forked from lijiext/lammps
patch 11Apr17
This commit is contained in:
Steve Plimpton
parent
49dd9449b8
commit
4da8c1c4e2
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@ -1,7 +1,7 @@
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<!-- HTML_ONLY -->
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<!-- HTML_ONLY -->
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<HEAD>
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<HEAD>
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<TITLE>LAMMPS Users Manual</TITLE>
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<TITLE>LAMMPS Users Manual</TITLE>
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<META NAME="docnumber" CONTENT="31 Mar 2017 version">
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<META NAME="docnumber" CONTENT="11 Apr 2017 version">
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<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
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<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
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<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
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<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
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</HEAD>
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</HEAD>
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@ -21,7 +21,7 @@
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<H1></H1>
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<H1></H1>
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LAMMPS Documentation :c,h3
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LAMMPS Documentation :c,h3
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31 Mar 2017 version :c,h4
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11 Apr 2017 version :c,h4
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Version info: :h4
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Version info: :h4
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@ -1155,7 +1155,7 @@ USER-OMP, t = OPT.
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"zero"_dihedral_zero.html,
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"zero"_dihedral_zero.html,
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"hybrid"_dihedral_hybrid.html,
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"hybrid"_dihedral_hybrid.html,
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"charmm (ko)"_dihedral_charmm.html,
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"charmm (ko)"_dihedral_charmm.html,
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"charmmfsh"_dihedral_charmm.html,
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"charmmfsw"_dihedral_charmm.html,
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"class2 (ko)"_dihedral_class2.html,
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"class2 (ko)"_dihedral_class2.html,
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"harmonic (io)"_dihedral_harmonic.html,
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"harmonic (io)"_dihedral_harmonic.html,
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"helix (o)"_dihedral_helix.html,
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"helix (o)"_dihedral_helix.html,
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@ -215,7 +215,7 @@ documentation for the formula it computes.
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"special_bonds"_special_bonds.html charmm
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"special_bonds"_special_bonds.html charmm
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"special_bonds"_special_bonds.html amber :ul
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"special_bonds"_special_bonds.html amber :ul
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NOTE: For CHARMM, the newer {charmmfsw} or {charmmfsh} styles were
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NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were
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released in March 2017. We recommend they be used instead of the
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released in March 2017. We recommend they be used instead of the
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older {charmm} styles. See discussion of the differences on the "pair
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older {charmm} styles. See discussion of the differences on the "pair
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charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
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charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
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@ -10,25 +10,25 @@ dihedral_style charmm command :h3
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dihedral_style charmm/intel command :h3
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dihedral_style charmm/intel command :h3
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dihedral_style charmm/kk command :h3
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dihedral_style charmm/kk command :h3
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dihedral_style charmm/omp command :h3
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dihedral_style charmm/omp command :h3
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dihedral_style charmmfsh command :h3
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dihedral_style charmmfsw command :h3
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[Syntax:]
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[Syntax:]
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dihedral_style style :pre
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dihedral_style style :pre
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style = {charmm} or {charmmfsh} :ul
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style = {charmm} or {charmmfsw} :ul
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[Examples:]
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[Examples:]
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dihedral_style charmm
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dihedral_style charmm
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dihedral_style charmmfsh
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dihedral_style charmmfsw
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dihedral_coeff 1 0.2 1 180 1.0
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dihedral_coeff 1 0.2 1 180 1.0
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dihedral_coeff 2 1.8 1 0 1.0
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dihedral_coeff 2 1.8 1 0 1.0
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dihedral_coeff 1 3.1 2 180 0.5 :pre
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dihedral_coeff 1 3.1 2 180 0.5 :pre
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[Description:]
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[Description:]
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The {charmm} and {charmmfsh} dihedral styles use the potential
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The {charmm} and {charmmfsw} dihedral styles use the potential
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:c,image(Eqs/dihedral_charmm.jpg)
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:c,image(Eqs/dihedral_charmm.jpg)
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@ -38,10 +38,12 @@ field (see comment on weighting factors below). See
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"(Cornell)"_#dihedral-Cornell for a description of the AMBER force
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"(Cornell)"_#dihedral-Cornell for a description of the AMBER force
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field.
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field.
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NOTE: The newer {charmmfsh} style was released in March 2017. We
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NOTE: The newer {charmmfsw} style was released in March 2017. We
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recommend it be used instead of the older {charmm} style when running
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recommend it be used instead of the older {charmm} style when running
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a simulation with the CHARMM force field and Coulomb cutoffs, via the
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a simulation with the CHARMM force field, either with long-range
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"pair_style lj/charmmfsw/coul/charmmfsh"_pair_charmm.html command.
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Coulombics or a Coulomb cutoff, via the "pair_style
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lj/charmmfsw/coul/long"_pair_charmm.html and "pair_style
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lj/charmmfsw/coul/charmmfsh"_pair_charmm.html commands respectively.
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Otherwise the older {charmm} style is fine to use. See the discussion
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Otherwise the older {charmm} style is fine to use. See the discussion
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below and more details on the "pair_style charmm"_pair_charmm.html doc
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below and more details on the "pair_style charmm"_pair_charmm.html doc
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page.
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page.
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@ -86,17 +88,18 @@ default). Otherwise 1-4 non-bonded interactions in dihedrals will be
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computed twice.
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computed twice.
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For simulations using the CHARMM force field with a Coulomb cutoff,
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For simulations using the CHARMM force field with a Coulomb cutoff,
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the difference between the {charmm} and {charmmfsh} styles is in the
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the difference between the {charmm} and {charmmfsw} styles is in the
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computation of the 1-4 non-bond interactions, though only if the
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computation of the 1-4 non-bond interactions, though only if the
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distance between the two atoms is within the switching region of the
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distance between the two atoms is within the switching region of the
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pairwise potential defined by the corresponding CHARMM pair style,
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pairwise potential defined by the corresponding CHARMM pair style,
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i.e. within the outer cutoff specified for the pair style. The
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i.e. within the outer cutoff specified for the pair style. The
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{charmmfsh} style should only be used when using the "pair_style
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{charmmfsw} style should only be used when using the corresponding
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lj/charmmfsw/coul/charmmfsh"_pair_charmm.html to make the Coulombic
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"pair_style lj/charmmfsw/coul/charmmfsw"_pair_charmm.html or
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pairwise calculations consistent. Use the {charmm} style with
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"pair_style lj/charmmfsw/coul/long"_pair_charmm.html commands. Use
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long-range Coulombics or the older "pair_style
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the {charmm} style with the older "pair_style"_pair_charmm.html
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lj/charmm/coul/charmm"_pair_charmm.html command. See the discussion
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commands that have just "charmm" in their style name. See the
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on the "CHARMM pair_style"_pair_charmm.html doc page for details.
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discussion on the "CHARMM pair_style"_pair_charmm.html doc page for
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details.
