forked from lijiext/lammps
1571 lines
56 KiB
HTML
1571 lines
56 KiB
HTML
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
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<HTML>
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<HEAD>
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<META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
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</HEAD>
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<BODY>
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<H2>
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LAMMPS Input Commands</H2>
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<P>
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<A HREF="README.html">Return</A> to top-level of LAMMPS documentation.</P>
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<P>
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This page contains a complete list of valid LAMMPS inputs. It will be
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easiest to understand if you read it while looking at sample input
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files such as those in the examples directory. </P>
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<P>
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The input file of commands is read by LAMMPS, one line at a time. Each
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command causes LAMMPS to take some action. Usually it simply causes
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some internal variable(s) to be set. Or it may cause a file to be read
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in or a simulation to be run. In general, commands can be listed in any
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order, although some commands require others to have been executed
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previously. </P>
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<P>
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LAMMPS continues to read successive lines from the input command file
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until the end-of-file is reached which causes LAMMPS to terminate. Thus
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new simulations can be run or current simulations continued by simply
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specifying additional commands in the input command file. </P>
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<P>
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The next section of this page gives an example of each command, some of
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which can be specified in multiple styles. Typically the commands take
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one or more parameters. The keyword for each command should begin in
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the leftmost column and all characters in the command and its
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parameters should be in lower-case. Parameters can be separated by
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arbitrary numbers of spaces and/or tabs (so long as the command fits on
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one line). The remainder of the line after the last parameter is
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ignored.</P>
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<P>
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The final section of this page gives a more detailed description of
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each command with its associated parameters. It also lists the default
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parameters associated with each command. When performing a simulation,
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you only need specify a particular command if you do not want to use
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the default settings.</P>
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<UL>
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<LI>
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<A HREF="#_cch3_931277449">Categories of Commands with Examples</A>
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<LI>
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<A HREF="#_cch3_931277455">Alphabetic Listing of Commands</A>
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</UL>
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<HR>
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<H3>
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<A NAME="_cch3_931277449">Categories of Commands withExamples</A></H3>
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<UL>
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<LI>
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<A HREF="#_cch3_930960479">Basic Settings</A>
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<LI>
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<A HREF="#_cch3_930960485">Output Control</A>
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<LI>
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<A HREF="#_cch3_930960490">Ensemble Control</A>
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<LI>
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<A HREF="#_cch3_930960495">Nonbond Force Field</A>
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<LI>
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<A HREF="#_cch3_930960501">Bonded Force Field</A>
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<LI>
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<A HREF="#_cch3_930960506">Atom Creation</A>
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<LI>
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<A HREF="#_cch3_930960510">Velocity Creation</A>
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<LI>
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<A HREF="#_cch3_930960516">Constraint Creation</A>
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<LI>
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<A HREF="#_cch3_930960521">Dynamics or Minimization</A>
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</UL>
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<HR>
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<H3>
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<A NAME="_cch3_930960479">Basic Settings </A></H3>
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<PRE>
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<A HREF="#_cch3_931276588">comments</A>
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<A HREF="#_cch3_931276596">units</A> real
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<A HREF="#_cch3_931276604">dimension</A> 3
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<A HREF="#_cch3_931276612">periodicity</A> 0 0 0
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<A HREF="#_cch3_931276624">processor grid</A> 10 10 10
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<A HREF="#_cch3_931276632">newton flag</A> 3
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<A HREF="#_cch3_931276638">timestep</A> 1.0
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<A HREF="#_cch3_931276645">respa</A> 2 2 4
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<A HREF="#_cch3_931276654">neighbor</A> 2.0 0 1 10 1
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<A HREF="#_cch3_931276666">special bonds</A> 0.0 0.0 0.4
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_930960485">Output Control</A></H3>
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<PRE>
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<A HREF="#_cch3_931276675">thermo flag</A> 50
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<A HREF="#_cch3_931276681">thermo style</A> 0
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<A HREF="#_cch3_931276687">true flag</A> 0
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<A HREF="#_cch3_931276696">dump atoms</A> 100 filename
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<A HREF="#_cch3_931276703">dump velocities</A> 100 filename
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<A HREF="#_cch3_931276712">dump forces</A> 100 filename
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<A HREF="#_cch3_931276719">restart</A> 1000 file1 file2
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<A HREF="#_cch3_931276727">diagnostic</A> diffusion 100 filename 3 1.0 -1.0 2.5
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_930960490">Ensemble Control</A></H3>
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<PRE>
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<A HREF="#_cch3_931276742">temp control</A> none
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<A HREF="#_cch3_931276742">temp control</A> rescale 300.0 300.0 100 20.0
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<A HREF="#_cch3_931276742">temp control</A> replace 300.0 300.0 50 12345678
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<A HREF="#_cch3_931276742">temp control</A> langevin 50.0 50.0 0.01 123456
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<A HREF="#_cch3_931276742">temp control</A> nose/hoover 300.0 300.0 0.01
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<A HREF="#_cch3_931276784">press control</A> none
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<A HREF="#_cch3_931276784">press control</A> nose/hoover 1.0 1.0 0.001
