forked from lijiext/lammps
Merge pull request #445 from Pakketeretet2/extract_for_bond
Extract for bond
This commit is contained in:
sjplimp
GitHub
commit
06cebb9fb4
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@ -22,6 +22,11 @@ attribute = {pair} or {kspace} or {atom} :l
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pparam = parameter to adapt over time
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I,J = type pair(s) to set parameter for
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v_name = variable with name that calculates value of pparam
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{bond} args = bstyle bparam I v_name
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bstyle = bond style name, e.g. harmonic
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bparam = parameter to adapt over time
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I = type bond to set parameter for
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v_name = variable with name that calculates value of bparam
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{kspace} arg = v_name
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v_name = variable with name that calculates scale factor on K-space terms
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{atom} args = aparam v_name
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@ -42,7 +47,10 @@ keyword = {scale} or {reset} :l
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fix 1 all adapt 1 pair soft a 1 1 v_prefactor
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fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
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fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
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fix 1 all adapt 10 atom diameter v_size :pre
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fix 1 all adapt 10 atom diameter v_size
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variable ramp_up equal "ramp(0.01,0.5)"
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fix stretch all adapt 1 bond harmonic r0 1 v_ramp_up :pre
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[Description:]
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@ -192,6 +200,19 @@ fix 1 all adapt 1 pair soft a * * v_prefactor :pre
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:line
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The {bond} keyword uses the specified variable to change the value of
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a bond coefficient over time, very similar to how the {pair} keyword
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operates. The only difference is that now a bond coefficient for a
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given bond type is adapted.
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Currently {bond} does not support bond_style hybrid nor bond_style
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hybrid/overlay as bond styles. The only bonds that currently are
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working with fix_adapt are
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"harmonic"_bond_harmonic.html: k,r0: type bonds :tb(c=3,s=:)
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:line
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The {kspace} keyword used the specified variable as a scale factor on
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the energy, forces, virial calculated by whatever K-Space solver is
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defined by the "kspace_style"_kspace_style.html command. If the
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@ -13,6 +13,7 @@
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#include <math.h>
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#include <stdlib.h>
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#include <string.h>
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#include "bond_harmonic.h"
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#include "atom.h"
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#include "neighbor.h"
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@ -26,7 +27,10 @@ using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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BondHarmonic::BondHarmonic(LAMMPS *lmp) : Bond(lmp) {}
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BondHarmonic::BondHarmonic(LAMMPS *lmp) : Bond(lmp)
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{
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reinitflag = 1;
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}
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/* ---------------------------------------------------------------------- */
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@ -196,3 +200,16 @@ double BondHarmonic::single(int type, double rsq, int i, int j,
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if (r > 0.0) fforce = -2.0*rk/r;
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return rk*dr;
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}
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/* ----------------------------------------------------------------------
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Return ptr to internal members upon request.
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------------------------------------------------------------------------ */
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void *BondHarmonic::extract( char *str, int &dim )
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{
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dim = 1;
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if( strcmp(str,"kappa")==0) return (void*) k;
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if( strcmp(str,"r0")==0) return (void*) r0;
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return NULL;
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}
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@ -36,6 +36,7 @@ class BondHarmonic : public Bond {
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void read_restart(FILE *);
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void write_data(FILE *);
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double single(int, double, int, int, double &);
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virtual void *extract(char *, int &);
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protected:
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double *k,*r0;
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11
src/bond.cpp
11
src/bond.cpp
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@ -292,3 +292,14 @@ double Bond::memory_usage()
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bytes += comm->nthreads*maxvatom*6 * sizeof(double);
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return bytes;
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}
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/* -----------------------------------------------------------------------
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Reset all type-based bond params via init.