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Note that for AMBER force fields, which use pair styles with "lj/cut",
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Note that for AMBER force fields, which use pair styles with "lj/cut",
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the special_bonds 1-4 scaling factor should be set to the AMBER
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the special_bonds 1-4 scaling factor should be set to the AMBER
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@ -104,7 +107,7 @@ defaults (1/2 and 5/6) and all the dihedral weighting factors (4th
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coeff above) must be set to 0.0. In this case, you can use any pair
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coeff above) must be set to 0.0. In this case, you can use any pair
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style you wish, since the dihedral does not need any Lennard-Jones
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style you wish, since the dihedral does not need any Lennard-Jones
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parameter information and will not compute any 1-4 non-bonded
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parameter information and will not compute any 1-4 non-bonded
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interactions. Likewise the {charmm} or {charmmfsh} styles are
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interactions. Likewise the {charmm} or {charmmfsw} styles are
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identical in this case since no 1-4 non-bonded interactions are
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identical in this case since no 1-4 non-bonded interactions are
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computed.
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computed.
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@ -99,9 +99,10 @@ artifacts.
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NOTE: The newer {charmmfsw} or {charmmfsh} styles were released in
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NOTE: The newer {charmmfsw} or {charmmfsh} styles were released in
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March 2017. We recommend they be used instead of the older {charmm}
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March 2017. We recommend they be used instead of the older {charmm}
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styles. Eventually code from the new styles will propagate into the
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styles. This includes the newer "dihedral_style
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related pair styles (e.g. implicit, accelerator, free energy
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charmmfsw"_dihedral_charmm.html command. Eventually code from the new
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variants).
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styles will propagate into the related pair styles (e.g. implicit,
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accelerator, free energy variants).
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The general CHARMM formulas are as follows
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The general CHARMM formulas are as follows
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@ -9,11 +9,10 @@ boundary p p p
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atom_style full
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atom_style full
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bond_style harmonic
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bond_style harmonic
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angle_style charmm
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angle_style charmm
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dihedral_style charmm
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dihedral_style charmmfsw
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improper_style harmonic
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improper_style harmonic
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pair_style lj/charmm/coul/charmm 8 12
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pair_style lj/charmmfsw/coul/charmmfsh 8 12
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#pair_style lj/charmmfsw/coul/charmmfsh 8 12
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pair_modify mix arithmetic
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pair_modify mix arithmetic
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fix cmap all cmap charmm22.cmap
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fix cmap all cmap charmm22.cmap
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@ -1,201 +0,0 @@
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LAMMPS (5 Oct 2016)
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# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
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units real
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neigh_modify delay 2 every 1
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#newton off
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boundary p p p
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atom_style full
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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pair_style lj/charmm/coul/charmm 8 12
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#pair_style lj/charmmfsw/coul/charmmfsh 8 12
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pair_modify mix arithmetic
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fix cmap all cmap charmm22.cmap
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Reading potential file charmm22.cmap with DATE: 2016-09-26
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fix_modify cmap energy yes
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read_data gagg.data fix cmap crossterm CMAP
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orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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34 atoms
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scanning bonds ...
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4 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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scanning dihedrals ...
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12 = max dihedrals/atom
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scanning impropers ...
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1 = max impropers/atom
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reading bonds ...
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33 bonds
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reading angles ...
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57 angles
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reading dihedrals ...
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75 dihedrals
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reading impropers ...
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7 impropers
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4 = max # of 1-2 neighbors
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7 = max # of 1-3 neighbors
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13 = max # of 1-4 neighbors