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<A HREF="#_cch3_931276810">press_x control</A> nose/hoover 1.0 1.0 0.001
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<A HREF="#_cch3_931276810">press_y control</A> nose/hoover 1.0 1.0 0.001
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<A HREF="#_cch3_931276810">press_z control</A> nose/hoover 1.0 1.0 0.001
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_930960495">Nonbond Force Field</A></H3>
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<PRE>
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<A HREF="#_cch3_931276833">nonbond style</A> none
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<A HREF="#_cch3_931276833">nonbond style</A> lj/cutoff 10.0 0
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<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 10.0
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<A HREF="#_cch3_931276833">nonbond style</A> lj/smooth 8.0 10.0
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<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 8.0 10.0
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<A HREF="#_cch3_931276833">nonbond style</A> lj/shift 10.0 0
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<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 2.0 10.0
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<A HREF="#_cch3_931276833">nonbond style</A> soft 2.5
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<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 30.0 2.5
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<A HREF="#_cch3_931276833">nonbond style</A> class2/cutoff 10.0 0
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<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 10.0
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<A HREF="#_cch3_931276900">mixing style</A> geometric
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<A HREF="#_cch3_931276910">coulomb style</A> none
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<A HREF="#_cch3_931276910">coulomb style</A> cutoff 10.0
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<A HREF="#_cch3_931276910">coulomb style</A> smooth 8.0 10.0
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<A HREF="#_cch3_931276910">coulomb style</A> ewald 10.0 1.0E-4
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<A HREF="#_cch3_931276910">coulomb style</A> pppm 10.0 1.0E-4
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<A HREF="#_cch3_931276941">pppm mesh</A> 32 32 64
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<A HREF="#_cch3_931276947">pppm order</A> 5
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<A HREF="#_cch3_931276953">dielectric</A> 1.0
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_930960501">Bonded Force Field</A></H3>
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<PRE>
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<A HREF="#_cch3_931276958">bond style</A> none
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<A HREF="#_cch3_931276958">bond style</A> harmonic
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<A HREF="#_cch3_931276970">bond coeff</A> 1 100.0 3.45
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<A HREF="#_cch3_931276958">bond style</A> fene/standard
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<A HREF="#_cch3_931276970">bond coeff</A> 1 30.0 1.5 1.0 1.0
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<A HREF="#_cch3_931276958">bond style</A> fene/shift
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<A HREF="#_cch3_931276970">bond coeff</A> 1 30.0 1.5 1.0 1.0 0.2
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<A HREF="#_cch3_931276958">bond style</A> nonlinear
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<A HREF="#_cch3_931276970">bond coeff</A> 1 28.0 0.748308 0.166667
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<A HREF="#_cch3_931276958">bond style</A> class2
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<A HREF="#_cch3_931277007">angle style</A> none
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<A HREF="#_cch3_931277007">angle style</A> harmonic
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<A HREF="#_cch3_931277007">angle style</A> class2
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<A HREF="#_cch3_931277020">dihedral style</A> none
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<A HREF="#_cch3_931277020">dihedral style</A> harmonic
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<A HREF="#_cch3_931277020">dihedral style</A> class2
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<A HREF="#_cch3_931277042">improper style</A> none
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<A HREF="#_cch3_931277042">improper style</A> harmonic
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<A HREF="#_cch3_931277042">improper style</A> class2
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_930960506">Atom Creation</A></H3>
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<PRE>
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<A HREF="#_cch3_931277059">read data</A> filename
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<A HREF="#_cch3_931277070">read restart</A> filename
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_930960510">Velocity Creation</A></H3>
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<PRE>
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<A HREF="#_cch3_931277080">create group</A> types 1 3
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<A HREF="#_cch3_931277080">create group</A> region 0.0 1.0 0.0 1.0 INF 1.0
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<A HREF="#_cch3_931277080">create group</A> remainder
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<A HREF="#_cch3_931277097">create temp</A> uniform 300.0 12345678
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<A HREF="#_cch3_931277097">create temp</A> gaussian 300.0 12345678
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<A HREF="#_cch3_931277097">create temp</A> velocity 0.0 0.0 0.0
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_930960516">Constraint Creation</A></H3>
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<PRE>
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<A HREF="#_cch3_931277114">fix style</A> none
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<A HREF="#_cch3_931277114">fix style</A> 1 setforce 0.0 NULL 0.0
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<A HREF="#_cch3_931277114">fix style</A> 1 addforce 1.0 0.0 0.0
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<A HREF="#_cch3_931277114">fix style</A> 1 aveforce 1.0 0.0 0.0
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<A HREF="#_cch3_931277114">fix style</A> 1 rescale 300.0 300.0 100 20.0
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<A HREF="#_cch3_931277114">fix style</A> 1 langevin 50.0 50.0 0.01 12345 1 1 1
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<A HREF="#_cch3_931277114">fix style</A> 1 nose/hoover 50.0 50.0 0.01
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<A HREF="#_cch3_931277114">fix style</A> 1 springforce 10.0 NULL NULL 1.0
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<A HREF="#_cch3_931277114">fix style</A> 1 dragforce 10.0 -5.0 NULL 2.0 1.0
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<A HREF="#_cch3_931277163">assign fix</A> 1 atom 200
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<A HREF="#_cch3_931277163">assign fix</A> 1 molecule 50
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<A HREF="#_cch3_931277163">assign fix</A> 1 type 2
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<A HREF="#_cch3_931277163">assign fix</A> 1 region 0.0 1.0 INF INF 0.0 1.0
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<A HREF="#_cch3_931277163">assign fix</A> 1 remainder
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_930960521">Dynamics or Minimization</A></H3>
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<PRE>
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<A HREF="#_cch3_931277185">reset timestep</A> 0
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<A HREF="#_cch3_931277194">run</A> 1000
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<A HREF="#_cch3_931277200">min style</A> hftn
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<A HREF="#_cch3_931277206">min file</A> filename
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<A HREF="#_cch3_931277212">minimize</A> 0.0001 9999 50000
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_931277455">Alphabetic Listing of Commands:</A></H3>
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<HR>
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<H3>
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<A NAME="_cch3_931277007">angle style </A></H3>
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<UL>
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<LI>
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none = compute no angles
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<LI>
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harmonic = harmonic angles (class 1)
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<LI>
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class2 = class 2 angles (and associated cross terms)
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</UL>
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<PRE>
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define style of angle interactions to use for all 3-body terms
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angle style determines how many angle coefficients the program expects to
