Made fix adapt work with bond_harmonic. (28e86917) · Commits · 郑智淋 / lammps

doc/src/fix_adapt.txt

+22 −1

Original line number	Diff line number	Diff line
		@@ -22,6 +22,11 @@ attribute = {pair} or {kspace} or {atom} :l
		pparam = parameter to adapt over time
		I,J = type pair(s) to set parameter for
		v_name = variable with name that calculates value of pparam
		{bond} args = bstyle bparam I v_name
		bstyle = bond style name, e.g. harmonic
		bparam = parameter to adapt over time
		I = type bond to set parameter for
		v_name = variable with name that calculates value of bparam
		{kspace} arg = v_name
		v_name = variable with name that calculates scale factor on K-space terms
		{atom} args = aparam v_name
		@@ -42,7 +47,10 @@ keyword = {scale} or {reset} :l
		fix 1 all adapt 1 pair soft a 1 1 v_prefactor
		fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
		fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
		fix 1 all adapt 10 atom diameter v_size :pre
		fix 1 all adapt 10 atom diameter v_size

		variable ramp_up equal "ramp(0.01,0.5)"
		fix stretch all adapt 1 bond harmonic r0 1 v_ramp_up :pre

		[Description:]

		@@ -192,6 +200,19 @@ fix 1 all adapt 1 pair soft a * * v_prefactor :pre

		:line

		The {bond} keyword uses the specified variable to change the value of
		a bond coefficient over time, very similar to how the {pair} keyword
		operates. The only difference is that now a bond coefficient for a
		given bond type is adapted.

		Currently {bond} does not support bond_style hybrid nor bond_style
		hybrid/overlay as bond styles. The only bonds that currently are
		working with fix_adapt are

		"harmonic"_bond_harmonic.html: k,r0: type bonds :tb(c=3,s=:)

		:line

		The {kspace} keyword used the specified variable as a scale factor on
		the energy, forces, virial calculated by whatever K-Space solver is
		defined by the "kspace_style"_kspace_style.html command. If the

src/bond.cpp

+11 −0

Original line number	Diff line number	Diff line
		@@ -292,3 +292,14 @@ double Bond::memory_usage()
		bytes += comm->nthreadsmaxvatom6 * sizeof(double);
		return bytes;
		}

		/* -----------------------------------------------------------------------
		Reset all type-based bond params via init.
		-------------------------------------------------------------------------- */
		void Bond::reinit()
		{
		if (!reinitflag)
		error->all(FLERR,"Fix adapt interface to this bond style not supported");

		init();
		}

src/bond.h

+4 −0

Original line number	Diff line number	Diff line
		@@ -30,6 +30,8 @@ class Bond : protected Pointers {
		double virial[6]; // accumulated virial
		double eatom,*vatom; // accumulated per-atom energy/virial

		int reinitflag; // 1 if compatible with fix adapt and alike

		// KOKKOS host/device flag and data masks

		ExecutionSpace execution_space;
		@@ -49,6 +51,8 @@ class Bond : protected Pointers {
		virtual void write_data(FILE *) {}
		virtual double single(int, double, int, int, double &) = 0;
		virtual double memory_usage();
		virtual void extract(char , int &) {return NULL;}
		virtual void reinit();

		void write_file(int, char**);

src/fix_adapt.cpp

+111 −2

Original line number	Diff line number	Diff line
		@@ -16,6 +16,7 @@
		#include <stdlib.h>
		#include "fix_adapt.h"
		#include "atom.h"
		#include "bond.h"
		#include "update.h"
		#include "group.h"
		#include "modify.h"
		@@ -35,7 +36,7 @@ using namespace LAMMPS_NS;
		using namespace FixConst;
		using namespace MathConst;

		enum{PAIR,KSPACE,ATOM};
		enum{PAIR,KSPACE,ATOM,BOND};
		enum{DIAMETER,CHARGE};