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16 = max # of special neighbors
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special_bonds charmm
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fix 1 all nve
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#fix 1 all nvt temp 300 300 100.0
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#fix 2 all shake 1e-9 500 0 m 1.0
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velocity all create 0.0 12345678 dist uniform
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thermo 1000
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thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp
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timestep 2.0
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run 100000
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 2 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7 -> bins = 12 12 12
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Memory usage per processor = 14.6355 Mbytes
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Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro
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0 26.542777 -0.93822087 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023
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1000 28.673005 -0.47724367 0.80029132 3.151679 4.4684446 -2.3928648 0.18604953
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2000 27.67955 -1.170342 0.72018905 4.0400131 4.4713764 -2.5490207 0.21834436
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3000 29.256656 -0.35856055 0.73303546 3.7411606 4.4710568 -2.8939692 0.37728884
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4000 30.097549 -1.1353905 0.79007053 3.0688444 4.4091469 -2.3383587 0.20743631
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5000 28.357525 -1.0723742 0.9180297 3.6579424 4.8792664 -2.3185572 0.088366962
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6000 29.214175 -0.95299225 0.81926009 3.6805429 4.6742897 -2.9343577 0.26697813
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7000 27.018614 -0.52423475 0.72502764 3.8840137 4.7780956 -2.3916009 0.24952584
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8000 29.682167 -1.0939711 0.76111486 3.1090116 4.9359719 -2.5662984 0.1411154
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9000 27.909695 -0.80905986 0.78952533 4.203187 4.1301204 -2.000402 0.088859259
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10000 27.480298 -0.86273377 1.1293962 4.3857421 4.899282 -3.3895621 0.12126215
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11000 28.303203 -1.0221152 0.62762348 4.055414 4.5863024 -2.5842816 0.17996907
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12000 28.311127 -0.94227367 0.91859012 3.6673926 4.7018632 -3.902715 0.30065704
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13000 30.818607 -1.5220116 0.95710386 3.3364371 4.543427 -3.0423067 0.16712905
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14000 27.643736 -1.0144117 0.95806952 4.1046912 4.800236 -4.0534389 0.29293405
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15000 27.660491 -1.0390086 0.78061056 4.1139174 4.7197202 -2.3670379 0.22126985
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16000 27.845157 -0.63654502 0.78007478 3.9365994 4.949418 -3.1470214 0.22335355
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17000 28.44772 -1.0255112 0.70402007 4.0573343 4.2887527 -2.2099596 0.048050962
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18000 27.128323 -0.96218536 1.1327159 4.3222585 4.326607 -2.2881766 0.13491257
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19000 27.337633 -0.78999574 0.80152298 4.2239689 4.7073478 -2.2924164 0.12710292
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20000 27.780537 -0.46458072 0.79707671 3.7232618 4.943417 -2.5290628 0.26191223
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21000 26.435484 -0.7803224 1.0753217 4.4196051 5.9945933 -2.3340925 0.16448475
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22000 28.619429 -1.1623149 0.9401731 3.8508844 5.1636737 -2.5551846 0.25318434
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23000 28.399338 -0.79700962 0.85575503 4.488526 4.5975422 -2.5663549 0.13601693
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24000 29.645532 -1.158744 0.83180313 3.8193399 4.60319 -2.6847864 0.24260466
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25000 28.695339 -1.4802204 0.76583757 3.6786272 4.8959496 -2.3627896 0.080867326
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26000 28.149711 -1.029689 0.79383806 3.7885067 4.3345813 -2.1041553 0.14598209
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27000 29.580373 -1.0525813 1.0262723 3.7767318 4.6119758 -2.2802386 0.088556038
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28000 28.44308 -0.93411225 0.8794395 3.948079 4.780246 -2.1814583 0.14340149
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|
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29000 29.335621 -1.6087988 0.71803091 3.7819186 4.6688385 -2.4282242 0.16061111
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30000 28.706138 -1.3938241 0.67713818 4.031275 4.4756505 -2.1807056 0.11461356
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31000 27.451944 0.010297225 0.65064883 3.6402029 4.3607811 -2.5511516 0.12637237
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32000 27.070878 -1.103158 1.1932199 5.1329709 4.5201653 -2.2224479 0.11215427
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33000 29.889976 -1.6228316 0.69407996 3.5361991 4.3502767 -1.9847454 0.09089949
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34000 28.223151 -0.927208 1.043253 3.4650939 5.1028142 -2.8127219 0.10648823
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35000 27.985986 -0.48153861 0.63878449 3.3724641 4.9551679 -2.6565919 0.12123115
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36000 28.580688 -1.4500694 1.055762 4.0490064 4.423782 -2.3103578 0.072747638
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37000 29.192947 -0.49678176 1.1146731 2.9233947 4.5738603 -2.4376144 0.22874047
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38000 26.954594 -0.53812359 0.79230685 4.3356989 5.0284656 -2.3791255 0.0486081
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39000 27.567555 -0.57870028 0.73614374 4.191991 4.9209556 -2.6122044 0.08635571
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40000 28.494172 -0.79057135 0.79072816 4.1893209 4.4826919 -2.4179635 0.14612898
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41000 28.44904 -1.1002948 0.93405654 4.3586358 4.4338415 -2.2950944 0.15705834
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42000 28.95725 -1.0297067 1.1632348 4.274711 4.9979487 -2.7611464 0.15944725
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43000 28.640394 -0.70938882 0.68100893 3.1844315 5.1817454 -2.2837487 0.14189233
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44000 27.997558 -1.0115099 0.59125208 4.0883422 4.6033907 -2.2775964 0.094273258
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|
||||||
45000 27.67163 -0.67992747 1.1225552 3.9020703 4.8171056 -2.1952679 0.041418433
|
|
||||||
46000 28.822607 -0.6687953 0.74160059 3.3193715 4.5546965 -2.3024572 0.047569065
|
|
||||||
47000 29.20147 -1.4456785 0.79223353 3.8288813 4.5811826 -2.5154936 0.061230141
|
|
||||||
48000 27.843026 -1.0222301 0.87322137 4.3432743 4.4266307 -2.1414153 0.06802794
|
|
||||||
49000 28.199573 -1.1887794 1.2781088 4.0779644 4.5881353 -2.319775 0.094803547
