setup issues with fix numdiff (0723bf3d) · Commits · 郑智淋 / lammps

examples/numdiff/in.numdiff

+2 −2

Original line number	Diff line number	Diff line
		@@ -21,8 +21,8 @@ variable errx atom fx-f_numdiff[1]
		variable erry atom fy-f_numdiff[2]
		variable errz atom fz-f_numdiff[3]

		write_dump all custom tmp.error f_numdiff[1] f_numdiff[2] f_numdiff[3]

		dump forces all custom 200 force_error.dump v_errx v_erry v_errz
		thermo 200
		run 2000

src/fix_numdiff.cpp

+44 −11

Original line number	Diff line number	Diff line
		@@ -71,7 +71,13 @@ FixNumDiff::FixNumDiff(LAMMPS lmp, int narg, char *arg) :
		numdiff_forces = NULL;
		temp_x = NULL;
		temp_f = NULL;
		array_atom = NULL;

		// perform initial allocation of atom-based arrays
		// zero numdiff_forces since dump may access it on timestep 0
		// zero numdiff_forces since a variable may access it before first run

		reallocate();
		force_clear(numdiff_forces);
		}

		/* ---------------------------------------------------------------------- */
		@@ -127,6 +133,26 @@ void FixNumDiff::init()

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

		void FixNumDiff::setup(int vflag)
		{
		if (strstr(update->integrate_style,"verlet"))
		post_force(vflag);
		else {
		((Respa *) update->integrate)->copy_flevel_f(ilevel_respa);
		post_force_respa(vflag,ilevel_respa,0);
		((Respa *) update->integrate)->copy_f_flevel(ilevel_respa);
		}
		}

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

		void FixNumDiff::min_setup(int vflag)
		{
		post_force(vflag);
		}

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

		void FixNumDiff::post_force(int vflag)
		{
		if (update->ntimestep % nevery) return;
		@@ -159,16 +185,7 @@ void FixNumDiff::calculate_forces()

		// grow arrays if necessary

		if (atom->nlocal + atom->nghost > maxatom) {
		memory->destroy(numdiff_forces);
		memory->destroy(temp_x);
		memory->destroy(temp_f);
		maxatom = atom->nmax;
		memory->create(numdiff_forces,maxatom,3,"numdiff:numdiff_force");
		memory->create(temp_x,maxatom,3,"numdiff:temp_x");
		memory->create(temp_f,maxatom,3,"numdiff:temp_f");
		array_atom = numdiff_forces;
		}
		if (atom->nlocal + atom->nghost > maxatom) reallocate();

		// store copy of current forces for owned and ghost atoms

		@@ -304,6 +321,22 @@ void FixNumDiff::force_clear(double **forces)
		if (nbytes) memset(&forces[0][0],0,3*nbytes);
		}

		/* ----------------------------------------------------------------------
		reallocated local per-atoms arrays
		------------------------------------------------------------------------- */

		void FixNumDiff::reallocate()
		{
		memory->destroy(numdiff_forces);
		memory->destroy(temp_x);
		memory->destroy(temp_f);
		maxatom = atom->nmax;
		memory->create(numdiff_forces,maxatom,3,"numdiff:numdiff_force");
		memory->create(temp_x,maxatom,3,"numdiff:temp_x");
		memory->create(temp_f,maxatom,3,"numdiff:temp_f");
		array_atom = numdiff_forces;
		}

		/* ----------------------------------------------------------------------
		memory usage of local atom-based arrays
		------------------------------------------------------------------------- */

src/fix_numdiff.h

+3 −0

Original line number	Diff line number	Diff line
		@@ -30,6 +30,8 @@ class FixNumDiff : public Fix {
		~FixNumDiff();
		int setmask();
		void init();
		void setup(int);
		void min_setup(int);
		void post_force(int);
		void post_force_respa(int, int, int);
		void min_post_force(int);
		@@ -55,6 +57,7 @@ private:
		void restore_atoms(int, int);
		double update_energy();
		void force_clear(double **);
		void reallocate();
		};

		}

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