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find in a "Angle Coeffs" entry in the data file,
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thus the style must be set (if not using default)
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before using the "read data" command (if the data file contains a
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"Angle Coeffs" entry)
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coefficients for all angle types must be defined in data (or restart)
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file by "Angle Coeffs" entry before a run is performed
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style of "none" erases all previously defined angle coefficients, must
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reset style to something else before defining new coefficients
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Default = harmonic
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_931277163">assign fix </A></H3>
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<UL>
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<LI>
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1st parameter = constraint #
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<LI>
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2nd parameter = style of group of atoms
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<LI>
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3rd-Nth parameters = coeffs 1 to N-2
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</UL>
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<PRE>
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styles:
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</PRE>
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<UL>
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<LI>
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atom = single atom
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<LI>
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molecule = all atoms in a particular molecule
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<LI>
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type = single atom type
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<LI>
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region = geometric region of atoms
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<LI>
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remainder = rest of unconstrained atoms
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</UL>
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<PRE>
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coeffs: atom
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(1) global atom #
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molecule
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(1) molecule #
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type
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(1) atom type
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region
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(1) lower x bound of region
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(2) upper x bound of region
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(3) lower y bound of region
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(4) upper y bound of region
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(5) lower z bound of region
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(6) upper z bound of region
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remainder
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no other parameters required
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assign a group of atoms to a particular constraint
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use appropriate number of coeffs for a particular style
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the constraint itself is defined by the "fix style" command
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multiple groups of atoms can be assigned to the same constraint
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an atom can be assigned to multiple constraints, the contraints will be
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applied in the reverse order they are assigned to that atom
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(e.g. each timestep, the last fix assigned to an atom will be applied
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to it first, then the next-to-last applied second, etc)
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for style region, a coeff of INF means + or - infinity (all the way
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to the boundary)
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_931276970">bond coeff </A></H3>
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<UL>
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<LI>
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1st parameter = bond type #
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<LI>
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2nd-Nth parameters = coeffs 1 to N-1
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</UL>
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<PRE>
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coeffs: harmonic
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(1) K (energy units)
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(2) r0 (distance units)
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fene/standard
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(1) k for FENE portion (energy/distance^2 units)
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(2) r0 for FENE portion (distance units)
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(3) epsilon for LJ portion (energy units)
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(4) sigma for LJ portion (distance units)
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fene/shift
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(1) k for FENE (energy/distance^2 units)
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(2) r0 for FENE after shift is performed (distance units)
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(3) epsilon for LJ (energy units)
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(4) sigma for LJ after shift is performed (distance units)
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(5) delta shift distance (distance units)
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nonlinear
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(1) epsilon (energy units)
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(2) r0 (distance units)
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(3) lamda (distance units)
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class 2
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currently not enabled for "bond coeff" command
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must be specified in data file (see "read data" command)
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define (or override) bond coefficients for an individual bond type
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use appropriate number of coeffs for a particular style
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these coefficients can also be set in data file
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by "Bond Coeffs" entry, the most recently defined coefficients are used
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Default = no settings
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_931276958">bond style </A></H3>
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<UL>
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<LI>
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none = compute no bonds
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<LI>
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harmonic = harmonic springs
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<LI>
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fene/standard = attractive cosine, repulsive LJ
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<LI>
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fene/shift = same as fene/standard with shift of bond distance
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<LI>
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nonlinear = non-linear finite-extension spring (van Swol)
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<LI>
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class2 = class 2 bonds
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</UL>
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<PRE>
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define style of bond interactions to use between all bonded atoms
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bond style determines how many bond coefficients the program expects to
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find in a "Bond Coeffs" entry in the data file or when using the
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"bond coeff" command, thus the style must be set (if not using default)
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before using the "read data" command (if the data file contains a
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"Bond Coeffs" entry)
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coefficients for all bond types must be defined in data (or restart)