|
|
||||||
50000 28.759212 -1.354416 0.68534569 3.8394841 4.2308134 -2.1281844 0.1395951
|
|
||||||
51000 27.876455 -1.5705462 0.76557156 4.5335223 4.523708 -2.203702 0.14679803
|
|
||||||
52000 27.930587 -1.2277489 0.96071516 3.960953 5.1152188 -2.4101451 0.060949521
|
|
||||||
53000 27.031236 -1.4746477 1.2341141 5.0540975 4.3656865 -2.1288513 0.092725656
|
|
||||||
54000 28.809394 -1.1162427 0.94350207 3.4013958 4.4755547 -2.3342811 0.18855912
|
|
||||||
55000 28.948415 -1.1560418 0.6260139 3.5386373 4.5244978 -2.340212 0.17474657
|
|
||||||
56000 28.048368 -0.95784532 0.76432571 4.1404665 4.4570033 -2.0899628 0.045693628
|
|
||||||
57000 28.707642 -1.366574 0.9907873 3.729903 4.3131997 -2.2777698 0.065420213
|
|
||||||
58000 26.361663 -1.0424403 1.0452563 5.0977108 4.7035231 -2.3101244 0.13671642
|
|
||||||
59000 29.218218 -1.2210564 0.62435875 3.4236327 4.5481681 -2.1575943 0.037984042
|
|
||||||
60000 27.655546 -1.1053224 0.86323501 3.7641375 4.8946898 -2.2422249 0.077725979
|
|
||||||
61000 27.252108 -1.3744824 1.1150806 5.0444848 4.4878135 -2.2743829 0.058331257
|
|
||||||
62000 27.163469 -1.1715781 0.72099321 4.5295501 4.9509918 -2.2993961 0.050401105
|
|
||||||
63000 29.581575 -1.2238537 0.86303245 3.1194038 5.2218965 -2.5002427 0.055032632
|
|
||||||
64000 27.897822 -1.1011516 0.74540883 4.2869228 4.3394269 -2.2552393 0.1403321
|
|
||||||
65000 27.083245 -1.0633392 0.92771724 5.0805224 4.2747962 -2.2388039 0.064196692
|
|
||||||
66000 29.072723 -1.5514209 0.89798805 4.2600224 4.4261812 -2.3524752 0.15067414
|
|
||||||
67000 27.308181 -0.72224802 0.97109517 4.5074578 4.4559352 -2.1381121 0.089297603
|
|
||||||
68000 27.505686 -0.43855431 0.80785812 4.1917251 5.0157721 -2.3382145 0.11105164
|
|
||||||
69000 29.041681 -0.64735378 0.89874684 3.3891579 4.3753361 -2.2320941 0.14716747
|
|
||||||
70000 29.735756 -1.7061457 0.9206878 3.5767878 4.3851664 -2.2516304 0.097196062
|
|
||||||
71000 28.224352 -0.92217702 0.86093586 3.9507157 4.5596589 -2.2173397 0.089116669
|
|
||||||
72000 29.282336 -1.056142 0.65185725 3.8735742 4.4839333 -2.4314756 0.071909704
|
|
||||||
73000 26.257283 -0.64273826 0.98300685 5.063943 5.045958 -2.5544375 0.2180275
|
|
||||||
74000 28.825119 -0.97736616 0.87201848 3.55875 4.3653309 -2.2303567 0.098963875
|
|
||||||
75000 29.239507 -0.96508809 0.74517323 3.4306236 4.7651921 -2.6077732 0.17883654
|
|
||||||
76000 27.349841 -0.50990238 1.1183613 4.4252451 4.4097775 -2.4125794 0.18483606
|
|
||||||
77000 28.130197 -1.4081219 0.94921357 4.2572132 4.5162849 -2.4013797 0.073744606
|
|
||||||
78000 28.235774 -0.9214321 0.6324981 3.8697686 4.8092154 -2.2272847 0.092108346
|
|
||||||
79000 26.732846 -0.55949486 1.0989617 5.0088609 4.4930687 -2.277945 0.03855146
|
|
||||||
80000 28.529208 -0.94244671 0.79407482 3.961106 4.3930011 -2.3127726 0.091124948
|
|
||||||
81000 29.603852 -1.6116062 1.060847 3.7824932 4.151001 -1.9139868 0.19875986
|
|
||||||
82000 28.232876 -1.1833011 1.0182713 3.4195758 5.1394333 -2.4632697 0.28501012
|
|
||||||
83000 29.565482 -1.3479552 0.99056973 3.7851802 4.4781011 -2.7872481 0.2031991
|
|
||||||
84000 28.780274 -1.3073882 1.0512637 4.004638 4.502282 -2.3789146 0.015656202
|
|
||||||
85000 27.262312 -1.1305346 1.203524 4.7938623 4.1747105 -2.0952844 0.054240361
|
|
||||||
86000 28.157348 -1.0662817 0.81163796 3.9912709 4.8320213 -2.255237 0.14698333
|
|
||||||
87000 28.445543 -1.3365026 0.78156195 4.4767689 4.4457575 -2.5008786 0.13879386
|
|
||||||
88000 27.656717 -1.1490599 0.87974869 4.4629952 4.7023033 -2.3258145 0.081904139
|
|
||||||
89000 28.838821 -1.020709 0.85587929 3.7110705 4.4938307 -2.4914483 0.11447952
|
|
||||||
90000 27.356497 -0.59107077 0.81879666 4.5209332 4.4703836 -2.3806717 0.071307775
|
|
||||||
91000 27.780445 -0.80564513 0.94752313 3.8468943 4.2924253 -2.1011134 0.1118672
|
|
||||||
92000 28.555276 -1.3514732 0.80826674 3.9590742 4.5775954 -2.4891232 0.054254978
|
|
||||||
93000 28.747267 -1.2133243 0.75507246 4.1319789 4.9048611 -2.4913887 0.13045693
|
|
||||||
94000 27.479343 -0.69973695 0.99696121 3.5966229 4.549025 -2.4155312 0.41745762
|
|
||||||
95000 27.726945 -1.1905026 1.1120842 4.7433275 4.5386861 -2.7947142 0.33671682
|
|
||||||
96000 28.021114 -1.0341645 0.6663033 4.2397505 4.6203984 -1.9904034 0.10972565
|
|
||||||
97000 28.382022 -1.3916008 1.180588 4.0729621 4.6741792 -2.554927 0.13462346
|
|
||||||
98000 27.895969 -0.7496449 1.3072185 4.2611888 4.3726077 -2.1320701 0.15376665
|
|
||||||
99000 28.517889 -1.2183957 1.279778 3.957647 4.2638434 -2.2888407 0.042705003
|
|
||||||
100000 28.109211 -1.2538948 0.83671785 4.3734766 4.544545 -2.3076497 0.042189096
|
|
||||||
Loop time of 2.84552 on 1 procs for 100000 steps with 34 atoms
|
|
||||||
|
|
||||||
Performance: 6072.706 ns/day, 0.004 hours/ns, 35142.973 timesteps/s
|
|
||||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.94207 | 0.94207 | 0.94207 | 0.0 | 33.11
|
|
||||||
Bond | 1.6125 | 1.6125 | 1.6125 | 0.0 | 56.67
|
|
||||||
Neigh | 0.0073986 | 0.0073986 | 0.0073986 | 0.0 | 0.26
|
|
||||||
Comm | 0.012739 | 0.012739 | 0.012739 | 0.0 | 0.45
|
|
||||||
Output | 0.00075531 | 0.00075531 | 0.00075531 | 0.0 | 0.03
|
|
||||||
Modify | 0.21483 | 0.21483 | 0.21483 | 0.0 | 7.55
|
|
||||||
Other | | 0.05524 | | | 1.94
|
|
||||||
|
|
||||||
Nlocal: 34 ave 34 max 34 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 0 ave 0 max 0 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 395 ave 395 max 395 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 395
|
|
||||||
Ave neighs/atom = 11.6176
|
|
||||||
Ave special neighs/atom = 9.52941
|
|
||||||
Neighbor list builds = 237
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:02
|
|
||||||
|
|
@ -1,201 +0,0 @@
|
||||||
LAMMPS (5 Oct 2016)
|
|
||||||
# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
|
|
||||||
|
|
||||||
units real
|
|
||||||
neigh_modify delay 2 every 1
|
|
||||||
#newton off
|
|
||||||
|
|
||||||
boundary p p p
|
|
||||||
|
|
||||||
atom_style full
|
|
||||||
bond_style harmonic
|
|
||||||
angle_style charmm
|
|
||||||
dihedral_style charmm
|
|
||||||
improper_style harmonic
|
|
||||||
|
|
||||||
pair_style lj/charmm/coul/charmm 8 12
|
|
||||||
#pair_style lj/charmmfsw/coul/charmmfsh 8 12
|
|
||||||
pair_modify mix arithmetic
|
|
||||||
|
|
||||||
fix cmap all cmap charmm22.cmap
|
|
||||||
Reading potential file charmm22.cmap with DATE: 2016-09-26
|
|
||||||
fix_modify cmap energy yes
|
|
||||||
|
|
||||||
read_data gagg.data fix cmap crossterm CMAP
|
|
||||||
orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
34 atoms
|
|
||||||
scanning bonds ...
|
|
||||||
4 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
6 = max angles/atom
|
|
||||||
scanning dihedrals ...
|
|
||||||
12 = max dihedrals/atom
|
|
||||||
scanning impropers ...
|
|
||||||
1 = max impropers/atom
|
|
||||||
reading bonds ...
|
|
||||||
33 bonds
|
|
||||||
reading angles ...
|
|
||||||
57 angles
|
|
||||||
reading dihedrals ...
|
|
||||||
75 dihedrals
|
|
||||||
reading impropers ...
|
|
||||||
7 impropers
|
|
||||||
4 = max # of 1-2 neighbors
|
|
||||||
7 = max # of 1-3 neighbors
|
|
||||||
13 = max # of 1-4 neighbors
|
|
||||||
16 = max # of special neighbors
|
|
||||||
|
|
||||||
special_bonds charmm
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
#fix 1 all nvt temp 300 300 100.0
|
|
||||||
#fix 2 all shake 1e-9 500 0 m 1.0
|
|
||||||
|
|
||||||
velocity all create 0.0 12345678 dist uniform
|
|
||||||
|
|
||||||
thermo 1000
|
|
||||||
thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp
|
|
||||||
timestep 2.0
|
|
||||||
|
|
||||||
run 100000
|
|
||||||
Neighbor list info ...
