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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4578 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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50
doc/temper.html
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@ -54,15 +54,47 @@ time. Each attempted swap of temperatures is either accepted or
rejected based on a Boltzmann-weighted Metropolis criterion which uses
<I>seed2</I> in the random number generator.
</P>
<P>The last argument <I>index</I> is optional and is used when restarting a
tempering run from a set of restart files (one for each replica) which
had previously swapped to new temperatures. The <I>index</I> value (from 0
to N-1, where N is the # of replicas) identifies which temperature the
replica was simulating on the timestep the restart files were written.
Obviously, this argument must be a variable so that each partition has
the correct value. Set the variable to the <I>N</I> values listed in the
log file for the previous run for the replica temperatures at that
timestep. For example if the log file listed
<P>As a tempering run proceeds, multiple log files and screen output
files are created, one per replica. By default these files are named
log.lammps.M and screen.M where M is the replica number from 0 to N-1,
with N = # of replicas. See the <A HREF = "Section_start.html#2_6">section on command-line
switches</A> for info on how to change these
names.
</P>
<P>The main screen and log file (log.lammps) will list information about
which temperature is assigned to each replica at each thermodynamic
output timestep. E.g. for a simulation with 16 replicas:
</P>
<PRE>Running on 16 partitions of processors
Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15
0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
500 1 0 3 2 5 4 6 7 8 9 10 11 12 13 14 15
1000 2 0 4 1 5 3 6 7 8 9 10 11 12 14 13 15
1500 2 1 4 0 5 3 6 7 9 8 10 11 12 14 13 15
2000 2 1 3 0 6 4 5 7 10 8 9 11 12 14 13 15
2500 2 1 3 0 6 4 5 7 11 8 9 10 12 14 13 15
...
</PRE>
<P>The column headings T0 to TN-1 mean which temperature is currently
assigned to the replica 0 to N-1. Thus the columns represent replicas
and the value in each column is its temperature (also numbered 0 to
N-1). For example, a 0 in the 4th column (column T3, step 2500) means
that the 4th replica is assigned temperature 0, i.e. the lowest
temperature. You can verify this time sequence of temperature
assignments for the Nth replica by comparing the Nth column of screen
output to the thermodynamic data in the corresponding log.lammps.N or
screen.N files as time proceeds.
</P>
<P>The last argument <I>index</I> in the temper command is optional and is
used when restarting a tempering run from a set of restart files (one
for each replica) which had previously swapped to new temperatures.
The <I>index</I> value (from 0 to N-1, where N is the # of replicas)
identifies which temperature the replica was simulating on the
timestep the restart files were written. Obviously, this argument
must be a variable so that each partition has the correct value. Set
the variable to the <I>N</I> values listed in the log file for the previous
run for the replica temperatures at that timestep. For example if the
log file listed the following for a simulation with 5 replicas:
</P>
<PRE>500000 2 4 0 1 3
</PRE>

50
doc/temper.txt
View File

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