count each force computation as one simulation step. this avoids accessing uninitialized data, too. (286112ff) · Commits · 郑智淋 / lammps

examples/USER/phonon/dynamical_matrix_command/Manual.md

deleted100755 → 0

+0 −48

Original line number	Diff line number	Diff line
		# dynamical_matrix command

		## Syntax

		```
		dynamical_matrix group-ID style args keyword value ...
		```

		* group-ID = ID of group of atoms to displace
		* style = regular or eskm
		```
		regular args = gamma
		gamma = finite difference displacement length
		eskm args = gamma
		gamma = finite difference displacement length
		```
		* zero or more keyword/value pairs may be appended
		* keyword = file or binary
		```
		file value = output_file
		output_file = name of file to dump the dynamical matrix into
		binary values = yes or no or gzip
		```

		## Examples

		```
		dynamical_matrix 1 regular 0.000001
		dynamical_matrix 1 eskm 0.000001
		dynamical_matrix 3 regular 0.00004 file dynmat.dat
		dynamical_matrix 5 eskm 0.00000001 file dynamical.dat binary yes
		```

		## Description

		Calculate the dynamical matrix of the selected group.

		## Restrictions

		None

		## Related commands

		None

		## Default

		The option defaults are file = "dynmat.dyn", binary = no

+3 −1

Original line number	Diff line number	Diff line
		@@ -258,6 +258,7 @@ void DynamicalMatrix::calculateMatrix()

		if (comm->me == 0 && screen) fprintf(screen,"Calculating Dynamical Matrix...\n");

		update->nsteps = 0;
		for (bigint i=1; i<=natoms; i++){
		local_idx = atom->map(i);
		for (bigint alpha=0; alpha<3; alpha++){
		@@ -390,6 +391,7 @@ void DynamicalMatrix::update_force()
		comm->reverse_comm();
		timer->stamp(Timer::COMM);
		}
		++ update->nsteps;
		}

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

+3 −1

Original line number	Diff line number	Diff line
		@@ -247,6 +247,7 @@ void ThirdOrder::calculateMatrix()

		if (comm->me == 0 && screen) fprintf(screen,"Calculating Anharmonic Dynamical Matrix...\n");

		update->nsteps = 0;
		for (bigint i=1; i<=natoms; i++){
		local_idx = atom->map(i);
		for (bigint alpha=0; alpha<3; alpha++){
		@@ -411,6 +412,7 @@ void ThirdOrder::update_force()
		comm->reverse_comm();
		timer->stamp(Timer::COMM);
		}
		++ update->nsteps;
		}

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