|
|
||||||
1 neighbor list requests
|
|
||||||
update every 1 steps, delay 2 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 14
|
|
||||||
ghost atom cutoff = 14
|
|
||||||
binsize = 7 -> bins = 12 12 12
|
|
||||||
Memory usage per processor = 15.9307 Mbytes
|
|
||||||
Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro
|
|
||||||
0 26.542777 -0.93822087 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023
|
|
||||||
1000 28.673005 -0.47724367 0.80029132 3.151679 4.4684446 -2.3928648 0.18604953
|
|
||||||
2000 27.67955 -1.170342 0.72018905 4.0400131 4.4713764 -2.5490207 0.21834436
|
|
||||||
3000 29.256656 -0.35856055 0.73303546 3.7411606 4.4710568 -2.8939692 0.37728884
|
|
||||||
4000 30.097549 -1.1353905 0.79007053 3.0688444 4.4091469 -2.3383587 0.20743631
|
|
||||||
5000 28.357525 -1.0723742 0.9180297 3.6579424 4.8792663 -2.3185572 0.088366962
|
|
||||||
6000 29.214175 -0.95299239 0.81926011 3.6805428 4.6742897 -2.9343578 0.26697816
|
|
||||||
7000 27.018614 -0.52423469 0.72502751 3.8840141 4.7780958 -2.3916014 0.24952572
|
|
||||||
8000 29.682494 -1.0940368 0.76113051 3.1089345 4.9357863 -2.5662256 0.14112613
|
|
||||||
9000 27.853918 -0.7913741 0.79503268 4.2177256 4.146792 -2.00475 0.090585666
|
|
||||||
10000 27.13754 -0.80551128 1.1325023 4.4718283 5.2460631 -3.4947725 0.11893125
|
|
||||||
11000 28.277434 -1.4897448 0.90075953 4.1895717 4.3594269 -1.9553119 0.090222212
|
|
||||||
12000 28.630973 -1.222206 0.67796385 3.3905661 4.9691334 -2.9052721 0.13897658
|
|
||||||
13000 28.593007 -0.95684026 0.75585196 3.7242568 4.7417932 -2.3893117 0.2074121
|
|
||||||
14000 26.147115 -0.6026921 0.93591488 5.1292829 4.9821952 -2.2571835 0.11872421
|
|
||||||
15000 26.29432 -0.82424162 1.048979 4.5569495 5.1189308 -2.9750422 0.16195676
|
|
||||||
16000 29.189992 -0.80998247 0.74093508 3.8299275 4.4536688 -2.5497538 0.19155639
|
|
||||||
17000 25.878012 -0.3519646 1.0988924 4.7359591 5.3923098 -2.7211029 0.13405223
|
|
||||||
18000 27.726135 -0.28229987 0.63072344 4.1777888 4.7237271 -2.2177157 0.15939372
|
|
||||||
19000 27.153504 -0.66477422 0.77910129 4.2036117 5.113851 -2.3494315 0.094793307
|
|
||||||
20000 28.044833 -1.2835827 0.88745367 3.9955526 4.5077788 -3.0116467 0.17197859
|
|
||||||
21000 27.205696 -0.74090037 1.0023251 4.3421733 4.912671 -2.3473271 0.26089356
|
|
||||||
22000 27.385785 -0.93740972 0.84554838 4.562743 4.883866 -2.2110955 0.11573301
|
|
||||||
23000 27.05534 -0.95605442 0.96719024 3.9277618 5.0359014 -2.6135949 0.21368061
|
|
||||||
24000 28.273378 -0.97543103 0.8983443 4.2067985 4.4782971 -2.4230505 0.30311692
|
|
||||||
25000 27.477789 -0.20383849 0.8380706 3.8037992 4.8312504 -2.5831791 0.093843746
|
|
||||||
26000 30.344199 -1.9773473 0.92882437 3.7821405 4.5176677 -2.3020968 0.2194307
|
|
||||||
27000 27.32767 -0.9803839 0.92988865 3.7611603 5.0328211 -2.4647656 0.18213622
|
|
||||||
28000 27.34208 -1.037938 0.74488346 4.1727342 4.7056812 -2.2718346 0.17741362
|
|
||||||
29000 27.682777 -0.51006495 0.57074224 4.7332237 4.7080462 -2.0491512 0.2130517
|
|
||||||
30000 24.925731 0.13670248 0.84976065 4.4143762 6.0677158 -3.5479173 0.28059419
|
|
||||||
31000 28.623419 -0.90725708 1.0710501 3.6930688 4.6639301 -2.2225373 0.20988139
|
|
||||||
32000 27.732286 -1.1948367 0.89230134 4.4398373 4.8923907 -3.5849327 0.49167488
|
|
||||||
33000 28.800772 -1.5319589 0.93455495 4.1634728 4.6107706 -2.3503486 0.22636535
|
|
||||||
34000 27.374398 -1.0957453 0.89450276 3.9829508 4.991786 -2.3548834 0.15869465
|
|
||||||
35000 28.38753 -0.89261166 0.90000776 3.536864 4.4293294 -2.4218118 0.10640557
|
|
||||||
36000 27.713974 0.088038031 0.85190574 3.8969601 4.6256355 -2.7935475 0.34671662
|
|
||||||
37000 29.13007 -1.378597 0.74412556 3.131538 4.6458653 -2.9373734 0.38035616
|
|
||||||
38000 28.556573 -1.4055344 1.139984 4.0035753 4.2938358 -2.489329 0.25338326
|
|
||||||
39000 26.447036 -1.1829705 0.87032438 5.0804461 4.5772023 -2.7346466 0.32165802
|
|
||||||
40000 27.991454 -0.64295679 0.61020872 4.165871 4.4623087 -2.2244194 0.13826991
|
|
||||||
41000 29.483296 -1.2400745 0.66926627 3.3473666 4.5766617 -2.3051145 0.12171554
|
|
||||||
42000 26.948627 -1.2162288 1.1440628 4.3993073 5.1176533 -2.4734485 0.15497709
|
|
||||||
43000 28.04459 -0.26543193 0.83647367 3.5160747 4.6964397 -2.2805068 0.12618821
|
|
||||||
44000 28.213608 -1.216128 0.9132792 4.0206483 4.9483599 -2.3387049 0.10132022
|
|
||||||
45000 28.283506 -1.0390766 0.86113772 4.504509 4.7209088 -2.3043085 0.14588362
|
|
||||||
46000 27.433853 -0.57912107 0.78448334 4.5998579 5.1181394 -2.6165094 0.18722528
|
|
||||||
47000 27.552939 -1.1128925 0.80087638 4.3448001 4.8062869 -2.4296883 0.2702479
|
|
||||||
48000 28.874034 -1.3242519 0.71770727 3.5648565 4.4671824 -2.2608958 0.16115978
|
|
||||||
49000 29.216186 -1.2210307 0.76937497 3.9260628 4.7550577 -2.7316081 0.085505664
|
|
||||||
50000 28.065856 -1.1545547 0.86953819 4.4137666 4.732157 -2.4450867 0.23320539
|
|
||||||
51000 26.308975 -0.99728352 0.90408444 4.2400186 5.6340425 -2.2090554 0.079882158
|
|
||||||
52000 28.517571 -1.5027398 0.83520278 3.8176552 4.3001251 -2.0731682 0.1665375
|
|
||||||
53000 28.77579 -1.3564268 0.97253881 3.6866407 4.8532347 -2.5330776 0.17668411
|
|
||||||
54000 29.135315 -1.0994106 0.67605671 3.6819254 4.3134408 -1.9796929 0.076951331
|
|
||||||
55000 26.168938 -0.76247492 0.88784685 4.6533473 6.0484793 -2.1334561 0.036876985
|
|
||||||
56000 27.471775 -0.68648837 1.0576168 4.0354311 4.4767052 -2.2368959 0.24950568
|
|
||||||
57000 29.787083 -1.4914384 1.0702944 3.5388133 4.5173097 -2.6694464 0.27937092
|
|
||||||
58000 28.705448 -1.3016617 0.63337853 3.9552713 4.4119825 -1.8774657 0.17540021
|
|
||||||
59000 29.130155 -0.91647363 0.84384883 3.1076903 4.5346348 -2.3457338 0.16674486
|
|
||||||
60000 26.874199 -0.81598034 1.3432151 5.1322624 4.9545484 -2.9566615 0.25950486
|
|
||||||
61000 27.401306 -0.82895856 1.1636949 4.020154 4.5745928 -2.601466 0.18061051
|
|
||||||
62000 28.930313 -1.5231967 0.85173243 4.3517328 4.4878662 -2.5859205 0.1755493
|
|
||||||
63000 26.56874 0.026147233 0.60836216 4.4231618 4.4390677 -2.1721849 0.08594237