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file by "Bond Coeffs" entry or by "bond coeffs" commands before a run
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is performed
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style of "none" erases all previously defined bond coefficients, must
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reset style to something else before defining new coefficients
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Default = harmonic
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_931276588">comments </A></H3>
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<PRE>
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blank lines are ignored
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everything on a line after the last parameter is ignored
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lines starting with a # are echoed into the log file
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</PRE>
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<HR>
|
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<H3>
|
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<A NAME="_cch3_931276910">coulomb style </A></H3>
|
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<UL>
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<LI>
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1st parameter = style of pairwise Coulomb interactions
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<LI>
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2nd-Nth parameters = coeffs 1 to N-1
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</UL>
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<PRE>
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styles:
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</PRE>
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<UL>
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<LI>
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none = no Coulomb interactions are computed
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<LI>
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cutoff = use a simple cutoff
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<LI>
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smooth = use a switch region that goes smoothly to zero
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<LI>
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ewald = use Ewald summations for long-range effects
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<LI>
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pppm = use particle-mesh Ewald for long-range effects
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</UL>
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<PRE>
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coeffs: none
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no other parameters required
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cutoff
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(1) cutoff distance (distance units)
|
|
smooth
|
|
(1) inner cutoff (distance units)
|
|
(2) outer cutoff (distance units)
|
|
ewald
|
|
(1) cutoff distance for near-field portion (distance units)
|
|
(2) accuracy criterion
|
|
pppm
|
|
(1) cutoff distance for near-field portion (distance units)
|
|
(2) accuracy criterion
|
|
|
|
use appropriate number of coeffs for a particular style
|
|
if simulated system has no charges, must set "coulomb style none" to
|
|
prevent LAMMPS from doing useless nonbond work
|
|
accuracy criterion means "one part in value" - e.g. 1.0E-4
|
|
Ewald and PPPM accuracy criterion are used in conjunction with cutoff
|
|
to partition work between short-range and long-range routines
|
|
accuracy criterion effectively determines how many k-space vectors are used
|
|
to approximate the energy and forces
|
|
for PPPM, accuracy criterion determines mesh spacing (see "particle mesh"
|
|
command)
|
|
for PPPM, must be running on power-of-2 number of processors for FFTs
|
|
must use periodic boundary conditions in conjuction with Ewald and PPPM
|
|
cannot use any styles other than none with nonbond style = lj/shift or
|
|
nonbond style = soft
|
|
Coulomb style = smooth should be used with nonbond style = lj/switch,
|
|
and both should use same inner and outer cutoffs
|
|
for smooth style, outer cutoff must be > inner cutoff
|
|
for smooth style, atom pairs less than the inner cutoff distance use
|
|
usual Coulomb, pairs between inner and outer are smoothed, and the
|
|
potential goes to 0.0 at the outer cutoff
|
|
for smooth style, force is continuously differentiable everywhere
|
|
|
|
Default = cutoff 10.0
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931277080">create group </A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = style of group of atoms
|
|
<LI>
|
|
2nd-Nth parameters = coeffs 1 to N-1
|
|
</UL>
|
|
<PRE>
|
|
styles:
|
|
</PRE>
|
|
<UL>
|
|
<LI>
|
|
types = range of atom types
|
|
<LI>
|
|
region = geometric region of atoms
|
|
<LI>
|
|
remainder = rest of uninitialized atoms
|
|
</UL>
|
|
<PRE>
|
|
coeffs: types
|
|
(1) lowest atom type
|
|
(2) highest atom type
|
|
region
|
|
(1) lower x bound of region
|
|
(2) upper x bound of region
|
|
(3) lower y bound of region
|
|
(4) upper y bound of region
|
|
(5) lower z bound of region
|
|
(6) upper z bound of region
|
|
remainder
|
|
no other parameters required
|
|
|
|
used with "create temp" commmand to initialize velocities of atoms
|
|
by default, the "create temp" command initializes the velocities of all atoms,
|
|
this command limits the initialization to a group of atoms
|
|
this command is only in force for the next "create temp" command, any
|
|
subsequent "create temp" command is applied to all atoms (unless the
|
|
"create group" command is used again)
|
|
for style types, only atoms with a type such that lo-type <= type <= hi-type
|
|
will be initialized by "create temp"
|
|
for style types, lo-type can equal hi-type if just want to specify one type
|
|
for style region, only atoms within the specified spatial region
|
|
will be initialized by "create temp"
|
|
for style region, a coeff of INF means + or - infinity (all the way
|
|
to the boundary)
|
|
for style remainder, only previously uninitialized atoms
|
|
will be initialized by "create temp"
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931277097">create temp</A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = style of temperature creation
|
|
<LI>
|
|
2nd-Nth parameters = coeffs 1 to N-1
|
|
</UL>
|
|
<PRE>
|
|
styles:
|
|
</PRE>
|
|
<UL>
|
|
<LI>
|
|
uniform = uniform distribution of velocities
|
|
<LI>
|
|
gaussian = gaussian distribution of velocities
|
|
<LI>
|
|
velocity = assign specific initial velocity to each atom
|
|
</UL>
|
|
<PRE>
|
|
coeffs: uniform
|
|
(1) target T (temperature units)
|
|
(2) random # seed (0 < seed <= 8 digits)
|
|
gaussian
|
|
(1) target T (temperature units)
|
|
(2) random # seed (0 < seed <= 8 digits)
|
|
velocity
|
|
(1) x velocity component (velocity units)
|
|
(2) y velocity component (velocity units)
|
|
(3) z velocity component (velocity units)
|
|
|
|
initialize velocities of atoms to a specified temperature
|
|
use appropriate number of coeffs for a particular style
|
|
cannot be done before a data or restart file is read
|
|
by default, velocities are created for all atoms - this can be overridden
|
|
by "create group" command
|
|
for uniform and Gaussian styles velocities are created in
|
|
processor-independent fashion - is slower but gives the same initial
|
|
state independent of # of processors
|
|
for uniform and Gaussian styles the momentum of the initialized atoms is
|
|
also zeroed, but only if all atoms are being initialized
|
|
for uniform and Gaussian styles, RN are generated with Park/Miller RNG
|
|
for velocity style in 2-d simulations, still specify z velocity component,
|
|
even though it is ignored
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276727">diagnostic</A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = nametag of a user routine added to diagnostic.f file
|
|
<LI>
|
|
2nd parameter = call this user routine every this # of timesteps
|
|
<LI>
|
|
3rd parameter = file name for this routine's diagnostic output
|
|
<LI>
|
|
4th parameter = # of remaining parameters (0 to 5)
|
|
<LI>
|
|
5th-9th parameters = optional parameters to pass to user routine
|
|
</UL>
|
|
<PRE>
|
|
call a user-defined diagnostic routine every this many timesteps
|
|
this command can be used multiple times to call different routines
|
|
at different frequencies, that use different parameters, and that
|
|
send output to different files
|
|
value of 0 for 2nd parameter means never call this particular routine
|
|
this command causes any previous file associated with this user routine
|
|
to be closed
|
|
new filename can exist, will be overwritten
|
|
if the file name specified is "none", then no file is opened
|
|
each routine that is added to diagnostic.f and enabled with a
|
|
"diagnostic" command will be called at the beginning and end of
|
|
each "run" and every so many timesteps during the run
|
|
the diagnostic.f file has further information on how to create
|
|
routines that operate on internal LAMMPS data, do their own file output,
|
|
perform different operations (e.g. setup and clean-up) depending
|
|
on when they are called, etc
|
|
the user routines must be compiled and linked into LAMMPS
|
|
the optional 5th-9th parameters are stored in program variables which
|
|
can be accessed by the diagnostic routine
|
|
|
|
Default = none
