Merge pull request #1937 from jibril-b-coulibaly/fixadapt (4acdd161) · Commits · 郑智淋 / lammps

doc/src/fix_adapt.rst

+11 −14

Original line number	Diff line number	Diff line
		@@ -14,7 +14,7 @@ Syntax
		* adapt = style name of this fix command
		* N = adapt simulation settings every this many timesteps
		* one or more attribute/arg pairs may be appended
		* attribute = pair or kspace or atom
		* attribute = pair or bond or kspace or atom

		.. parsed-literal::

		@@ -86,8 +86,8 @@ the end of a simulation. Even if reset is specified as yes\ , a
		restart file written during a simulation will contain the modified
		settings.

		If the scale keyword is set to no\ , then the value the parameter is
		set to will be whatever the variable generates. If the scale
		If the scale keyword is set to no\ , then the value of the altered
		parameter will be whatever the variable generates. If the scale
		keyword is set to yes\ , then the value of the altered parameter will
		be the initial value of that parameter multiplied by whatever the
		variable generates. I.e. the variable is now a "scale factor" applied
		@@ -319,26 +319,23 @@ The atom keyword enables various atom properties to be changed. The
		current list of atom parameters that can be varied by this fix:

		* charge = charge on particle
		* diameter = diameter of particle
		* diameter, or, diameter/disc = diameter of particle

		The v_name argument of the atom keyword is the name of an
		:doc:`equal-style variable <variable>` which will be evaluated each time
		this fix is invoked to set the parameter to a new value. It should be
		specified as v_name, where name is the variable name. See the
		this fix is invoked to set, or scale the parameter to a new value.
		It should be specified as v_name, where name is the variable name. See the
		discussion above describing the formulas associated with equal-style
		variables. The new value is assigned to the corresponding attribute
		for all atoms in the fix group.

		.. note::

		The atom keyword works this way whether the scale keyword is
		set to no or yes\ . I.e. the use of scale yes is not yet supported
		by the atom keyword.

		If the atom parameter is diameter and per-atom density and per-atom
		mass are defined for particles (e.g. :doc:`atom_style granular <atom_style>`), then the mass of each particle is also
		changed when the diameter changes (density is assumed to stay
		constant).
		changed when the diameter changes. The mass is set from the particle volume
		for 3d systems (density is assumed to stay constant). For 2d, the default is
		for LAMMPS to model particles with a radius attribute as spheres.
		However, if the atom parameter is diameter/disc, then the mass is
		set from the particle area (the density is assumed to be in mass/distance^2 units).

		For example, these commands would shrink the diameter of all granular
		particles in the "center" group from 1.0 to 0.1 in a linear fashion

src/fix_adapt.cpp

+40 −25

Original line number	Diff line number	Diff line
		@@ -15,6 +15,7 @@
		#include <cstring>
		#include "atom.h"
		#include "bond.h"
		#include "domain.h"
		#include "update.h"
		#include "group.h"
		#include "modify.h"
		@@ -139,9 +140,11 @@ nadapt(0), id_fix_diam(NULL), id_fix_chg(NULL), adapt(NULL)
		} else if (strcmp(arg[iarg],"atom") == 0) {
		if (iarg+3 > narg) error->all(FLERR,"Illegal fix adapt command");
		adapt[nadapt].which = ATOM;
		if (strcmp(arg[iarg+1],"diameter") == 0) {
		if (strcmp(arg[iarg+1],"diameter") == 0 \|\| strcmp(arg[iarg+1],"diameter/disc") == 0) {
		adapt[nadapt].aparam = DIAMETER;
		diamflag = 1;
		discflag = 0;
		if (strcmp(arg[iarg+1],"diameter/disc") == 0) discflag = 1;
		} else if (strcmp(arg[iarg+1],"charge") == 0) {
		adapt[nadapt].aparam = CHARGE;
		chgflag = 1;
		@@ -235,7 +238,6 @@ int FixAdapt::setmask()

		void FixAdapt::post_constructor()
		{
		if (!resetflag) return;
		if (!diamflag && !chgflag) return;

		// new id = fix-ID + FIX_STORE_ATTRIBUTE
		@@ -251,7 +253,7 @@ void FixAdapt::post_constructor()
		newarg[4] = (char *) "1";
		newarg[5] = (char *) "1";

		if (diamflag) {
		if (diamflag && atom->radius_flag) {
		int n = strlen(id) + strlen("_FIX_STORE_DIAM") + 1;
		id_fix_diam = new char[n];
		strcpy(id_fix_diam,id);
		@@ -274,7 +276,7 @@ void FixAdapt::post_constructor()
		}
		}

		if (chgflag) {
		if (chgflag && atom->q_flag) {
		int n = strlen(id) + strlen("_FIX_STORE_CHG") + 1;
		id_fix_chg = new char[n];
		strcpy(id_fix_chg,id);
		@@ -428,6 +430,10 @@ void FixAdapt::init()
		if (ad->aparam == DIAMETER) {
		if (!atom->radius_flag)
		error->all(FLERR,"Fix adapt requires atom attribute diameter");
		if (!atom->rmass_flag)
		error->all(FLERR,"Fix adapt requires atom attribute mass");
		if (discflag && domain->dimension!=2)
		error->all(FLERR,"Fix adapt requires 2d simulation");
		}
		if (ad->aparam == CHARGE) {
		if (!atom->q_flag)
		@@ -568,38 +574,44 @@ void FixAdapt::change_settings()
		// also scale rmass to new value

		if (ad->aparam == DIAMETER) {
		int mflag = 0;
		if (atom->rmass_flag) mflag = 1;
		double density;

		// Get initial diameter if `scale` keyword is used

		double *vec = fix_diam->vstore;
		double *radius = atom->radius;
		double *rmass = atom->rmass;
		int *mask = atom->mask;
		int nlocal = atom->nlocal;
		int nall = nlocal + atom->nghost;

		if (mflag == 0) {
		for (i = 0; i < nall; i++)
		if (mask[i] & groupbit)
		radius[i] = 0.5*value;
		} else {
		for (i = 0; i < nall; i++)
		if (mask[i] & groupbit) {
		density = rmass[i] / (4.0MY_PI/3.0
		if (discflag) density = rmass[i] / (MY_PI * radius[i]*radius[i]);
		else density = rmass[i] / (4.0MY_PI/3.0
		radius[i]radius[i]radius[i]);
		radius[i] = 0.5*value;
		rmass[i] = 4.0MY_PI/3.0
		if (scaleflag) radius[i] = value * vec[i];
		else radius[i] = 0.5*value;
		if (discflag) rmass[i] = MY_PI * radius[i]radius[i] density;
		else rmass[i] = 4.0MY_PI/3.0
		radius[i]radius[i]radius[i] * density;
		}
		}

		} else if (ad->aparam == CHARGE) {

		// Get initial charge if `scale` keyword is used

		double *vec = fix_chg->vstore;
		double *q = atom->q;
		int *mask = atom->mask;
		int nlocal = atom->nlocal;
		int nall = nlocal + atom->nghost;

		for (i = 0; i < nall; i++)
		if (mask[i] & groupbit) q[i] = value;
		if (mask[i] & groupbit) {
		if (scaleflag) q[i] = value * vec[i];
		else q[i] = value;
		}
		}
		}
		}
		@@ -607,7 +619,7 @@ void FixAdapt::change_settings()
		modify->addstep_compute(update->ntimestep + nevery);

		// re-initialize pair styles if any PAIR settings were changed
		// ditto for bond styles if any BOND setitings were changes
		// ditto for bond styles if any BOND settings were changed
		// this resets other coeffs that may depend on changed values,
		// and also offset and tail corrections

		@@ -670,10 +682,13 @@ void FixAdapt::restore_settings()

		for (int i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {
		density = rmass[i] / (4.0MY_PI/3.0
		if(discflag) density = rmass[i] / (MY_PI * radius[i]*radius[i]);
		else density = rmass[i] / (4.0MY_PI/3.0
		radius[i]radius[i]radius[i]);
		radius[i] = vec[i];
		rmass[i] = 4.0MY_PI/3.0 radius[i]radius[i]radius[i] * density;
		if(discflag) rmass[i] = MY_PI * radius[i]radius[i] density;
		else rmass[i] = 4.0MY_PI/3.0
		radius[i]radius[i]radius[i] * density;
		}
		}
		if (chgflag) {

src/fix_adapt.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -47,6 +47,7 @@ class FixAdapt : public Fix {
		int nlevels_respa;
		char id_fix_diam,id_fix_chg;
		class FixStore fix_diam,fix_chg;
		int discflag;

		struct Adapt {
		int which,ivar;

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