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-------------------------------------------------------------------------- */
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void Bond::reinit()
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{
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if (!reinitflag)
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error->all(FLERR,"Fix adapt interface to this bond style not supported");
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init();
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}
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@ -30,6 +30,8 @@ class Bond : protected Pointers {
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double virial[6]; // accumulated virial
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double *eatom,**vatom; // accumulated per-atom energy/virial
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int reinitflag; // 1 if compatible with fix adapt and alike
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// KOKKOS host/device flag and data masks
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ExecutionSpace execution_space;
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@ -49,6 +51,8 @@ class Bond : protected Pointers {
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virtual void write_data(FILE *) {}
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virtual double single(int, double, int, int, double &) = 0;
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virtual double memory_usage();
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virtual void *extract(char *, int &) {return NULL;}
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virtual void reinit();
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void write_file(int, char**);
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@ -16,6 +16,7 @@
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#include <stdlib.h>
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#include "fix_adapt.h"
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#include "atom.h"
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#include "bond.h"
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#include "update.h"
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#include "group.h"
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#include "modify.h"
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@ -35,7 +36,7 @@ using namespace LAMMPS_NS;
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using namespace FixConst;
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using namespace MathConst;
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enum{PAIR,KSPACE,ATOM};
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enum{PAIR,KSPACE,ATOM,BOND};
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enum{DIAMETER,CHARGE};
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/* ---------------------------------------------------------------------- */
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@ -68,6 +69,10 @@ nadapt(0), id_fix_diam(NULL), id_fix_chg(NULL), adapt(NULL)
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if (iarg+3 > narg) error->all(FLERR,"Illegal fix adapt command");
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nadapt++;
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iarg += 3;
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} else if (strcmp(arg[iarg],"bond") == 0 ){
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if (iarg+5 > narg) error->all(FLERR,"Illegal fix adapt command");
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nadapt++;
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iarg += 5;
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} else break;
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}
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@ -103,6 +108,25 @@ nadapt(0), id_fix_diam(NULL), id_fix_chg(NULL), adapt(NULL)
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} else error->all(FLERR,"Illegal fix adapt command");
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nadapt++;
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iarg += 6;
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} else if (strcmp(arg[iarg],"bond") == 0 ){
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if (iarg+5 > narg) error->all(FLERR, "Illegal fix adapt command");
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adapt[nadapt].which = BOND;
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int n = strlen(arg[iarg+1]) + 1;
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adapt[nadapt].bstyle = new char[n];
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strcpy(adapt[nadapt].bstyle,arg[iarg+1]);
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n = strlen(arg[iarg+2]) + 1;
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adapt[nadapt].bparam = new char[n];
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adapt[nadapt].bond = NULL;
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strcpy(adapt[nadapt].bparam,arg[iarg+2]);
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force->bounds(FLERR,arg[iarg+3],atom->ntypes,
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adapt[nadapt].ilo,adapt[nadapt].ihi);
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if (strstr(arg[iarg+4],"v_") == arg[iarg+4]) {
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n = strlen(&arg[iarg+4][2]) + 1;
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adapt[nadapt].var = new char[n];
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strcpy(adapt[nadapt].var,&arg[iarg+4][2]);
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} else error->all(FLERR,"Illegal fix adapt command");
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nadapt++;
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iarg += 5;
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} else if (strcmp(arg[iarg],"kspace") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
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adapt[nadapt].which = KSPACE;
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@ -160,6 +184,13 @@ nadapt(0), id_fix_diam(NULL), id_fix_chg(NULL), adapt(NULL)
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for (int m = 0; m < nadapt; m++)
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if (adapt[m].which == PAIR)
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memory->create(adapt[m].array_orig,n+1,n+1,"adapt:array_orig");
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// allocate bond style arrays:
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n = atom->nbondtypes;
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for (int m = 0; m < nadapt; ++m)
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if (adapt[m].which == BOND)
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// For now just use same storage and fake it to be one-dimensional:
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memory->create(adapt[m].vector_orig,n+1,"adapt:vector_orig");
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}
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/* ---------------------------------------------------------------------- */
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@ -172,6 +203,10 @@ FixAdapt::~FixAdapt()
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delete [] adapt[m].pstyle;
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delete [] adapt[m].pparam;
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memory->destroy(adapt[m].array_orig);
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} else if (adapt[m].which == BOND) {
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delete [] adapt[m].bstyle;
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delete [] adapt[m].bparam;
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memory->destroy(adapt[m].vector_orig);
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}
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}
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delete [] adapt;
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@ -282,6 +317,7 @@ void FixAdapt::init()
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// setup and error checks
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anypair = 0;
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anybond = 0;
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for (int m = 0; m < nadapt; m++) {
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Adapt *ad = &adapt[m];
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@ -350,7 +386,44 @@ void FixAdapt::init()
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}
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delete [] pstyle;
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} else if (ad->which == BOND){
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ad->bond = NULL;
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anybond = 1;
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// Use same routines from pair to strip any suffices:
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int n = strlen(ad->bstyle) + 1;
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char *bstyle = new char[n];
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strcpy(bstyle,ad->bstyle);
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if (lmp->suffix_enable) {
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int len = 2 + strlen(bstyle) + strlen(lmp->suffix);
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char *bsuffix = new char[len];
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strcpy(bsuffix,bstyle);
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strcat(bsuffix,"/");
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strcat(bsuffix,lmp->suffix);
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ad->bond = force->bond_match(bsuffix);
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delete [] bsuffix;
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}
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// If not set grab regular one instead:
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if (ad->bond == NULL) ad->bond = force->bond_match(bstyle);
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if (ad->bond == NULL )
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error->all(FLERR,"Fix adapt bond style does not exist");
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void *ptr = ad->bond->extract(ad->bparam,ad->bdim);
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if (ptr == NULL)
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error->all(FLERR,"Fix adapt bond style param not supported");
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// For bond styles you should use a vector
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if (ad->bdim == 1) ad->vector = (double *) ptr;
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if (strcmp(force->bond_style,"hybrid") == 0 ||
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strcmp(force->bond_style,"hybrid_overlay") == 0)
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error->all(FLERR,"Fix adapt does not support bond_style hybrid");
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delete [] bstyle;
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} else if (ad->which == KSPACE) {
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if (force->kspace == NULL)
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error->all(FLERR,"Fix adapt kspace style does not exist");
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@ -368,7 +441,7 @@ void FixAdapt::init()
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}
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}
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// make copy of original pair array values
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// make copy of original pair/bond array values
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for (int m = 0; m < nadapt; m++) {
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Adapt *ad = &adapt[m];
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@ -378,7 +451,12 @@ void FixAdapt::init()
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ad->array_orig[i][j] = ad->array[i][j];
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}else if (ad->which == PAIR && ad->pdim == 0){
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ad->scalar_orig = *ad->scalar;
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}else if (ad->which == BOND && ad->bdim == 1){
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for (i = ad->ilo; i <= ad->ihi; ++i )
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ad->vector_orig[i] = ad->vector[i];
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}
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}
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// fixes that store initial per-atom values
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@ -470,6 +548,18 @@ void FixAdapt::change_settings()
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ad->array[i][j] = value;
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}
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// set bond type array values:
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} else if (ad->which == BOND) {
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if (ad->bdim == 1){
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if (scaleflag)
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for (i = ad->ilo; i <= ad->ihi; ++i )
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ad->vector[i] = value*ad->vector_orig[i];
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else
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for (i = ad->ilo; i <= ad->ihi; ++i )
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ad->vector[i] = value;
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}
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// set kspace scale factor
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} else if (ad->which == KSPACE) {
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@ -532,6 +622,14 @@ void FixAdapt::change_settings()
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}
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}
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}
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if (anybond) {
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for (int m = 0; m < nadapt; ++m ) {
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Adapt *ad = &adapt[m];
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if (ad->which == BOND) {
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ad->bond->reinit();
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}
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}
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}
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// reset KSpace charges if charges have changed
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@ -554,6 +652,12 @@ void FixAdapt::restore_settings()
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ad->array[i][j] = ad->array_orig[i][j];
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}
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} else if (ad->which == BOND) {
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if (ad->pdim == 1) {
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for (int i = ad->ilo; i <= ad->ihi; i++)
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ad->vector[i] = ad->vector_orig[i];
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}
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} else if (ad->which == KSPACE) {
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*kspace_scale = 1.0;
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@ -588,6 +692,7 @@ void FixAdapt::restore_settings()
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}
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if (anypair) force->pair->reinit();
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if (anybond) force->bond->reinit();
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if (chgflag && force->kspace) force->kspace->qsum_qsq();
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}
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@ -43,7 +43,7 @@ class FixAdapt : public Fix {
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private:
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int nadapt,resetflag,scaleflag;
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int anypair;
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int anypair, anybond;
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int nlevels_respa;
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char *id_fix_diam,*id_fix_chg;
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class FixStore *fix_diam,*fix_chg;
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@ -52,12 +52,15 @@ class FixAdapt : public Fix {
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int which,ivar;
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char *var;
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char *pstyle,*pparam;
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char *bstyle,*bparam;
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int ilo,ihi,jlo,jhi;
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int pdim;
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int pdim,bdim;
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double *scalar,scalar_orig;
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double *vector,*vector_orig;
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double **array,**array_orig;
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int aparam;
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class Pair *pair;
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class Bond *bond;
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};
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Adapt *adapt;
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