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276953">dielectric </A></H3>
|
|
<PRE>
|
|
set dielectric constant to this value
|
|
|
|
Default = 1.0
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931277020">dihedral style </A></H3>
|
|
<UL>
|
|
<LI>
|
|
none = compute no dihedrals
|
|
<LI>
|
|
harmonic = harmonic dihedrals (class 1)
|
|
<LI>
|
|
class2 = class 2 dihedrals (and associated cross terms)
|
|
</UL>
|
|
<PRE>
|
|
define style of dihedral interactions to use for all 4-body terms
|
|
dihedral style determines how many dihedral coefficients the program expects to
|
|
find in a "Dihedral Coeffs" entry in the data file,
|
|
thus the style must be set (if not using default)
|
|
before using the "read data" command (if the data file contains a
|
|
"Dihedral Coeffs" entry)
|
|
coefficients for all dihedral types must be defined in data (or restart)
|
|
file by "Dihedral Coeffs" entry before a run is performed
|
|
style of "none" erases all previously defined dihedral coefficients, must
|
|
reset style to something else before defining new coefficients
|
|
|
|
Default = harmonic
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276604">dimension </A></H3>
|
|
<UL>
|
|
<LI>
|
|
specify 3 for 3-d or 2 for 2-d run
|
|
</UL>
|
|
<PRE>
|
|
for a 2-d run, assumes all z-coords are set to 0.0 in "read data" or
|
|
"read restart" files and program creates no z velocities
|
|
this command sets the processor grid to default values for 2-d or 3-d
|
|
so must be used before "processor grid" command
|
|
must be set before data or restart file is read
|
|
|
|
Default = 3
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276696">dump atoms </A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = # of timesteps
|
|
<LI>
|
|
2nd parameter = file name
|
|
</UL>
|
|
<PRE>
|
|
dump all atom positions to a file every this many timesteps
|
|
positions are also dumped at the start and end of every run
|
|
value of 0 means never dump
|
|
any previous file is closed
|
|
new filename can exist, will be overwritten
|
|
atom positions in dump file are in "box" units (0.0 to 1.0) in each dimension
|
|
|
|
Default = 0
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276712">dump forces </A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = # of timesteps
|
|
<LI>
|
|
2nd parameter = file name
|
|
</UL>
|
|
<PRE>
|
|
dump all atom forces to a file every this many timesteps
|
|
forces are also dumped at the start and end of every run
|
|
any previous file is closed
|
|
new filename can exist, will be overwritten
|
|
value of 0 means never dump
|
|
|
|
Default = 0
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276703">dump velocities </A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = # of timesteps
|
|
<LI>
|
|
2nd parameter = file name
|
|
</UL>
|
|
<PRE>
|
|
dump all atom velocities to a file every this many timesteps
|
|
velocities are also dumped at the start and end of every run
|
|
any previous file is closed
|
|
new filename can exist, will be overwritten
|
|
value of 0 means never dump
|
|
|
|
Default = 0
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931277114">fix style </A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = constraint # (except for none)
|
|
<LI>
|
|
2nd parameter = style of that constraint
|
|
<LI>
|
|
3rd-Nth parameters = coeffs 1 to N-2
|
|
</UL>
|
|
<PRE>
|
|
styles:
|
|
</PRE>
|
|
<UL>
|
|
<LI>
|
|
none = erase all constraints and all atom assignments
|
|
<LI>
|
|
setforce = set force on each atom in group
|
|
<LI>
|
|
addforce = add a force to each atom in group
|
|
<LI>
|
|
aveforce = apply an external force to group of atoms such that every
|
|
atom is accelerated the same
|
|
<LI>
|
|
rescale = thermostat a group of atoms by rescaling their velocities
|
|
<LI>
|
|
langevin = thermostat a group of atoms by the Langevin method
|
|
<LI>
|
|
nose/hoover = thermostat a group of atoms by the Nose/Hoover method
|
|
<LI>
|
|
springforce = apply a spring force to each atom in group
|
|
<LI>
|
|
dragforce = drag each atom in group to a specified position
|
|
</UL>
|
|
<PRE>
|
|
coeffs: none
|
|
no other parameters required (use "none" as 1st parameter)
|
|
setforce
|
|
(1) x component of set force (in force units)
|
|
(2) y component of set force (in force units)
|
|
(3) z component of set force (in force units)
|
|
addforce
|
|
(1) x component of added force (in force units)
|
|
(2) y component of added force (in force units)
|
|
(3) z component of added force (in force units)
|
|
aveforce
|
|
(1) x comp of added average force per atom (in force units)
|
|
(2) y comp of added average force per atom (in force units)
|
|
(3) z comp of added average force per atom (in force units)
|
|
rescale
|
|
(1) desired T at beginning of run
|
|
(2) desired T at end of run
|
|
(3) check for rescaling every this many timesteps
|
|
(4) T window outside of which velocities will be rescaled
|
|
langevin
|
|
(1) desired T at beginning of run
|
|
(2) desired T at end of run
|
|
(3) Langevin damping parameter (inverse time units)
|
|
(4) random seed to use for white noise (0 < seed <= 8 digits)
|
|
(5) 0/1 = off/on x dimension
|
|
(6) 0/1 = off/on y dimension
|
|
(7) 0/1 = off/on z dimension
|
|
nose/hoover
|
|
(1) desired T at beginning of run
|
|
(2) desired T at end of run
|
|
(3) frequency constant for friction force (inverse time units)
|
|
springforce
|
|
(1) x position of spring origin
|
|
(2) y position
|
|
(3) z position
|
|
(4) force constant k (so that k*distance = force units)
|
|
dragforce
|
|
(1) x position to drag atom towards
|
|
(2) y position
|
|
(3) z position
|
|
(4) force magnitude f (in force units)
|
|
(5) delta outside of which to apply force (in distance units)
|
|
|
|
define a constraint
|
|
cannot skip a constraint number, all must be used before a run is performed
|
|
use appropriate number of coeffs for a particular style
|
|
which atoms the constraint will affect is set by the "assign fix" command
|
|
all of the constraints (except for rescale) are applied every timestep
|
|
all specified temperatures are in temperature units
|
|
for style setforce, a coeff of NULL means do not alter that force component
|
|
for style aveforce, average force on the group of fixed atoms is computed,
|
|
then new average force is added in and actual force on each atom is set
|
|
to new total value -> has effect of applying same force to entire group
|
|
of atoms
|
|
thermostatting constraints (rescale, langevin, nose/hoover) cannot be used in
|
|
conjuction with global "temp control", since they conflict and will
|
|
cause atom velocities to be reset twice
|
|
if multiple Langevin constraints are specified the Marsaglia RNG will
|
|
only use the last RNG seed specified for initialization
|
|
meaning of thermostatting coefficients is same as in "temp control" command
|
|
style springforce is designed to be applied to an entire group of atoms
|
|
en masse (e.g. an umbrella force on an entire molecule)
|
|
for style springforce, the center of mass r0 of the group of atoms is computed,
|
|
then a restoring force = -k*(r-r0)*mass/masstotal is applied to each
|
|
atom in the group where mass = mass of the atom and masstotal = mass of
|
|
all the atoms in the group - thus "k" should represent the total
|
|
force on the group of atoms (not per atom)
|
|
for style springforce, a xyz position of NULL means do not include that
|
|
dimension in the distance or force computation
|
|
for style dragforce, apply a drag force of magnitude f to each atom in the
|
|
group in the direction (r-r0) where r0 = (x,y,z) - do not apply the force if
|
|
the atom is within a distance delta of r0
|
|
for style dragforce, a xyz position of NULL means do not include that
|
|
dimension in the distance or force computation
|
|
|
|
Default = none
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931277042">improper style </A></H3>
|
|
<UL>
|
|
<LI>
|
|
none = compute no impropers
|
|
<LI>
|
|
harmonic = harmonic impropers (class 1) (V = k*phi*phi)
|
|
<LI>
|
|
cvff = cvff improper (class 1 variant) (V = K*(1 +/- cos(n*phi))
|
|
<LI>
|
|
class2 = class 2 Wilson out-of-plane (V = K*chi*chi)
|
|
</UL>
|
|
<PRE>
|
|
define style of improper interactions to use for all trigonal centers
|
|
in class2 case, dictates that angle-angle terms be included for all
|
|
trigonal and tetrahedral centers
|
|
in above formulas, phi = improper torsion, chi = Wilson out-of-plane
|
|
improper style determines how many improper coefficients the program
|
|
expects to find in a "Improper Coeffs" entry in the data file,
|
|
thus the style must be set (if not using default)
|
|
before using the "read data" command (if the data file contains a
|
|
"Improper Coeffs" entry)
|
|
coefficients for all improper types must be defined in data (or restart)
|
|
file by "Improper Coeffs" entry before a run is performed
|
|
style of "none" erases all previously defined improper coefficients, must
|
|
reset style to something else before defining new coefficients
|
|
|
|
Default = harmonic
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931277206">min file </A></H3>
|
|
<PRE>
|
|
name of file to write minimization iteration info to
|
|
filename can exist, will be overwritten when minimization occurs
|
|
if no file is specified, no minimization output will be written to a file
|
|
|
|
Default = none
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931277200">min style </A></H3>
|
|
<UL>
|
|
<LI>
|
|
htfn = Hessian-free truncated Newton method
|
|
</UL>
|
|
<PRE>
|
|
choose minimization algorithm to use when "minimize" command is performed
|
|
currently, only htfn style is available
|
|
|
|
Default = htfn