		/* ---------------------------------------------------------------------- */
		@@ -68,6 +69,10 @@ nadapt(0), id_fix_diam(NULL), id_fix_chg(NULL), adapt(NULL)
		if (iarg+3 > narg) error->all(FLERR,"Illegal fix adapt command");
		nadapt++;
		iarg += 3;
		} else if (strcmp(arg[iarg],"bond") == 0 ){
		if (iarg+5 > narg) error->all(FLERR,"Illegal fix adapt command");
		nadapt++;
		iarg += 5;
		} else break;
		}

		@@ -103,6 +108,25 @@ nadapt(0), id_fix_diam(NULL), id_fix_chg(NULL), adapt(NULL)
		} else error->all(FLERR,"Illegal fix adapt command");
		nadapt++;
		iarg += 6;
		} else if (strcmp(arg[iarg],"bond") == 0 ){
		if (iarg+5 > narg) error->all(FLERR, "Illegal fix adapt command");
		adapt[nadapt].which = BOND;
		int n = strlen(arg[iarg+1]) + 1;
		adapt[nadapt].bstyle = new char[n];
		strcpy(adapt[nadapt].bstyle,arg[iarg+1]);
		n = strlen(arg[iarg+2]) + 1;
		adapt[nadapt].bparam = new char[n];
		adapt[nadapt].bond = NULL;
		strcpy(adapt[nadapt].bparam,arg[iarg+2]);
		force->bounds(FLERR,arg[iarg+3],atom->ntypes,
		adapt[nadapt].ilo,adapt[nadapt].ihi);
		if (strstr(arg[iarg+4],"v_") == arg[iarg+4]) {
		n = strlen(&arg[iarg+4][2]) + 1;
		adapt[nadapt].var = new char[n];
		strcpy(adapt[nadapt].var,&arg[iarg+4][2]);
		} else error->all(FLERR,"Illegal fix adapt command");
		nadapt++;
		iarg += 5;
		} else if (strcmp(arg[iarg],"kspace") == 0) {
		if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
		adapt[nadapt].which = KSPACE;
		@@ -160,6 +184,13 @@ nadapt(0), id_fix_diam(NULL), id_fix_chg(NULL), adapt(NULL)
		for (int m = 0; m < nadapt; m++)
		if (adapt[m].which == PAIR)
		memory->create(adapt[m].array_orig,n+1,n+1,"adapt:array_orig");

		// allocate bond style arrays:
		n = atom->nbondtypes;
		for (int m = 0; m < nadapt; ++m)
		if (adapt[m].which == BOND)
		// For now just use same storage and fake it to be one-dimensional:
		memory->create(adapt[m].vector_orig,n+1,"adapt:vector_orig");
		}

		/* ---------------------------------------------------------------------- */
		@@ -172,6 +203,10 @@ FixAdapt::~FixAdapt()
		delete [] adapt[m].pstyle;
		delete [] adapt[m].pparam;
		memory->destroy(adapt[m].array_orig);
		} else if (adapt[m].which == BOND) {
		delete [] adapt[m].bstyle;
		delete [] adapt[m].bparam;
		memory->destroy(adapt[m].vector_orig);
		}
		}
		delete [] adapt;
		@@ -282,6 +317,7 @@ void FixAdapt::init()
		// setup and error checks

		anypair = 0;
		anybond = 0;

		for (int m = 0; m < nadapt; m++) {
		Adapt *ad = &adapt[m];
		@@ -350,6 +386,47 @@ void FixAdapt::init()
		}

		delete [] pstyle;
		} else if (ad->which == BOND){
		ad->bond = NULL;
		anybond = 1;
		// Use same routines from pair to strip any suffices:

		int n = strlen(ad->bstyle) + 1;
		char *bstyle = new char[n];
		strcpy(bstyle,ad->bstyle);

		if (lmp->suffix_enable) {
		int len = 2 + strlen(bstyle) + strlen(lmp->suffix);
		char *bsuffix = new char[len];
		strcpy(bsuffix,bstyle);
		strcat(bsuffix,"/");
		strcat(bsuffix,lmp->suffix);
		ad->bond = force->bond_match(bsuffix);
		delete [] bsuffix;
		}
		// If not set grab regular one instead:
		if (ad->bond == NULL) ad->bond = force->bond_match(bstyle);
		if (ad->bond == NULL )
		error->all(FLERR,"Fix adapt bond style does not exist");

		void *ptr = ad->bond->extract(ad->bparam,ad->bdim);
		if( comm->me == 0 ){
		fprintf(screen,"Attempting to extract %s\n", ad->bparam);
		fprintf(screen,"Got back %p\n", ptr);
		}

		if (ptr == NULL)
		error->all(FLERR,"Fix adapt bond style param not supported");

