re-writting relax_box method (0912054f) · Commits · 郑智淋 / lammps

src/min_adaptglok.cpp

+44 −16

Changes for src/min_adaptglok.cpp: 44 added lines, 16 removed lines.
Original line number	Diff line number	Diff line
		@@ -16,6 +16,7 @@
		#include "universe.h"
		#include "atom.h"
		#include "force.h"
		#include "pair.h"
		#include "update.h"
		#include "output.h"
		#include "timer.h"
		@@ -26,6 +27,8 @@
		#include "domain.h"
		#include "neighbor.h"
		#include "comm.h"
		#include "irregular.h"
		#include "change_box.h"

		using namespace LAMMPS_NS;

		@@ -68,6 +71,12 @@ void MinAdaptGlok::init()
		vdotf_negatif = 0;

		if (relaxbox_flag){

		// require the box to be orthogonal

		if (domain->triclinic)
		error->all(FLERR,"Cannot use boxrelax with triclinic box");

		int icompute = modify->find_compute("thermo_press");
		pressure = modify->compute[icompute];
		}
		@@ -134,25 +143,30 @@ void MinAdaptGlok::save_box_state()
		deform the simulation box and remap the particles
		------------------------------------------------------------------------- */

		void MinAdaptGlok::relax_box()
		void MinAdaptGlok::relax_box1()
		{
		int i,n;

		}

		void MinAdaptGlok::relax_box()
		{
		// rescale simulation box and scale atom coords for all atoms
		// based on change_box.cpp

		int i,n;
		double **x = atom->x;
		double epsilon,disp;
		double *current_pressure_v;
		int *mask = atom->mask;
		n = atom->nlocal + atom->nghost;
		save_box_state();

		// convert pertinent atoms and rigid bodies to lamda coords
		int nlocal = atom->nlocal;

		domain->x2lamda(n);
		domain->pbc();
		domain->reset_box();
		save_box_state();
		neighbor->setup_bins();
		comm->exchange();
		comm->borders();
		neighbor->build(1);

		// ensure the virial is tallied, update the flag

		pressure->addstep(update->ntimestep);
		update->vflag_global = update->ntimestep;

		@@ -163,20 +177,34 @@ void MinAdaptGlok::relax_box()
		epsilon = pressure->scalar / relaxbox_mod;
		for (int i = 0; i < 3; i++) {
		if (relaxbox_flag == 2) epsilon = pressure->vector[i] / relaxbox_mod;
		disp = domain->boxhi[i] * epsilon * relaxbox_rate;
		disp = domain->h[i] * epsilon * relaxbox_rate;
		if (fabs(disp) > dmax) disp > 0.0 ? disp = dmax : disp = -1 * dmax;
		domain->boxhi[i] += p_flag[i] * disp;
		domain->boxlo[i] -= p_flag[i] * disp * 0.5;
		domain->boxhi[i] += p_flag[i] * disp * 0.5;
		}

		// reset global and local box to new size/shape

		domain->set_initial_box();
		domain->set_global_box();
		domain->set_local_box();

		// convert atoms and back to box coords

		domain->lamda2x(n);
		// convert atoms to lamda coords, using last box state
		// convert atoms back to box coords, using current box state
		// save current box state
		for (i = 0; i < nlocal; i++)
		domain->x2lamda(x[i],x[i],boxlo,h_inv);
		for (i = 0; i < nlocal; i++)
		domain->lamda2x(x[i],x[i]);
		save_box_state();

		// move atoms back inside simulation box and to new processors
		// use remap() instead of pbc()
		// in case box moved a long distance relative to atoms

		imageint *image = atom->image;
		for (i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
		domain->reset_box();

		}

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

src/min_adaptglok.h

+1 −0

Changes for src/min_adaptglok.h: 1 added line, 0 removed lines.
Original line number	Diff line number	Diff line
		@@ -33,6 +33,7 @@ class MinAdaptGlok : public Min {
		void reset_vectors();
		void save_box_state();
		void relax_box();
		void relax_box1();
		int iterate(int);

		private:

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