_s);
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memory->destroy(gle_tmp1);
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memory->destroy(gle_tmp2);
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}
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/* ---------------------------------------------------------------------- */
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int FixGLE::setmask()
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{
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int mask = 0;
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mask |= INITIAL_INTEGRATE;
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mask |= FINAL_INTEGRATE;
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mask |= INITIAL_INTEGRATE_RESPA;
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mask |= FINAL_INTEGRATE_RESPA;
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return mask;
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}
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/* ------- Initializes one-time quantities for GLE ---------------------- */
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void FixGLE::init()
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{
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dogle = 1;
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dtv = update->dt;
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dtf = 0.5 * update->dt * force->ftm2v;
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// set force prefactors
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if (!atom->rmass) {
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for (int i = 1; i <= atom->ntypes; i++) {
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sqrt_m[i] = sqrt(atom->mass[i]);
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}
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}
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if (utils::strmatch(update->integrate_style,"^respa")) {
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nlevels_respa = ((Respa *) update->integrate)->nlevels;
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step_respa = ((Respa *) update->integrate)->step;
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}
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||||
|
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init_gle();
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}
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||||
|
||||
/* ------- Initializes integrator matrices (change with T and dt) ------- */
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void FixGLE::init_gle()
|
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{
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// compute Langevin terms
|
||||
|
||||
double *tmp1 = new double[ns1sq];
|
||||
double *tmp2 = new double[ns1sq];
|
||||
|
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for (int i=0; i<ns1sq; ++i) {
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tmp1[i]=-A[i]*update->dt*0.5*gle_every;
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tmp2[i]=S[i]=0.0;
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}
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GLE::MatrixExp(ns+1,tmp1,T);
|
||||
|
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GLE::MyMult(ns+1,ns+1,ns+1,T,C,tmp1);
|
||||
GLE::MyTrans(ns+1,T,tmp2);
|
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GLE::MyMult(ns+1,ns+1,ns+1,tmp1,tmp2,S);
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||||
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||||
for (int i=0; i<ns1sq; ++i) tmp1[i]=C[i]-S[i];
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||||
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||||
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
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||||
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 (utils::strmatch(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 nullptr;
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
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 = (double)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;
|
||||
// pack buf[0] this way because other fixes unpack it
|
||||
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
|
||||
// unpack the Nth first values this way because other fixes pack them
|
||||
|
||||
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;
|
||||
}
|
||||
Reference in New Issue
Block a user