patch 17Mar17 (4a90bca7) · Commits · 郑智淋 / lammps

doc/src/Manual.txt

+2 −2

Original line number	Diff line number	Diff line
		<!-- HTML_ONLY -->
		<HEAD>
		<TITLE>LAMMPS Users Manual</TITLE>
		<META NAME="docnumber" CONTENT="10 Mar 2017 version">
		<META NAME="docnumber" CONTENT="17 Mar 2017 version">
		<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
		<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
		</HEAD>
		@@ -21,7 +21,7 @@
		<H1></H1>

		LAMMPS Documentation :c,h3
		10 Mar 2017 version :c,h4
		17 Mar 2017 version :c,h4

		Version info: :h4

doc/src/Section_commands.txt

+1 −0

Original line number	Diff line number	Diff line
		@@ -687,6 +687,7 @@ package"_Section_start.html#start_3.
		"eos/cv"_fix_eos_cv.html,
		"eos/table"_fix_eos_table.html,
		"eos/table/rx"_fix_eos_table_rx.html,
		"filter/corotate"_fix_filter_corotate.html,
		"flow/gauss"_fix_flow_gauss.html,
		"gle"_fix_gle.html,
		"grem"_fix_grem.html,

doc/src/fix_filter_corotate.txt

+24 −21

Original line number	Diff line number	Diff line
		@@ -31,26 +31,29 @@ fix cor all filter/corotate b 4 19 a 3 5 2 :pre

		[Description:]

		This fix implements a corotational filter for a mollified impulse method. In
		biomolecular simulations, it allows the usage of larger timesteps for
		long-range electrostatic interactions. For details, see "(Fath)"_#Fath2017.

		When using "run_style respa"_run_style.html for a biomolecular simulation with high-frequency covalent
		bonds, the outer time-step is restricted to below ~ 4fs due to resonance
		problems. This fix filters the outer stage of the respa and thus a larger
		(outer) time-step can be used. Since in large biomolecular simulations the
		computation of the long-range electrostatic contributions poses a major
		bottleneck, this can significantly accelerate the simulation.

		The filter computes a cluster decomposition of the molecular structure following
		the criteria indicated by the options a, b, t and m. This process is similar to
		the approach in "fix shake"_fix_shake.html, however, the clusters are not kept
		contrained. Instead, the position is slightly modified only for the computation
		of long-range forces. A good cluster decomposition constitutes in building
		clusters which contain the fastest covalent bonds inside clusters.

		If the clusters are chosen suitably, the "run_style respa"_run_style.html is stable for outer
		time-steps of at least 8fs.
		This fix implements a corotational filter for a mollified impulse
		method. In biomolecular simulations, it allows the usage of larger
		timesteps for long-range electrostatic interactions. For details, see
		"(Fath)"_#Fath2017.

		When using "run_style respa"_run_style.html for a biomolecular
		simulation with high-frequency covalent bonds, the outer time-step is
		restricted to below ~ 4fs due to resonance problems. This fix filters
		the outer stage of the respa and thus a larger (outer) time-step can
		be used. Since in large biomolecular simulations the computation of
		the long-range electrostatic contributions poses a major bottleneck,
		this can significantly accelerate the simulation.

		The filter computes a cluster decomposition of the molecular structure
		following the criteria indicated by the options a, b, t and m. This
		process is similar to the approach in "fix shake"_fix_shake.html,
		however, the clusters are not kept contrained. Instead, the position
		is slightly modified only for the computation of long-range forces. A
		good cluster decomposition constitutes in building clusters which
		contain the fastest covalent bonds inside clusters.

		If the clusters are chosen suitably, the "run_style
		respa"_run_style.html is stable for outer time-steps of at least 8fs.

		:line

src/RIGID/fix_shake.cpp

+1 −0

Original line number	Diff line number	Diff line
		@@ -66,6 +66,7 @@ FixShake::FixShake(LAMMPS lmp, int narg, char *arg) :
		virial_flag = 1;
		create_attribute = 1;
		dof_flag = 1;

		// error check

		molecular = atom->molecular;

src/fix_store_state.cpp

+6 −3

Original line number	Diff line number	Diff line
		@@ -38,7 +38,8 @@ enum{KEYWORD,COMPUTE,FIX,VARIABLE,DNAME,INAME};

		FixStoreState::FixStoreState(LAMMPS lmp, int narg, char *arg) :
		Fix(lmp, narg, arg),
		nvalues(0), which(NULL), argindex(NULL), value2index(NULL), ids(NULL), values(NULL),
		nvalues(0), which(NULL), argindex(NULL), value2index(NULL),
		ids(NULL), values(NULL),
		vbuf(NULL), pack_choice(NULL)
		{
		if (narg < 5) error->all(FLERR,"Illegal fix store/state command");
		@@ -1046,7 +1047,8 @@ void FixStoreState::pack_ysu(int n)

		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit)
		vbuf[n] = (x[i][1]-boxylo)*invyprd + (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
		vbuf[n] = (x[i][1]-boxylo)*invyprd +
		(image[i] >> IMGBITS & IMGMASK) - IMGMAX;
		else vbuf[n] = 0.0;
		n += nvalues;
		}
		@@ -1158,7 +1160,8 @@ void FixStoreState::pack_iy(int n)
		int nlocal = atom->nlocal;

		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) vbuf[n] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
		if (mask[i] & groupbit)
		vbuf[n] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
		else vbuf[n] = 0.0;
		n += nvalues;
		}

Admin message