Merge branch 'master' into coulomb-refactoring (9d8d88d0) · Commits · 郑智淋 / lammps

doc/src/Manual.txt

+2 −2

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		<!-- HTML_ONLY -->
		<HEAD>
		<TITLE>LAMMPS Users Manual</TITLE>
		<META NAME="docnumber" CONTENT="26 Jan 2017 version">
		<META NAME="docnumber" CONTENT="21 Feb 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
		26 Jan 2017 version :c,h4
		21 Feb 2017 version :c,h4

		Version info: :h4

doc/src/Section_commands.txt

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		@@ -969,7 +969,7 @@ KOKKOS, o = USER-OMP, t = OPT.
		"lubricateU/poly"_pair_lubricateU.html,
		"meam"_pair_meam.html,
		"mie/cut (o)"_pair_mie.html,
		"morse (got)"_pair_morse.html,
		"morse (gkot)"_pair_morse.html,
		"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
		"nm/cut (o)"_pair_nm.html,
		"nm/cut/coul/cut (o)"_pair_nm.html,
		@@ -1076,7 +1076,7 @@ KOKKOS, o = USER-OMP, t = OPT.
		"none"_bond_none.html,
		"zero"_bond_zero.html,
		"hybrid"_bond_hybrid.html,
		"class2 (o)"_bond_class2.html,
		"class2 (ko)"_bond_class2.html,
		"fene (iko)"_bond_fene.html,
		"fene/expand (o)"_bond_fene_expand.html,
		"harmonic (ko)"_bond_harmonic.html,
		@@ -1109,7 +1109,7 @@ USER-OMP, t = OPT.
		"zero"_angle_zero.html,
		"hybrid"_angle_hybrid.html,
		"charmm (ko)"_angle_charmm.html,
		"class2 (o)"_angle_class2.html,
		"class2 (ko)"_angle_class2.html,
		"cosine (o)"_angle_cosine.html,
		"cosine/delta (o)"_angle_cosine_delta.html,
		"cosine/periodic (o)"_angle_cosine_periodic.html,
		@@ -1145,7 +1145,7 @@ USER-OMP, t = OPT.
		"zero"_dihedral_zero.html,
		"hybrid"_dihedral_hybrid.html,
		"charmm (ko)"_dihedral_charmm.html,
		"class2 (o)"_dihedral_class2.html,
		"class2 (ko)"_dihedral_class2.html,
		"harmonic (io)"_dihedral_harmonic.html,
		"helix (o)"_dihedral_helix.html,
		"multi/harmonic (o)"_dihedral_multi_harmonic.html,
		@@ -1177,7 +1177,7 @@ USER-OMP, t = OPT.
		"none"_improper_none.html,
		"zero"_improper_zero.html,
		"hybrid"_improper_hybrid.html,
		"class2 (o)"_improper_class2.html,
		"class2 (ko)"_improper_class2.html,
		"cvff (io)"_improper_cvff.html,
		"harmonic (ko)"_improper_harmonic.html,
		"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

doc/src/Section_errors.txt

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		@@ -22,7 +22,7 @@ either conceptually, or as printed out by the program.

		12.1 Common problems :link(err_1),h4

		If two LAMMPS runs do not produce the same answer on different
		If two LAMMPS runs do not produce the exact same answer on different
		machines or different numbers of processors, this is typically not a
		bug. In theory you should get identical answers on any number of
		processors and on any machine. In practice, numerical round-off can
		@@ -80,12 +80,24 @@ order. If you mess this up, LAMMPS will often flag the error, but it
		may also simply read a bogus argument and assign a value that is
		valid, but not what you wanted. E.g. trying to read the string "abc"
		as an integer value of 0. Careful reading of the associated doc page
		for the command should allow you to fix these problems. Note that
		some commands allow for variables to be specified in place of numeric
		constants so that the value can be evaluated and change over the
		course of a run. This is typically done with the syntax {v_name} for
		a parameter, where name is the name of the variable. This is only
		allowed if the command documentation says it is.
		for the command should allow you to fix these problems. In most cases,
		where LAMMPS expects to read a number, either integer or floating point,
		it performs a stringent test on whether the provided input actually
		is an integer or floating-point number, respectively, and reject the
		input with an error message (for instance, when an integer is required,
		but a floating-point number 1.0 is provided):