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931277212">minimize </A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = stopping tolerance (in force units)
|
|
<LI>
|
|
2nd parameter = max iterations of minimizer
|
|
<LI>
|
|
3rd parameter = max number of force or energy evaluations
|
|
</UL>
|
|
<PRE>
|
|
perform an energy minimization of the atomic coordinates of the system
|
|
uses algorithm selected with "min style" command
|
|
minimization stops if any of 3 criteria are met:
|
|
(1) largest force component < stopping tolerance
|
|
(2) # of iterations > max iterations
|
|
(3) # of force and energy evaluations > max evaluations
|
|
for good convergence, should specify use of smooth nonbond force fields
|
|
that have continuous second derivatives, set "coulomb style" to "smooth",
|
|
set nonbond style to "lj/smooth" or use a long cutoff
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276900">mixing style </A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = style of mixing used to generate i-j nonbond
|
|
interactions
|
|
</UL>
|
|
<PRE>
|
|
styles:
|
|
</PRE>
|
|
<UL>
|
|
<LI>
|
|
geometric = sqrt(i*j) for both epsilon and sigma
|
|
<LI>
|
|
arithmetic = sqrt(i*j) for epsilon, (i+j)/2 for sigma
|
|
<LI>
|
|
sixthpower = see force_fields.txt file for details
|
|
</UL>
|
|
<PRE>
|
|
determine the kind of mixing rule that is applied to generate nonbond
|
|
coefficients for interactions between type i and type j atoms
|
|
mixing rules are used only when nonbond coeffs are input in a "read data" file
|
|
for nonbond style "soft", only epsilons (prefactor A) are input - they are
|
|
always mixed geometrically, regardless of mixing style setting
|
|
|
|
Default = geometric for all nonbond styles except class2/cutoff
|
|
sixthpower for nonbond style class2/cutoff
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276654">neighbor </A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = skin distance in distance units
|
|
<LI>
|
|
2nd parameter = neighboring style: 0 = N^2, 1 = binning
|
|
<LI>
|
|
3rd parameter = build neighbor list every this many steps (see next
|
|
param)
|
|
<LI>
|
|
4th parameter = delay building until after this many steps since last
|
|
build
|
|
<LI>
|
|
5th parameter = build criteria: 0 = always build, 1 = only build if
|
|
some atom has moved 1/2 or more of the skin thickness
|
|
</UL>
|
|
<PRE>
|
|
factors that affect how and when neighbor lists are constructed
|
|
skin must be large enough that all atoms needed for bond
|
|
interactions are also acquired by interprocessor communication
|
|
last parameter incurs extra checking and communication to test against
|
|
skin thickness, but may mean neighbor list is created less often
|
|
when RESPA is run, the 3rd and 4th parameters refer to the
|
|
nonbond (short-range) timestepping
|
|
defaults = 2.0 0 1 10 1
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276632">newton flag </A></H3>
|
|
<PRE>
|
|
turn off or on Newton's 3rd law for bond and non-bond force computation
|
|
</PRE>
|
|
<UL>
|
|
<LI>
|
|
value = 0 -> no Newton's 3rd law for either
|
|
<LI>
|
|
value = 1 -> Newton's 3rd law only for bonded computations
|
|
<LI>
|
|
value = 2 -> Newton's 3rd law only for non-bonded computations
|
|
<LI>
|
|
value = 3 -> Newton's 3rd law for both bonded and non-bonded
|
|
computations
|
|
</UL>
|
|
<PRE>
|
|
no Newton's 3rd law means more force computation and less communication
|
|
yes Newton's 3rd law means less force computation and more communication
|
|
which choice is faster is problem dependent on N, # of processors,
|
|
and cutoff length(s)
|
|
expect for round-off errors, setting this flag should not affect answers,
|
|
only run time
|
|
must be set before data or restart file is read
|
|
|
|
Default = 3
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276848">nonbond coeff</A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = 1st atom type
|
|
<LI>
|
|
2nd parameter = 2nd atom type
|
|
<LI>
|
|
3rd-Nth parameters = coeffs 1 to N-2
|
|
</UL>
|
|
<PRE>
|
|
coeffs: lj/cutoff
|
|
(1) epsilon (energy units)
|
|
(2) sigma (distance units)
|
|
(3) cutoff (distance units)
|
|
lj/smooth
|
|
(1) epsilon (energy units)
|
|
(2) sigma (distance units)
|
|
(3) inner cutoff (distance units)
|
|
(4) outer cutoff (distance units)
|
|
lj/shift
|
|
(1) epsilon (energy units)
|
|
(2) sigma (distance units)
|
|
(3) delta shift distance (distance units)
|
|
(4) cutoff (distance units)
|
|
soft
|
|
(1) prefactor A at start of run (energy units)
|
|
(2) prefactor A at end of run (energy units)
|
|
(3) cutoff (distance units)
|
|
class2/cutoff
|
|
(1) epsilon (energy units)
|
|
(2) sigma (distance units)
|
|
(3) cutoff (distance units)
|
|
|
|
define (or override) nonbond coefficients for an individual atom type pair
|
|
use appropriate number of coeffs for a particular style
|
|
1st atom type must be <= 2nd atom type
|
|
all cutoffs are in global units, not local sigma units
|
|
(e.g. in reduced units a setting of "lj/cutoff 1.0 1.2 2.5" means a
|
|
cutoff of 2.5, not 1.2*2.5)
|
|
turn off a particular type pair interaction by setting the
|
|
cutoff to 0.0 (both cutoffs to zero for lj/smooth option)
|
|
for soft style, prefactor A is ramped from starting value to
|
|
ending value during run
|
|
these coefficients (except the cutoffs) can also be set in data file
|
|
by "Nonbond Coeffs" entry and associated mixing rules, the cutoffs can
|
|
be set (globally) via the "nonbond style" command, the most
|
|
recently defined coefficients/cutoffs are used
|
|
|
|
Default = no settings
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276833">nonbond style </A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = style of pairwise nonbond interactions (other than
|
|
Coulombic)
|
|
<LI>
|
|
2nd-Nth parameters = coeffs 1 to N-1
|
|
</UL>
|
|
<PRE>
|
|
styles:
|
|
</PRE>
|
|
<UL>
|
|
<LI>
|
|
none = no nonbond interactions are computed
|
|
<LI>
|
|
lj/cutoff = LJ with a cutoff
|
|
<LI>
|
|
lj/smooth = LJ with a switched region that goes smoothly to zero
|
|
<LI>
|
|
lj/shift = same as lj/cutoff with shift of interparticle distance
|
|
<LI>
|
|
soft = cosine potential with time-varying prefactor
|
|
</UL>
|
|
<PRE>
|
|
coeffs: none
|
|
no other parameters required
|
|
lj/cutoff
|
|
(1) cutoff (distance units)
|
|
(2) offset flag (0 or 1)
|
|
lj/smooth
|
|
(1) inner cutoff (distance units)
|
|
(2) outer cutoff (distance units)
|
|
lj/shift
|
|
(1) cutoff (distance units)
|
|
(2) offset flag (0 or 1)
|
|
soft
|
|
(1) cutoff (distance units)
|
|
class2/cutoff
|
|
(1) cutoff (distance units)
|
|
(2) offset flag (0 or 1)
|
|
|
|
define style of pairwise nonbond interactions to use between all atom types
|
|
use appropriate number of coeffs for a particular style
|
|
this is separate from charge interactions (see "coulomb style" command)
|
|
nonbond style determines how many nonbond coefficients the program expects to
|
|
find in a "Nonbond Coeffs" entry in the data file or when using the
|
|
"nonbond coeff" command, thus the style must be set (if not using default)
|
|
before using the "read data" command (if the data file contains a
|
|
"Nonbond Coeffs" entry)
|
|
coefficients for all atom type pairs must be defined in data (or restart)
|
|
file by "Nonbond Coeffs" entry or by "nonbond coeffs" commands before a run
|
|
is performed
|
|
style of "none" erases all previously defined nonbond coefficients, must
|
|
reset style to something else before defining new coefficients
|
|
for all styles (except none), this command sets the cutoff(s) for all type
|
|
pair interactions, thus overriding any previous settings by a "nonbond
|
|
coeff" command or that were read in from a restart file
|
|
for lj/cutoff, lj/shift, class2/cutoff styles,
|
|
offset flag only affects printout of thermodynamic energy
|
|
(not forces or dynamics), determines whether offset energy
|
|
is added in to LJ potential to make value at cutoff = 0.0,
|
|
flag = 0 -> do not add in offset energy,
|
|
flag = 1 -> add in offset energy
|
|
for lj/smooth style, outer cutoff must be > inner cutoff
|
|
for lj/smooth style, atom pairs less than the inner cutoff distance use
|
|
straight LJ, pairs between inner and outer use a smoothed LJ, and the
|
|
potential goes to 0.0 at the outer cutoff
|
|
for lj/smooth style, energy and forces are continuous at inner cutoff and go
|
|
smoothly to zero at outer cutoff
|
|
for lj/shift and soft styles, must set "coulomb style" to "none"
|
|
for lj/shift style, delta shift distances for each atom pair are set by
|
|
"Nonbond Coeffs" entry in data file or by "nonbond coeffs" command
|
|
for soft style, values of the prefactor "A", which is ramped from one
|
|
value to another during the run, are set by "Nonbond Coeffs" entry
|
|
in data file or by "nonbond coeffs" command
|
|
|
|
Default = lj/cutoff 10.0 0
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276612">periodicity </A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = periodic BC in x direction (0) yes, (1) no
|
|
<LI>
|
|
2nd parameter = periodic BC in y direction (0) yes, (1) no
|
|
<LI>
|
|
3rd parameter = periodic BC in z direction (0) yes, (1) no
|
|
</UL>
|
|
<PRE>
|
|
turn on/off periodicity in any of three dimensions
|
|
used in inter-particle distance computation and when particles move
|
|
to map (or not map) them back into periodic box
|
|
for a 2-d run (see "dimension" command), 3rd parameter must be
|
|
specified, but doesn't matter if it is 0 or 1
|
|
must be set before data or restart file is read
|
|
|
|
Default = 0 0 0 (periodic in all dimensions)
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276941">pppm mesh </A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = # of mesh points in x direction
|
|
<LI>
|
|
2nd parameter = # of mesh points in y direction
|
|
<LI>
|
|
3rd parameter = # of mesh points in z direction
|
|
</UL>
|
|
<PRE>
|
|
specify the mesh size used by coulomb style pppm
|
|
mesh dimensions that are power-of-two are fastest for FFTs, but any size
|
|
can be used that are supported by native machine libraries
|
|
this command is optional - if not used, a default
|
|
mesh size will be chosen to satisfy accuracy criterion - if used, the
|
|
specifed mesh size will override the default
|
|
|
|
Default = none
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276947">pppm order </A></H3>
|
|
<PRE>
|
|
specify the order of the interpolation function that is used by coulomb
|
|
style pppm to map particle charge to the particle mesh
|
|
order is roughly equivalent to how many mesh points a point charge
|
|
overlaps onto
|
|
|
|
Default = 5
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276784">press control </A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = style of pressure control
|
|
<LI>
|
|
2nd-Nth parameters = coeffs 1 to N-1
|
|
</UL>
|
|
<PRE>
|
|
styles:
|
|
</PRE>
|
|
<UL>
|
|
<LI>
|
|
none = no control
|
|
<LI>
|
|
nose/hoover = Nose-Hoover constant P
|
|
</UL>
|
|
<PRE>
|
|
coeffs: none
|
|
no other parameters required
|
|
nose/hoover
|
|
(1) desired P at beginning of run
|
|
(2) desired P at end of run
|
|
(3) frequency constant for volume adjust (inverse time units)
|
|
|
|
use appropriate number of coeffs for a particular style
|
|
all specified pressures are in pressure units
|
|
target pressure at intermediate points during run is a ramped value
|
|
between the beginning and ending pressure
|
|
for nose/hoover style, frequency constant is like an inverse "piston"
|
|
mass which determines how rapidly the pressure fluctuates in response to a
|
|
restoring force, large frequency -> small mass -> rapid fluctations
|
|
for nose/hoover style, units of frequency/damping constant are
|
|
inverse time, so a value of 0.001 means relax in a timespan on the
|
|
order of 1000 fmsec (real units) or 1000 tau (LJ units)
|
|
|
|
Default = none
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276810">press_x control </A></H3>
|
|
<H3>
|
|
press_y control </H3>
|
|
<H3>
|
|
press_z control </H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = style of pressure control
|
|
<LI>
|
|
2nd-Nth parameters = coeffs 1 to N-1
|
|
</UL>
|
|
<PRE>
|
|
styles:
|
|
</PRE>
|
|
<UL>
|
|
<LI>
|
|
none = no control
|
|
<LI>
|
|
nose/hoover = Nose-Hoover constant P
|
|
</UL>
|
|
<PRE>
|
|
coeffs: none
|
|
no other parameters required
|
|
nose/hoover
|
|
(1) desired P at beginning of run
|
|
(2) desired P at end of run
|
|
(3) frequency constant for volume adjust (inverse time units)
|
|
|
|
commands for anisotropic pressure control, any combination is allowed
|
|
for a component with style = none, the cell dimension in that direction
|
|
is held constant (constant volume)
|
|
use appropriate number of coeffs for a particular style
|
|
all specified pressures are in pressure units
|
|
target pressure at intermediate points during run is a ramped value
|
|
between the beginning and ending pressure
|
|
cannot be used with isotropic "press control" command
|
|
for nose/hoover style, frequency constant is like an inverse "piston"
|
|
mass which determines how rapidly the pressure fluctuates in response to a
|
|
restoring force, large frequency -> small mass -> rapid fluctations
|
|
for nose/hoover style, units of frequency/damping constant are
|
|
inverse time, so a value of 0.001 means relax in a timespan on the
|
|
order of 1000 fmsec (real units) or 1000 tau (LJ units)
|
|
|
|
Default = none
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276624">processor grid </A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = # of processors in x dimension
|
|
<LI>
|
|
2nd parameter = # of processors in y dimension
|
|
<LI>
|
|
3rd parameter = # of processors in z dimension
|
|
</UL>
|
|
<PRE>
|
|
specify 3-d grid of processors to map to physical simulation domain
|
|
for 2-d problem, specify N by M by 1 grid
|
|
program will choose these values to best map processor grid to physical
|
|
simulation box, only use this command if wish to override program choice
|
|
product of 3 parameters must equal total # of processors
|
|
must be set before data or restart file is read
|
|
|
|
Default = none
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931277059">read data </A></H3>
|
|
<PRE>
|
|
read the initial atom positions and bond info from the specified file
|
|
the format for the data file is specified in the file data_format
|
|
if a "Coeffs" entry is in data file, the appropriate "style" command
|
|
command must be used first (unless default setting is used) to tell
|
|
LAMMPS how many coefficients to expect
|
|
most "Coeffs" entries must be present in this file if a particular "style"
|
|
is desired, an exception are the "Nonbond Coeffs" and "Bond Coeffs" entries
|
|
which can be omitted if all the settings are made via "nonbond coeff"
|
|
and "bond coeff" commands
|
|
a "Nonbond Coeffs" entry only contains one set of coefficients for each
|
|
atom type, after being read-in the appropriate class I or class II mixing
|
|
rules are applied to compute the cross-type coefficients (see the file
|
|
data_format for more information)
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931277070">read restart </A></H3>
|
|
<PRE>
|
|
read atom positions and velocities and nonbond and bond coefficients
|
|
from specified file
|
|
allows continuation of a previous run
|
|
file is binary to enable exact restarts
|
|
do not have to restart on same # of processors, but can only do exact
|
|
restarts on same # of processors
|
|
when restart file is read, warnings are issued if certain parameters
|
|
in the restart file do not match current settings (e.g. newton flag,
|
|
dimension, periodicity, units) - this usually indicates an error
|
|
the restart file stores all nonbond and many-body styles and coefficients,
|
|
so reading the file will overwrite any current settings
|
|
the restart file stores the constraint assignments for each atom, but
|
|
not the constraints themselves, so they must still be specified with
|
|
the "fix style" command
|
|
for a restart do not use the "read data" and "create temp" commands
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931277185">reset timestep </A></H3>
|
|
<PRE>
|
|
explicitly reset the timestep to this value
|
|
the "read data" and "read restart" commands set the timestep to zero
|
|
and file value respectively, so this should be done after those commands
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276645">respa</A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = compute bond forces this many times for every one
|
|
3/4-body force call
|
|
<LI>
|
|
2nd parameter = compute 3/4-body forces this many times for every one
|
|
nonbond (short-range) force call
|
|
<LI>
|
|
3rd parameter = compute nonbond (short-range) forces this many times
|
|
for every one long-range force call
|
|
</UL>
|
|
<PRE>
|
|
factors that affect sub-cycling of force calculations within RESPA hierarchy
|
|
bonded intramolecular forces are calculated every innermost sub-timestep
|
|
bonded 3- and 4-body forces are computed every 1st parameter sub-timesteps
|
|
short-range nonbond pairwise forces (LJ, Coulombic) are computed every
|
|
(2nd parameter * 1st parameter) sub-timesteps
|
|
long-range (Ewald, PPPM) forces are computed every
|
|
(3rd parameter * 2nd parameter * 1st parameter) sub-timesteps
|
|
the timestepping for all 3 inner loops (bond, 3/4-body, nonbond) is performed
|
|
as sub-cycling within the long-range timestepping loop
|
|
the fastest (innermost) timestep size is set by the "timestep" command
|
|
when running RESPA, all input commands that specify numbers of timesteps
|
|
(e.g. run, thermo flag, restart flag, etc) refer to the outermost loop
|
|
of long-range timestepping
|
|
the only exception to this rule is the "neighbor" command, where the timestep
|
|
parameters refer to the nonbond (short-range) timestepping
|
|
setting all 3 parameters to 1 turns off RESPA
|
|
|
|
Default = 1 1 1 (no RESPA)
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276719">restart </A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = # of timesteps
|
|
<LI>
|
|
2nd parameter = 1st file name
|
|
<LI>
|
|
3rd parameter = 2nd file name
|
|
</UL>
|
|
<PRE>
|
|
create a restart file every this many timesteps
|
|
value of 0 means never create one
|
|
program will toggle between 2 filenames as the run progresses
|
|
so always have at least one good file even if the program dies in mid-write
|
|
restart file stores atom positions and velocities in binary form
|
|
allows program to restart from where it left off (see "read restart" commmand)
|
|
|
|
Default = 0
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931277194">run </A></H3>
|
|
<PRE>
|
|
run or continue dynamics for specified # of timesteps
|
|
must have performed "read data"/"create temp" or "read restart"
|
|
commands first
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276666">special bonds </A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = nonbond weight applied to 1st nearest neighbors
|
|
<LI>
|
|
2nd parameter = nonbond weight applied to 2nd nearest neighbors
|
|
<LI>
|
|
3rd parameter = nonbond weight applied to 3rd nearest neighbors
|
|
</UL>
|
|
<PRE>
|
|
weighting factors to turn on/off nonbond interactions of atom pairs that
|
|
are "close" in the molecular topology
|
|
1st nearest neighbors are a pair of atoms connected by a bond
|
|
2nd nearest neighbors are a pair of atoms 2 hops away, etc.
|
|
weight values are from 0.0 to 1.0 and are used to multiply the
|
|
energy and force interaction (both Coulombic and LJ) between the 2 atoms
|
|
weight of 0.0 means no interaction
|
|
weight of 1.0 means full interaction
|
|
|
|
Default = 0.0 0.0 0.4 (CHARMM standard)
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276742">temp control </A></H3>
|
|
<UL>
|
|
<LI>
|
|
1st parameter = style of temperature control
|
|
<LI>
|
|
2nd-Nth parameters = coeffs 1 to N-1
|
|
</UL>
|
|
<PRE>
|
|
styles:
|
|
</PRE>
|
|
<UL>
|
|
<LI>
|
|
none = no control
|
|
<LI>
|
|
rescale = instantaneous rescaling
|
|
<LI>
|
|
replace = Gaussian replacement
|
|
<LI>
|
|
nose/hoover = Nose-Hoover constant T
|
|
<LI>
|
|
langevin = Langevin white noise
|
|
</UL>
|
|
<PRE>
|
|
coeffs: none
|
|
no other parameters required
|
|
rescale
|
|
(1) desired T at beginning of run
|
|
(2) desired T at end of run
|
|
(3) check for rescaling every this many timesteps
|
|
(4) T window outside of which velocities will be rescaled
|
|
replace
|
|
(1) desired T at beginning of run
|
|
(2) desired T at end of run
|
|
(3) do Gaussian replacement every this many timesteps
|
|
(4) random # seed to use for replacement (0 < seed <= 8 digits)
|
|
langevin
|
|
(1) desired T at beginning of run
|
|
(2) desired T at end of run
|
|
(3) Langevin damping parameter (inverse time units)
|
|
(4) random seed to use for white noise (0 < seed <= 8 digits)
|
|
nose/hoover
|
|
(1) desired T at beginning of run
|
|
(2) desired T at end of run
|
|
(3) frequency constant for friction force (inverse time units)
|
|
|
|
use appropriate number of coeffs for a particular style
|
|
all specified temperatures are in temperature units
|
|
target temperature at intermediate points during run is a ramped value
|
|
between the beginning and ending temperatures
|
|
for rescale style, temperature is controlled by explicitly rescaling
|
|
velocities to exactly the target temperature
|
|
for rescale style, rescaling is only done if current temperature is
|
|
beyond the target temperature plus or minus the window value
|
|
for replace style, Gaussian RNs from the Marsaglia RNG are used
|
|
for langevin style, uniform RNs from the Marsaglia RNG are used
|
|
for replace and langevin styles, the seed is used to initialize the
|
|
Marsaglia RNG, on successive runs the RNG will just continue on
|
|
for replace and langevin styles, generated RNs depend on # of processors
|
|
so will not get same answers independent of # of processors
|
|
for replace and langevin styles, RNG states are not saved in restart file,
|
|
so cannot do an exact restart
|
|
for langevin style, damping parameter means small value -> less damping
|
|
for nose/hoover style, frequency constant is like an inverse "piston"
|
|
mass which determines how rapidly the temperature fluctuates in response to a
|
|
restoring force, large frequency -> small mass -> rapid fluctations
|
|
for langevin and nose/hoover styles, units of frequency/damping constant are
|
|
inverse time, so a value of 0.01 means relax in a timespan on the
|
|
order of 100 fmsec (real units) or 100 tau (LJ units)
|
|
|
|
Default = none
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276675">thermo flag </A></H3>
|
|
<PRE>
|
|
print thermodynamic info to screen and log file every this many timesteps
|
|
value of 0 means never print
|
|
|
|
Default = 0
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276681">thermo style </A></H3>
|
|
<PRE>
|
|
determines format of thermodynamic output to screen and log file
|
|
</PRE>
|
|
<UL>
|
|
<LI>
|
|
style = 0 -> standard output - about 5 lines per entry
|
|
<LI>
|
|
style = 1 -> reduced output - 1 line per entry
|
|
<LI>
|
|
style = 2 -> output with class 2 terms - about 8 lines per entry
|
|
</UL>
|
|
<PRE>
|
|
Default = 0
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276638">timestep </A></H3>
|
|
<PRE>
|
|
timestep size for MD run (time units)
|
|
when RESPA is run, the timestep size is for the innermost (bond) loop
|
|
|
|
Default = 1.0
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276687">true flag </A></H3>
|
|
<PRE>
|
|
read atom positions (see "read data" command) and dump atom positions
|
|
(see "dump flag" command) in one of 2 formats
|
|
</PRE>
|
|
<UL>
|
|
<LI>
|
|
flag = 0 -> read/dump only atom positions (remapped to periodic box)
|
|
<LI>
|
|
flag = 1 -> dump atom positions plus integer box counts
|
|
<LI>
|
|
flag = 2 -> read atom positions plus integer box counts
|
|
<LI>
|
|
flag = 3 -> read/dump atom positions plus integer box counts
|
|
</UL>
|
|
<PRE>
|
|
for each dimension, box count of "n" means add that many box lengths
|
|
to get "true" un-remapped position, "n" can be positive, negative, or zero
|
|
|
|
Default = 0
|
|
</PRE>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_931276596">units </A></H3>
|
|
<UL>
|
|
<LI>
|
|
real or lj
|
|
</UL>
|
|
<PRE>
|
|
set units to one of two options for all subsequent input parameters
|
|
|
|
option real = conventional units:
|
|
</PRE>
|
|
<UL>
|
|
<LI>
|
|
distance = Angstroms
|
|
<LI>
|
|
time = femtoseconds
|
|
<LI>
|
|
mass = grams/mole
|
|
<LI>
|
|
temperature = degrees K
|
|
<LI>
|
|
pressure = atmospheres
|
|
<LI>
|
|
energy = Kcal/mole
|
|
<LI>
|
|
velocity = Angstroms/femtosecond
|
|
<LI>
|
|
force = grams/mole * Angstroms/femtosecond^2
|
|
</UL>
|
|
<PRE>
|
|
option lj = LJ reduced units:
|
|
</PRE>
|
|
<UL>
|
|
<LI>
|
|
distance = sigmas
|
|
<LI>
|
|
time = reduced LJ tau
|
|
<LI>
|
|
temperature = reduced LJ temp
|
|
<LI>
|
|
pressure = reduced LJ pressure
|
|
<LI>
|
|
energy = epsilons
|
|
<LI>
|
|
velocity = sigmas/tau
|
|
<LI>
|
|
force = reduced LJ force (sigmas/tau^2)
|
|
</UL>
|
|
<PRE>
|
|
for LJ units, LAMMPS sets global epsilon,sigma,mass all equal to 1.0
|
|
subsequent input numbers in data and command file must be in these units
|
|
output numbers to screen and log and dump files will be in these units
|
|
must be set before data or restart file is read
|
|
|
|
Default = real
|
|
</PRE>
|
|
</BODY>
|
|
</HTML>
|