changes to integrate USER-BOCS into LAMMPS and to closer follow the LAMMPS programming/documentation style
This commit is contained in:
Axel Kohlmeyer
@ -122,6 +122,7 @@ Package, Description, Doc page, Example, Library
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Package, Description, Doc page, Example, Library
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"USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
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"USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
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"USER-BOCS"_#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
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"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
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"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
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"USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
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@ -1625,6 +1626,43 @@ examples/USER/awpmd :ul
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:line
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USER-BOCS package :link(USER-BOCS),h4
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[Contents:]
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This package provides "fix bocs"_fix_bocs.html, a modified version
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of "fix npt"_fix_nh.html which includes the pressure correction to
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the barostat as outlined in:
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N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
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accurately describe the structure, pressure, and compressibility of
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molecular liquids," J. Chem. Phys. 143, 243148 (2015).
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[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University)
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[Install or un-install:]
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make yes-user-bocs
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make machine :pre
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make no-user-bocs
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make machine :pre
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[Supporting info:]
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The USER-BOCS user package for LAMMPS is part of the BOCS software package:
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"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS
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See the following reference for information about the entire package:
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Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
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"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
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J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
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Example inputs are in the examples/USER/bocs folder.
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:line
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USER-CGDNA package :link(USER-CGDNA),h4
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[Contents:]
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112
doc/src/fix_bocs.txt
Normal file
112
doc/src/fix_bocs.txt
Normal file
@ -0,0 +1,112 @@
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<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix bocs command :h3
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[Syntax:]
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fix ID group-ID bocs keyword values ... :pre
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keyword = {temp} or {cgiso} or {analytic} or {linear_spline} or {cubic_spline}
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{temp} values = Tstart Tstop Tdamp
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{cgiso} values = Pstart Pstop Pdamp
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{basis set}
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{analytic} values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
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{linear_spline} values = input_filename
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{cubic_spline} values = input_filename :pre
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:ule
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[Examples:]
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fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 :pre
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fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre
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thermo_modify press 1_press :pre
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[Description:]
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These commands incorporate a pressure correction as described by
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Dunn and Noid in "(Dunn1)"_#bocs-Dunn1 to the standard MTTK
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barostat by Martyna et. al. in "(Martyna)"_#bocs-Martyna .
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The first half of the command mimics a standard fix npt command:
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fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp :pre
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The two differences are replacing {npt} with {bocs}, and replacing
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{iso}/{aniso}/{etc} with {cgiso}.
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The rest of the command details what form you would like to use for
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the pressure correction equation. The choices are: {analytic}, {linear_spline},
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or {cubic_spline}.
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With either spline method, the only argument that needs to follow it
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is the name of a file that contains the desired pressure correction
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as a function of volume. The file should be formatted so each line has:
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Volume_i, PressureCorrection_i :pre
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Note both the COMMA and the SPACE separating the volume's
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value and its corresponding pressure correction. The volumes in the file
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should be uniformly spaced. Both the volumes and the pressure corrections
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should be provided in the proper units, e.g. if you are using {units real},
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the volumes should all be in cubic angstroms, and the pressure corrections
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should all be in atomspheres. Furthermore, the table should start/end at a
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volume considerably smaller/larger than you expect your system to sample
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during the simulation. If the system ever reaches a volume outside of the
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range provided, the simulation will stop.
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With the {analytic} option, the arguments are as follows:
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... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N :pre
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Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you
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are using {units real}, {V_avg} should be in cubic angstroms, and the
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coefficients should all be in atmospheres * cubic angstroms.
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[Restrictions:]
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As this is computing a (modified) pressure, group-ID should be {all}.
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The pressure correction has only been tested for use with an isotropic
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pressure coupling in 3 dimensions.
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By default, LAMMPS will still report the normal value for the pressure
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if the pressure is printed via a {thermo} command, or if the pressures
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are written to a file every so often. In order to have LAMMPS report the
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modified pressure, you must include the {thermo_modify} command given in
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the examples. For the last argument in the command, you should put
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XXXX_press, where XXXX is the ID given to the fix bocs command (in the
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example, the ID of the fix bocs command is 1 ).
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This fix is part of the USER-BOCS package. It is only enabled if
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LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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[Related:]
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For more details about the pressure correction and the entire BOCS software
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package, visit the "BOCS package on github"_bocsgithub and read the release
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paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 .
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:link(bocsgithub,https://github.com/noid-group/BOCS)
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:line
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:link(bocs-Dunn1)
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[(Dunn1)] Dunn and Noid, J Chem Phys, 143, 243148 (2015).
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:link(bocs-Martyna)
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[(Martyna)] Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).
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:link(bocs-Dunn2)
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[(Dunn2)] Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).
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@ -20,6 +20,7 @@ Fixes :h1
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fix_ave_time
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fix_aveforce
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fix_balance
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fix_bocs
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fix_bond_break
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fix_bond_create
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fix_bond_swap
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@ -135,6 +135,7 @@ fix_ave_histo.html
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fix_ave_time.html
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fix_aveforce.html
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fix_balance.html
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fix_bocs.html
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fix_bond_break.html
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fix_bond_create.html
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fix_bond_swap.html
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