|
|
||||||
64000 26.729023 -0.76953985 0.76734633 4.5104288 5.0886456 -2.2118551 0.11339216
|
|
||||||
65000 28.900471 -1.3901477 0.86194657 4.2774976 4.498325 -2.3672362 0.20668335
|
|
||||||
66000 26.884253 -0.21198879 0.98509625 4.0843117 4.4344172 -2.3289416 0.23631017
|
|
||||||
67000 27.210888 -0.84075559 1.0396559 4.7253607 4.4314589 -2.2985702 0.19326507
|
|
||||||
68000 28.042102 -1.1898715 1.053534 3.8748712 4.4358449 -2.3998723 0.2431659
|
|
||||||
69000 28.939141 -1.6968936 0.98155912 4.0460838 5.0075204 -2.5547087 0.28645131
|
|
||||||
70000 27.15577 -0.85202797 1.1469079 4.7645212 4.6133209 -2.3410451 0.086576572
|
|
||||||
71000 25.507417 -0.27780727 0.95157881 4.8759406 4.853401 -2.9598705 0.41011008
|
|
||||||
72000 29.804703 -1.4847015 0.96345767 3.6797304 4.3678377 -2.4594626 0.14480206
|
|
||||||
73000 28.602798 -1.4906143 0.72497266 4.2442974 4.5360598 -2.3621638 0.14385651
|
|
||||||
74000 28.4928 -0.91319873 1.0377472 3.8033127 4.3991601 -2.4051911 0.095567428
|
|
||||||
75000 26.38168 -0.70733237 1.1557817 5.697939 4.5935618 -2.4285007 0.058980519
|
|
||||||
76000 27.16626 -0.83631031 0.84844246 4.7460887 4.5801472 -2.1260014 0.12845946
|
|
||||||
77000 29.040661 -1.3089499 0.80285084 4.664804 4.5215895 -2.6861939 0.13215598
|
|
||||||
78000 27.477871 -1.0600977 0.88595045 4.6264017 5.4095605 -2.474411 0.10987174
|
|
||||||
79000 26.151797 -0.55779685 0.91382436 4.99964 4.9184022 -2.2547241 0.22854038
|
|
||||||
80000 28.14523 -0.54460026 0.8982411 3.5374555 4.3785673 -2.3196807 0.088567964
|
|
||||||
81000 29.029941 -1.6467789 0.79042284 3.7269899 4.7407998 -2.3795824 0.1408727
|
|
||||||
82000 27.920287 -0.72798032 1.0076975 3.4449461 4.5621371 -2.8239074 0.25103454
|
|
||||||
83000 29.131054 -1.114367 0.76887285 3.459639 4.5163922 -2.607825 0.19991648
|
|
||||||
84000 28.249768 -0.69944068 1.0510846 4.0436296 4.6430538 -2.4213355 0.077299966
|
|
||||||
85000 28.06888 -0.62132922 0.91829312 4.1294147 4.3099557 -2.354063 0.15866186
|
|
||||||
86000 28.664264 -1.1022906 0.87831695 4.5773522 4.6045802 -2.9206875 0.33950063
|
|
||||||
87000 27.960967 -1.2852756 0.77694253 3.9011301 4.9114139 -3.2374868 0.3068138
|
|
||||||
88000 27.190678 -1.2803268 1.1545301 4.5769709 5.2404761 -2.3825838 0.10356039
|
|
||||||
89000 26.792931 -0.44516641 1.0236244 4.2007253 4.7098685 -2.3608551 0.034447062
|
|
||||||
90000 27.173991 -0.87185611 1.065719 4.1953618 4.6856408 -2.6539232 0.16957757
|
|
||||||
91000 28.626528 -1.239257 0.89524651 4.7048012 4.6344201 -2.7367901 0.43534143
|
|
||||||
92000 27.661812 -1.109044 0.92817391 5.0294489 4.3890711 -2.4108669 0.12570139
|
|
||||||
93000 28.156793 -1.0820907 0.92812693 4.938385 4.4901426 -2.4023366 0.30135781
|
|
||||||
94000 28.842149 -1.3524969 1.1451109 4.3125908 4.6959035 -2.6747199 0.2254607
|
|
||||||
95000 27.862247 -1.2119045 1.0218976 4.2614082 4.4931316 -2.6902934 0.16345201
|
|
||||||
96000 27.084973 -0.93738328 1.3984324 4.5647189 4.4232205 -2.2834097 0.11217888
|
|
||||||
97000 27.587078 -0.89397255 0.78218462 3.8944421 4.3981479 -2.4205318 0.16570942
|
|
||||||
98000 27.981746 -1.2380545 0.84847869 4.311441 4.7340377 -2.4270441 0.023565612
|
|
||||||
99000 27.476625 -0.8569146 0.82550381 4.1656963 4.4064921 -2.4169708 0.160814
|
|
||||||
100000 26.121325 -0.63610855 1.0803389 4.9257118 4.7073263 -2.4010334 0.066303044
|
|
||||||
Loop time of 2.693 on 4 procs for 100000 steps with 34 atoms
|
|
||||||
|
|
||||||
Performance: 6416.646 ns/day, 0.004 hours/ns, 37133.367 timesteps/s
|
|
||||||
98.4% CPU use with 4 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.065478 | 0.2501 | 0.63682 | 45.6 | 9.29
|
|
||||||
Bond | 0.066944 | 0.44772 | 0.88814 | 53.7 | 16.63
|
|
||||||
Neigh | 0.0076509 | 0.0077319 | 0.0078275 | 0.1 | 0.29
|
|
||||||
Comm | 0.57917 | 1.4166 | 1.9823 | 46.9 | 52.60
|
|
||||||
Output | 0.0033755 | 0.0035856 | 0.0037644 | 0.2 | 0.13
|
|
||||||
Modify | 0.03866 | 0.1366 | 0.23978 | 24.6 | 5.07
|
|
||||||
Other | | 0.4306 | | | 15.99
|
|
||||||
|
|
||||||
Nlocal: 8.5 ave 15 max 2 min
|
|
||||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
|
||||||
Nghost: 25.5 ave 32 max 19 min
|
|
||||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
|
||||||
Neighs: 98.75 ave 257 max 18 min
|
|
||||||
Histogram: 1 1 1 0 0 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 395
|
|
||||||
Ave neighs/atom = 11.6176
|
|
||||||
Ave special neighs/atom = 9.52941
|
|
||||||
Neighbor list builds = 294
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:02
|
|
||||||
|
|
@ -21,7 +21,7 @@
|
||||||
#include <mpi.h>
|
#include <mpi.h>
|
||||||
#include <math.h>
|
#include <math.h>
|
||||||
#include <stdlib.h>
|
#include <stdlib.h>
|
||||||
#include "dihedral_charmmfsh.h"
|
#include "dihedral_charmmfsw.h"
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "comm.h"
|
#include "comm.h"
|
||||||
#include "neighbor.h"
|
#include "neighbor.h"
|
||||||
|
|
@ -40,7 +40,7 @@ using namespace MathConst;
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
DihedralCharmmfsh::DihedralCharmmfsh(LAMMPS *lmp) : Dihedral(lmp)
|
DihedralCharmmfsw::DihedralCharmmfsw(LAMMPS *lmp) : Dihedral(lmp)
|
||||||
{
|
{
|
||||||
weightflag = 0;
|
weightflag = 0;
|
||||||
writedata = 1;
|
writedata = 1;
|
||||||
|
|
@ -48,7 +48,7 @@ DihedralCharmmfsh::DihedralCharmmfsh(LAMMPS *lmp) : Dihedral(lmp)
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
DihedralCharmmfsh::~DihedralCharmmfsh()
|
DihedralCharmmfsw::~DihedralCharmmfsw()
|
||||||
{
|
{
|
||||||
if (allocated && !copymode) {
|
if (allocated && !copymode) {
|
||||||
memory->destroy(setflag);
|
memory->destroy(setflag);
|
||||||
|
|
@ -63,7 +63,7 @@ DihedralCharmmfsh::~DihedralCharmmfsh()
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void DihedralCharmmfsh::compute(int eflag, int vflag)
|
void DihedralCharmmfsw::compute(int eflag, int vflag)
|
||||||
{
|
{
|
||||||
int i1,i2,i3,i4,i,m,n,type;
|
int i1,i2,i3,i4,i,m,n,type;
|
||||||
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
|
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
|
||||||
|
|
@ -322,7 +322,7 @@ void DihedralCharmmfsh::compute(int eflag, int vflag)