		// For bond styles you should use a vector

		if (ad->bdim == 1) ad->vector = (double *) ptr;

		if (strcmp(force->bond_style,"hybrid") == 0 \|\|
		strcmp(force->bond_style,"hybrid_overlay") == 0)
		error->all(FLERR,"Fix adapt does not support bond_style hybrid");

		delete [] bstyle;

		} else if (ad->which == KSPACE) {
		if (force->kspace == NULL)
		@@ -368,7 +445,7 @@ void FixAdapt::init()
		}
		}

		// make copy of original pair array values
		// make copy of original pair/bond array values

		for (int m = 0; m < nadapt; m++) {
		Adapt *ad = &adapt[m];
		@@ -378,7 +455,12 @@ void FixAdapt::init()
		ad->array_orig[i][j] = ad->array[i][j];
		}else if (ad->which == PAIR && ad->pdim == 0){
		ad->scalar_orig = *ad->scalar;

		}else if (ad->which == BOND && ad->bdim == 1){
		for (i = ad->ilo; i <= ad->ihi; ++i )
		ad->vector_orig[i] = ad->vector[i];
		}

		}

		// fixes that store initial per-atom values
		@@ -470,6 +552,18 @@ void FixAdapt::change_settings()
		ad->array[i][j] = value;
		}

		// set bond type array values:

		} else if (ad->which == BOND) {
		if (ad->pdim == 1){
		if (scaleflag)
		for (i = ad->ilo; i <= ad->ihi; ++i )
		ad->vector[i] = value*ad->vector_orig[i];
		else
		for (i = ad->ilo; i <= ad->ihi; ++i )
		ad->vector[i] = value;
		}

		// set kspace scale factor

		} else if (ad->which == KSPACE) {
		@@ -532,6 +626,14 @@ void FixAdapt::change_settings()
		}
		}
		}
		if (anybond) {
		for (int m = 0; m < nadapt; ++m ) {
		Adapt *ad = &adapt[m];
		if (ad->which == BOND) {
		ad->bond->reinit();
		}
		}
		}

		// reset KSpace charges if charges have changed

		@@ -554,6 +656,12 @@ void FixAdapt::restore_settings()
		ad->array[i][j] = ad->array_orig[i][j];
		}

		} else if (ad->which == BOND) {
		if (ad->pdim == 1) {
		for (int i = ad->ilo; i <= ad->ihi; i++)
		ad->vector[i] = ad->vector_orig[i];
		}

		} else if (ad->which == KSPACE) {
		*kspace_scale = 1.0;

		@@ -588,6 +696,7 @@ void FixAdapt::restore_settings()
		}

		if (anypair) force->pair->reinit();
		if (anybond) force->bond->reinit();
		if (chgflag && force->kspace) force->kspace->qsum_qsq();
		}

src/fix_adapt.h

+5 −2

Original line number	Diff line number	Diff line
		@@ -43,7 +43,7 @@ class FixAdapt : public Fix {

		private:
		int nadapt,resetflag,scaleflag;
		int anypair;
		int anypair, anybond;
		int nlevels_respa;
		char id_fix_diam,id_fix_chg;
		class FixStore fix_diam,fix_chg;
		@@ -52,12 +52,15 @@ class FixAdapt : public Fix {
		int which,ivar;
		char *var;
		char pstyle,pparam;
		char bstyle,bparam;
		int ilo,ihi,jlo,jhi;
		int pdim;
		int pdim,bdim;
		double *scalar,scalar_orig;
		double vector,vector_orig;
		double array,array_orig;
		int aparam;
		class Pair *pair;
		class Bond *bond;
		};

		Adapt *adapt;

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