Merge pull request #445 from Pakketeretet2/extract_for_bond (06cebb9f) · 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/MOLECULE/bond_harmonic.cpp

+18 −1

Original line number	Diff line number	Diff line
		@@ -13,6 +13,7 @@

		#include <math.h>
		#include <stdlib.h>
		#include <string.h>
		#include "bond_harmonic.h"
		#include "atom.h"
		#include "neighbor.h"
		@@ -26,7 +27,10 @@ using namespace LAMMPS_NS;

		/* ---------------------------------------------------------------------- */

		BondHarmonic::BondHarmonic(LAMMPS *lmp) : Bond(lmp) {}
		BondHarmonic::BondHarmonic(LAMMPS *lmp) : Bond(lmp)
		{
		reinitflag = 1;
		}

		/* ---------------------------------------------------------------------- */

		@@ -196,3 +200,16 @@ double BondHarmonic::single(int type, double rsq, int i, int j,
		if (r > 0.0) fforce = -2.0*rk/r;
		return rk*dr;
		}

		/* ----------------------------------------------------------------------
		Return ptr to internal members upon request.
		------------------------------------------------------------------------ */
		void BondHarmonic::extract( char str, int &dim )
		{
		dim = 1;
		if( strcmp(str,"kappa")==0) return (void*) k;
		if( strcmp(str,"r0")==0) return (void*) r0;
		return NULL;
		}

src/MOLECULE/bond_harmonic.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -36,6 +36,7 @@ class BondHarmonic : public Bond {
		void read_restart(FILE *);
		void write_data(FILE *);
		double single(int, double, int, int, double &);
		virtual void extract(char , int &);

		protected:
		double k,r0;

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**);

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