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void DihedralCharmmfsh::allocate()
|
void DihedralCharmmfsw::allocate()
|
||||||
{
|
{
|
||||||
allocated = 1;
|
allocated = 1;
|
||||||
int n = atom->ndihedraltypes;
|
int n = atom->ndihedraltypes;
|
||||||
|
|
@ -342,7 +342,7 @@ void DihedralCharmmfsh::allocate()
|
||||||
set coeffs for one type
|
set coeffs for one type
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void DihedralCharmmfsh::coeff(int narg, char **arg)
|
void DihedralCharmmfsw::coeff(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (narg != 5) error->all(FLERR,"Incorrect args for dihedral coefficients");
|
if (narg != 5) error->all(FLERR,"Incorrect args for dihedral coefficients");
|
||||||
if (!allocated) allocate();
|
if (!allocated) allocate();
|
||||||
|
|
@ -384,7 +384,7 @@ void DihedralCharmmfsh::coeff(int narg, char **arg)
|
||||||
error check and initialize all values needed for force computation
|
error check and initialize all values needed for force computation
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void DihedralCharmmfsh::init_style()
|
void DihedralCharmmfsw::init_style()
|
||||||
{
|
{
|
||||||
// insure use of CHARMM pair_style if any weight factors are non-zero
|
// insure use of CHARMM pair_style if any weight factors are non-zero
|
||||||
// set local ptrs to LJ 14 arrays setup by Pair
|
// set local ptrs to LJ 14 arrays setup by Pair
|
||||||
|
|
@ -392,14 +392,14 @@ void DihedralCharmmfsh::init_style()
|
||||||
if (weightflag) {
|
if (weightflag) {
|
||||||
int itmp;
|
int itmp;
|
||||||
if (force->pair == NULL)
|
if (force->pair == NULL)
|
||||||
error->all(FLERR,"Dihedral charmmfsh is incompatible with Pair style");
|
error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");
|
||||||
lj14_1 = (double **) force->pair->extract("lj14_1",itmp);
|
lj14_1 = (double **) force->pair->extract("lj14_1",itmp);
|
||||||
lj14_2 = (double **) force->pair->extract("lj14_2",itmp);
|
lj14_2 = (double **) force->pair->extract("lj14_2",itmp);
|
||||||
lj14_3 = (double **) force->pair->extract("lj14_3",itmp);
|
lj14_3 = (double **) force->pair->extract("lj14_3",itmp);
|
||||||
lj14_4 = (double **) force->pair->extract("lj14_4",itmp);
|
lj14_4 = (double **) force->pair->extract("lj14_4",itmp);
|
||||||
int *ptr = (int *) force->pair->extract("implicit",itmp);
|
int *ptr = (int *) force->pair->extract("implicit",itmp);
|
||||||
if (!lj14_1 || !lj14_2 || !lj14_3 || !lj14_4 || !ptr)
|
if (!lj14_1 || !lj14_2 || !lj14_3 || !lj14_4 || !ptr)
|
||||||
error->all(FLERR,"Dihedral charmmfsh is incompatible with Pair style");
|
error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");
|
||||||
implicit = *ptr;
|
implicit = *ptr;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -414,7 +414,7 @@ void DihedralCharmmfsh::init_style()
|
||||||
|
|
||||||
if (p_cutcoul == NULL || p_cutljinner == NULL ||
|
if (p_cutcoul == NULL || p_cutljinner == NULL ||
|
||||||
p_cutlj == NULL || p_dihedflag == NULL)
|
p_cutlj == NULL || p_dihedflag == NULL)
|
||||||
error->all(FLERR,"Dihedral charmmfsh is incompatible with Pair style");
|
error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");
|
||||||
|
|
||||||
dihedflag = *p_dihedflag;
|
dihedflag = *p_dihedflag;
|
||||||
cut_coul14 = *p_cutcoul;
|
cut_coul14 = *p_cutcoul;
|
||||||
|
|
@ -433,7 +433,7 @@ void DihedralCharmmfsh::init_style()
|
||||||
proc 0 writes out coeffs to restart file
|
proc 0 writes out coeffs to restart file
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void DihedralCharmmfsh::write_restart(FILE *fp)
|
void DihedralCharmmfsw::write_restart(FILE *fp)
|
||||||
{
|
{
|
||||||
fwrite(&k[1],sizeof(double),atom->ndihedraltypes,fp);
|
fwrite(&k[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||||
fwrite(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
|
fwrite(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
|
||||||
|
|
@ -446,7 +446,7 @@ void DihedralCharmmfsh::write_restart(FILE *fp)
|
||||||
proc 0 reads coeffs from restart file, bcasts them
|
proc 0 reads coeffs from restart file, bcasts them
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void DihedralCharmmfsh::read_restart(FILE *fp)
|
void DihedralCharmmfsw::read_restart(FILE *fp)
|
||||||
{
|
{
|
||||||
allocate();
|
allocate();
|
||||||
|
|
||||||
|
|
@ -474,7 +474,7 @@ void DihedralCharmmfsh::read_restart(FILE *fp)
|
||||||
proc 0 writes to data file
|
proc 0 writes to data file
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void DihedralCharmmfsh::write_data(FILE *fp)
|
void DihedralCharmmfsw::write_data(FILE *fp)
|
||||||
{
|
{
|
||||||
for (int i = 1; i <= atom->ndihedraltypes; i++)
|
for (int i = 1; i <= atom->ndihedraltypes; i++)
|
||||||
fprintf(fp,"%d %g %d %d %g\n",i,k[i],multiplicity[i],shift[i],weight[i]);
|
fprintf(fp,"%d %g %d %d %g\n",i,k[i],multiplicity[i],shift[i],weight[i]);
|
||||||
|
|
@ -13,22 +13,22 @@
|
||||||
|
|
||||||
#ifdef DIHEDRAL_CLASS
|
#ifdef DIHEDRAL_CLASS
|
||||||
|
|
||||||
DihedralStyle(charmmfsh,DihedralCharmmfsh)
|
DihedralStyle(charmmfsw,DihedralCharmmfsw)
|
||||||
|
|
||||||
#else
|
#else
|
||||||
|
|
||||||
#ifndef LMP_DIHEDRAL_CHARMMFSH_H
|
#ifndef LMP_DIHEDRAL_CHARMMFSW_H
|
||||||
#define LMP_DIHEDRAL_CHARMMFSH_H
|
#define LMP_DIHEDRAL_CHARMMFSW_H
|
||||||
|
|
||||||
#include <stdio.h>
|
#include <stdio.h>
|
||||||
#include "dihedral.h"
|
#include "dihedral.h"
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
class DihedralCharmmfsh : public Dihedral {
|
class DihedralCharmmfsw : public Dihedral {
|
||||||
public:
|
public:
|
||||||
DihedralCharmmfsh(class LAMMPS *);
|
DihedralCharmmfsw(class LAMMPS *);
|
||||||
virtual ~DihedralCharmmfsh();
|
virtual ~DihedralCharmmfsw();
|
||||||
virtual void compute(int, int);
|
virtual void compute(int, int);
|
||||||
virtual void coeff(int, char **);
|
virtual void coeff(int, char **);
|
||||||
virtual void init_style();
|
virtual void init_style();
|
||||||
|
|
@ -73,9 +73,9 @@ E: Incorrect weight arg for dihedral coefficients
|
||||||
|
|
||||||
Self-explanatory. Check the input script or data file.