		ERROR: Expected integer parameter in input script or data file :pre

		Some commands allow for using variable references in place of numeric
		constants so that the value can be evaluated and may change over the
		course of a run. This is typically done with the syntax {v_name} for a
		parameter, where name is the name of the variable. On the other hand,
		immediate variable expansion with the syntax ${name} is performed while
		reading the input and before parsing commands,

		NOTE: Using a variable reference (i.e. {v_name}) is only allowed if
		the documentation of the corresponding command explicitly says it is.

		Generally, LAMMPS will print a message to the screen and logfile and
		exit gracefully when it encounters a fatal error. Sometimes it will

doc/src/Section_howto.txt

+52 −29

Original line number	Diff line number	Diff line
		@@ -2573,7 +2573,7 @@ well.
		6.26 Adiabatic core/shell model :link(howto_26),h4

		The adiabatic core-shell model by "Mitchell and
		Finchham"_#MitchellFinchham is a simple method for adding
		Fincham"_#MitchellFincham is a simple method for adding
		polarizability to a system. In order to mimic the electron shell of
		an ion, a satellite particle is attached to it. This way the ions are
		split into a core and a shell where the latter is meant to react to
		@@ -2667,13 +2667,16 @@ bond_coeff 1 63.014 0.0
		bond_coeff 2 25.724 0.0 :pre

		When running dynamics with the adiabatic core/shell model, the
		following issues should be considered. Since the relative motion of
		the core and shell particles corresponds to the polarization, typical
		thermostats can alter the polarization behaviour, meaning the shell
		will not react freely to its electrostatic environment. This is
		critical during the equilibration of the system. Therefore
		it's typically desirable to decouple the relative motion of the
		core/shell pair, which is an imaginary degree of freedom, from the
		following issues should be considered. The relative motion of
		the core and shell particles corresponds to the polarization,
		hereby an instantaneous relaxation of the shells is approximated
		and a fast core/shell spring frequency ensures a nearly constant
		internal kinetic energy during the simulation.
		Thermostats can alter this polarization behaviour, by scaling the
		internal kinetic energy, meaning the shell will not react freely to
		its electrostatic environment.
		Therefore it is typically desirable to decouple the relative motion of
		the core/shell pair, which is an imaginary degree of freedom, from the
		real physical system. To do that, the "compute
		temp/cs"_compute_temp_cs.html command can be used, in conjunction with
		any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix
		@@ -2704,6 +2707,22 @@ fix thermostatequ all nve # integrator as needed f
		fix_modify thermoberendsen temp CSequ
		thermo_modify temp CSequ # output of center-of-mass derived temperature :pre

		The pressure for the core/shell system is computed via the regular
		LAMMPS convention by "treating the cores and shells as individual
		particles"_#MitchellFincham2. For the thermo output of the pressure
		as well as for the application of a barostat, it is necessary to
		use an additional "pressure"_compute_pressure compute based on the
		default "temperature"_compute_temp and specifying it as a second
		argument in "fix modify"_fix_modify.html and
		"thermo_modify"_thermo_modify.html resulting in:

		(...)
		compute CSequ all temp/cs cores shells
		compute thermo_press_lmp all pressure thermo_temp # pressure for individual particles
		thermo_modify temp CSequ press thermo_press_lmp # modify thermo to regular pressure
		fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4
		fix_modify press_bar temp CSequ press thermo_press_lmp # pressure modification for correct kinetic scalar :pre

		If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
		relative motion of the core and the shell should in theory be
		stable. However numerical fluctuation can introduce a small
		@@ -2724,24 +2743,18 @@ temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
		velocity all create 1427 134 bias yes temp CSequ
		velocity all scale 1427 temp CSequ :pre

		It is important to note that the polarizability of the core/shell
		pairs is based on their relative motion. Therefore the choice of
		spring force and mass ratio need to ensure much faster relative motion
		of the 2 atoms within the core/shell pair than their center-of-mass
		velocity. This allow the shells to effectively react instantaneously
		to the electrostatic environment. This fast movement also limits the
		timestep size that can be used.
		To maintain the correct polarizability of the core/shell pairs, the
		kinetic energy of the internal motion shall remain nearly constant.
		Therefore the choice of spring force and mass ratio need to ensure
		much faster relative motion of the 2 atoms within the core/shell pair
		than their center-of-mass velocity. This allows the shells to
		effectively react instantaneously to the electrostatic environment and
		limits energy transfer to or from the core/shell oscillators.
		This fast movement also dictates the timestep that can be used.

		The primary literature of the adiabatic core/shell model suggests that
		the fast relative motion of the core/shell pairs only allows negligible
		energy transfer to the environment. Therefore it is not intended to
		decouple the core/shell degree of freedom from the physical system
		during production runs. In other words, the "compute
		temp/cs"_compute_temp_cs.html command should not be used during
		production runs and is only required during equilibration. This way one
		is consistent with literature (based on the code packages DL_POLY or
		GULP for instance).

		energy transfer to the environment.
		The mentioned energy transfer will typically lead to a small drift
		in total energy over time. This internal energy can be monitored
		using the "compute chunk/atom"_compute_chunk_atom.html and "compute
		@@ -2761,15 +2774,21 @@ command, to use as input to the "compute
		chunk/atom"_compute_chunk_atom.html command to define the core/shell
		pairs as chunks.

		For example,
		For example if core/shell pairs are the only molecules:

		fix csinfo all property/atom i_CSID # property/atom command
		read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file
		compute prop all property/atom i_CSID
		read_data NaCl_CS_x0.1_prop.data
		compute prop all property/atom molecule
		compute cs_chunk all chunk/atom c_prop
		compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
		fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre

		For example if core/shell pairs and other molecules are present:

		fix csinfo all property/atom i_CSID # property/atom command
		read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file
		compute prop all property/atom i_CSID
		(...) :pre

		The additional section in the date file would be formatted like this:

		CS-Info # header of additional section :pre
		@@ -2890,9 +2909,13 @@ Phys, 79, 926 (1983).
		:link(Shinoda)
		[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).

		:link(MitchellFinchham)
		[(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
		:link(MitchellFincham)
		[(Mitchell and Fincham)] Mitchell, Fincham, J Phys Condensed Matter,
		5, 1031-1038 (1993).

		:link(MitchellFincham2)
		[(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter,
		6, 393-404 (1994).

		:link(howto-Lamoureux)
		[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)

doc/src/Section_start.txt

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		@@ -413,7 +413,7 @@ uses (for performing 1d FFTs) when running the particle-particle
		particle-mesh (PPPM) option for long-range Coulombics via the
		"kspace_style"_kspace_style.html command.

		LAMMPS supports various open-source or vendor-supplied FFT libraries
		LAMMPS supports common open-source or vendor-supplied FFT libraries
		for this purpose. If you leave these 3 variables blank, LAMMPS will
		use the open-source "KISS FFT library"_http://kissfft.sf.net, which is
		included in the LAMMPS distribution. This library is portable to all
		@@ -423,10 +423,9 @@ package in your build, you can also leave the 3 variables blank.

		Otherwise, select which kinds of FFTs to use as part of the FFT_INC
		setting by a switch of the form -DFFT_XXX. Recommended values for XXX
		are: MKL, SCSL, FFTW2, and FFTW3. Legacy options are: INTEL, SGI,
		ACML, and T3E. For backward compatability, using -DFFT_FFTW will use
		the FFTW2 library. Using -DFFT_NONE will use the KISS library
		described above.
		are: MKL or FFTW3. FFTW2 and NONE are supported as legacy options.
		Selecting -DFFT_FFTW will use the FFTW3 library and -DFFT_NONE will
		use the KISS library described above.

		You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
		so the compiler and linker can find the needed FFT header and library

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