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@ -54,15 +54,47 @@ time. Each attempted swap of temperatures is either accepted or
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rejected based on a Boltzmann-weighted Metropolis criterion which uses
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<I>seed2</I> in the random number generator.
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</P>
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<P>The last argument <I>index</I> is optional and is used when restarting a
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tempering run from a set of restart files (one for each replica) which
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had previously swapped to new temperatures. The <I>index</I> value (from 0
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to N-1, where N is the # of replicas) identifies which temperature the
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replica was simulating on the timestep the restart files were written.
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Obviously, this argument must be a variable so that each partition has
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the correct value. Set the variable to the <I>N</I> values listed in the
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log file for the previous run for the replica temperatures at that
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timestep. For example if the log file listed
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<P>As a tempering run proceeds, multiple log files and screen output
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files are created, one per replica. By default these files are named
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log.lammps.M and screen.M where M is the replica number from 0 to N-1,
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with N = # of replicas. See the <A HREF = "Section_start.html#2_6">section on command-line
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switches</A> for info on how to change these
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names.
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</P>
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<P>The main screen and log file (log.lammps) will list information about
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which temperature is assigned to each replica at each thermodynamic
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output timestep. E.g. for a simulation with 16 replicas:
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</P>
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<PRE>Running on 16 partitions of processors
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Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15
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0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
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500 1 0 3 2 5 4 6 7 8 9 10 11 12 13 14 15
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1000 2 0 4 1 5 3 6 7 8 9 10 11 12 14 13 15
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1500 2 1 4 0 5 3 6 7 9 8 10 11 12 14 13 15
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2000 2 1 3 0 6 4 5 7 10 8 9 11 12 14 13 15
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2500 2 1 3 0 6 4 5 7 11 8 9 10 12 14 13 15
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...
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</PRE>
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<P>The column headings T0 to TN-1 mean which temperature is currently
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assigned to the replica 0 to N-1. Thus the columns represent replicas
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and the value in each column is its temperature (also numbered 0 to
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N-1). For example, a 0 in the 4th column (column T3, step 2500) means
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that the 4th replica is assigned temperature 0, i.e. the lowest
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temperature. You can verify this time sequence of temperature
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assignments for the Nth replica by comparing the Nth column of screen
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output to the thermodynamic data in the corresponding log.lammps.N or
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screen.N files as time proceeds.
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</P>
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<P>The last argument <I>index</I> in the temper command is optional and is
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used when restarting a tempering run from a set of restart files (one
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for each replica) which had previously swapped to new temperatures.
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The <I>index</I> value (from 0 to N-1, where N is the # of replicas)
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identifies which temperature the replica was simulating on the
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timestep the restart files were written. Obviously, this argument
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must be a variable so that each partition has the correct value. Set
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the variable to the <I>N</I> values listed in the log file for the previous
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run for the replica temperatures at that timestep. For example if the
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log file listed the following for a simulation with 5 replicas:
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</P>
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<PRE>500000 2 4 0 1 3
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</PRE>
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@ -51,15 +51,47 @@ time. Each attempted swap of temperatures is either accepted or
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rejected based on a Boltzmann-weighted Metropolis criterion which uses
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{seed2} in the random number generator.
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The last argument {index} is optional and is used when restarting a
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tempering run from a set of restart files (one for each replica) which
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had previously swapped to new temperatures. The {index} value (from 0
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to N-1, where N is the # of replicas) identifies which temperature the
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replica was simulating on the timestep the restart files were written.
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Obviously, this argument must be a variable so that each partition has
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the correct value. Set the variable to the {N} values listed in the
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log file for the previous run for the replica temperatures at that
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timestep. For example if the log file listed
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As a tempering run proceeds, multiple log files and screen output
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files are created, one per replica. By default these files are named
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log.lammps.M and screen.M where M is the replica number from 0 to N-1,
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with N = # of replicas. See the "section on command-line
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switches"_Section_start.html#2_6 for info on how to change these
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names.
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The main screen and log file (log.lammps) will list information about
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which temperature is assigned to each replica at each thermodynamic
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output timestep. E.g. for a simulation with 16 replicas:
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Running on 16 partitions of processors
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Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15
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0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
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500 1 0 3 2 5 4 6 7 8 9 10 11 12 13 14 15
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1000 2 0 4 1 5 3 6 7 8 9 10 11 12 14 13 15
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1500 2 1 4 0 5 3 6 7 9 8 10 11 12 14 13 15
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2000 2 1 3 0 6 4 5 7 10 8 9 11 12 14 13 15
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2500 2 1 3 0 6 4 5 7 11 8 9 10 12 14 13 15
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... :pre
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The column headings T0 to TN-1 mean which temperature is currently
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assigned to the replica 0 to N-1. Thus the columns represent replicas
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and the value in each column is its temperature (also numbered 0 to
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N-1). For example, a 0 in the 4th column (column T3, step 2500) means
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that the 4th replica is assigned temperature 0, i.e. the lowest
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temperature. You can verify this time sequence of temperature
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assignments for the Nth replica by comparing the Nth column of screen
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output to the thermodynamic data in the corresponding log.lammps.N or
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screen.N files as time proceeds.
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The last argument {index} in the temper command is optional and is
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used when restarting a tempering run from a set of restart files (one
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for each replica) which had previously swapped to new temperatures.
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The {index} value (from 0 to N-1, where N is the # of replicas)
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identifies which temperature the replica was simulating on the
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timestep the restart files were written. Obviously, this argument
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must be a variable so that each partition has the correct value. Set
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the variable to the {N} values listed in the log file for the previous
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run for the replica temperatures at that timestep. For example if the
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log file listed the following for a simulation with 5 replicas:
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500000 2 4 0 1 3 :pre
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