|
Self-explanatory. Check the input script or data file.
|
||||||
|
|
||||||
E: Dihedral charmmfsh is incompatible with Pair style
|
E: Dihedral charmmfsw is incompatible with Pair style
|
||||||
|
|
||||||
Dihedral style charmmfsh must be used with a pair style charmm
|
Dihedral style charmmfsw must be used with a pair style charmm
|
||||||
in order for the 1-4 epsilon/sigma parameters to be defined.
|
in order for the 1-4 epsilon/sigma parameters to be defined.
|
||||||
|
|
||||||
*/
|
*/
|
||||||
|
|
@ -186,10 +186,10 @@ nadapt(0), id_fix_diam(NULL), id_fix_chg(NULL), adapt(NULL)
|
||||||
memory->create(adapt[m].array_orig,n+1,n+1,"adapt:array_orig");
|
memory->create(adapt[m].array_orig,n+1,n+1,"adapt:array_orig");
|
||||||
|
|
||||||
// allocate bond style arrays:
|
// allocate bond style arrays:
|
||||||
|
|
||||||
n = atom->nbondtypes;
|
n = atom->nbondtypes;
|
||||||
for (int m = 0; m < nadapt; ++m)
|
for (int m = 0; m < nadapt; ++m)
|
||||||
if (adapt[m].which == BOND)
|
if (adapt[m].which == BOND)
|
||||||
// For now just use same storage and fake it to be one-dimensional:
|
|
||||||
memory->create(adapt[m].vector_orig,n+1,"adapt:vector_orig");
|
memory->create(adapt[m].vector_orig,n+1,"adapt:vector_orig");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -389,7 +389,6 @@ void FixAdapt::init()
|
||||||
} else if (ad->which == BOND){
|
} else if (ad->which == BOND){
|
||||||
ad->bond = NULL;
|
ad->bond = NULL;
|
||||||
anybond = 1;
|
anybond = 1;
|
||||||
// Use same routines from pair to strip any suffices:
|
|
||||||
|
|
||||||
int n = strlen(ad->bstyle) + 1;
|
int n = strlen(ad->bstyle) + 1;
|
||||||
char *bstyle = new char[n];
|
char *bstyle = new char[n];
|
||||||
|
|
@ -404,7 +403,6 @@ void FixAdapt::init()
|
||||||
ad->bond = force->bond_match(bsuffix);
|
ad->bond = force->bond_match(bsuffix);
|
||||||
delete [] bsuffix;
|
delete [] bsuffix;
|
||||||
}
|
}
|
||||||
// If not set grab regular one instead:
|
|
||||||
if (ad->bond == NULL) ad->bond = force->bond_match(bstyle);
|
if (ad->bond == NULL) ad->bond = force->bond_match(bstyle);
|
||||||
if (ad->bond == NULL )
|
if (ad->bond == NULL )
|
||||||
error->all(FLERR,"Fix adapt bond style does not exist");
|
error->all(FLERR,"Fix adapt bond style does not exist");
|
||||||
|
|
@ -414,7 +412,7 @@ void FixAdapt::init()
|
||||||
if (ptr == NULL)
|
if (ptr == NULL)
|
||||||
error->all(FLERR,"Fix adapt bond style param not supported");
|
error->all(FLERR,"Fix adapt bond style param not supported");
|
||||||
|
|
||||||
// For bond styles you should use a vector
|
// for bond styles, use a vector
|
||||||
|
|
||||||
if (ad->bdim == 1) ad->vector = (double *) ptr;
|
if (ad->bdim == 1) ad->vector = (double *) ptr;
|
||||||
|
|
||||||
|
|
@ -449,10 +447,10 @@ void FixAdapt::init()
|
||||||
for (i = ad->ilo; i <= ad->ihi; i++)
|
for (i = ad->ilo; i <= ad->ihi; i++)
|
||||||
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
|
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
|
||||||
ad->array_orig[i][j] = ad->array[i][j];
|
ad->array_orig[i][j] = ad->array[i][j];
|
||||||
}else if (ad->which == PAIR && ad->pdim == 0){
|
} else if (ad->which == PAIR && ad->pdim == 0){
|
||||||
ad->scalar_orig = *ad->scalar;
|
ad->scalar_orig = *ad->scalar;
|
||||||
|
|
||||||
}else if (ad->which == BOND && ad->bdim == 1){
|
} else if (ad->which == BOND && ad->bdim == 1){
|
||||||
for (i = ad->ilo; i <= ad->ihi; ++i )
|
for (i = ad->ilo; i <= ad->ihi; ++i )
|
||||||
ad->vector_orig[i] = ad->vector[i];
|
ad->vector_orig[i] = ad->vector[i];
|
||||||
}
|
}
|
||||||
|
|
@ -612,8 +610,10 @@ void FixAdapt::change_settings()
|
||||||
modify->addstep_compute(update->ntimestep + nevery);
|
modify->addstep_compute(update->ntimestep + nevery);
|
||||||
|
|
||||||
// re-initialize pair styles if any PAIR settings were changed
|
// re-initialize pair styles if any PAIR settings were changed
|
||||||
|
// ditto for bond styles if any BOND setitings were changes
|
||||||
// this resets other coeffs that may depend on changed values,
|
// this resets other coeffs that may depend on changed values,
|
||||||
// and also offset and tail corrections
|
// and also offset and tail corrections
|
||||||
|
|
||||||
if (anypair) {
|
if (anypair) {
|
||||||
for (int m = 0; m < nadapt; m++) {
|
for (int m = 0; m < nadapt; m++) {
|
||||||
Adapt *ad = &adapt[m];
|
Adapt *ad = &adapt[m];
|
||||||
|
|
|
||||||
|
|
@ -1 +1 @@
|
||||||
#define LAMMPS_VERSION "31 Mar 2017"
|
#define LAMMPS_VERSION "11 Apr 2017"
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue