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Tweaked event output

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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5571 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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athomps
2011-01-22 01:03:17 +00:00
parent fa235e847c
commit 270bc5fdcb
2 changed files with 46 additions and 50 deletions
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48
doc/tad.html
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@ -119,7 +119,7 @@ performed. The logic for a TAD run is as follows:
update earliest event update earliest event
update tstop update tstop
reflect back into current basin reflect back into current basin
perform earliest event execute earliest event
</PRE> </PRE>
<P>Before this outer loop begins, the initial potential energy basin is <P>Before this outer loop begins, the initial potential energy basin is
identified by quenching (an energy minimization, see below) the identified by quenching (an energy minimization, see below) the
@ -155,7 +155,7 @@ and <I>neb_style</I> keywords.
<P>A key aspect of the TAD method is setting the stopping criterion <P>A key aspect of the TAD method is setting the stopping criterion
appropriately. If this criterion is too conservative, then many appropriately. If this criterion is too conservative, then many
events must be generated before one is finally performed. Conversely, events must be generated before one is finally executed. Conversely,
if this criterion is too aggressive, high-entropy high-barrier events if this criterion is too aggressive, high-entropy high-barrier events
will be over-sampled, while low-entropy low-barrier events will be will be over-sampled, while low-entropy low-barrier events will be
under-sampled. If the lowest pre-exponential factor is known fairly under-sampled. If the lowest pre-exponential factor is known fairly
@ -164,18 +164,7 @@ accurately, then it can be used to estimate <I>tmax</I>, and the value of
corresponds to 95% confidence. However, for systems where the dynamics corresponds to 95% confidence. However, for systems where the dynamics
are not well characterized (the most common case), it will be are not well characterized (the most common case), it will be
necessary to experiment with the values of <I>delta</I> and <I>tmax</I> to get a necessary to experiment with the values of <I>delta</I> and <I>tmax</I> to get a
good trade-off between accuracy and performance. To aid with this, for good trade-off between accuracy and performance.
each new event that is detected, a line is printed to the screen and
log output for the first partition, as follows:
</P>
<PRE>New event: t_hi = 1950 ievent = 2 eb = 2.97066 dt_lo = 114049 dt_hi/t_stop = 0.610293
</PRE>
<P><I>t_hi</I> is the timestep on which the event occurrred. <I>ievent</I> is the
event index, zero for the first event in each basin. <I>eb</I> is the
energy barrier for the event. <I>dt_lo</I> is the low-temperature time
since entering the basin. <I>dt_hi/t_stop</I> is a measure of how close
the stopping criterion is to being met (if > 1.0, then the criterion
is met).
</P> </P>
<P>A second key aspect is the choice of <I>t_hi</I>. A larger value greatly <P>A second key aspect is the choice of <I>t_hi</I>. A larger value greatly
increases the rate at which new events are generated. However, too increases the rate at which new events are generated. However, too
@ -190,16 +179,25 @@ statistics, NEB statistics, thermodynamic output by each replica, dump
files, and restart files. files, and restart files.
</P> </P>
<P>Event statistics are printed to the screen and master log.lammps file <P>Event statistics are printed to the screen and master log.lammps file
each time an event is performed. The quantities are the timestep, CPU each time an event is executed. The quantities are the timestep, CPU
time, clock, and event number. The timestep is the usual LAMMPS time, global event number N, local event number M,
event status, energy barrier, time margin, and clock.
The timestep is the usual LAMMPS
timestep, which corresponds to the high-temperature time at which the timestep, which corresponds to the high-temperature time at which the
event was detected, in units of timestep. The CPU time is the total event was detected, in units of timestep. The CPU time is the total
processor time since the start of the TAD run. The clock is the processor time since the start of the TAD run. The clock is the
low-temperature event time, in units of timestep. Each clock interval low-temperature event time, in units of timestep. Each clock interval
is equal to the timestep interval between events scaled by an is equal to the timestep interval between events scaled by an
exponential factor that depends on the hi/lo temperature ratio and the exponential factor that depends on the hi/lo temperature ratio and the
energy barrier for that event. The event number is a counter that energy barrier for that event. The global event number N is a counter
increments with each performed event. that increments with each executed event. The local event number
is a counter that resets to zero upon entering each new basin.
The event status is <I>E</I> when an event is executed, and
is <I>D</I> for an event that is detected, while <I>DF</I> is for a detected
event that is also the earliest (first) event at the low temperature.
The time margin is the ratio of the high temperature time in the current
basin to the stopping time. This last number can be used to judge
whether the stopping time is too short or too long (see above).
</P> </P>
<P>The NEB statistics are written to the file specified by the <I>neb_log</I> <P>The NEB statistics are written to the file specified by the <I>neb_log</I>
keyword. If the keyword value is "none", then no NEB statistics are keyword. If the keyword value is "none", then no NEB statistics are
@ -222,12 +220,12 @@ printed in each replica's log file, giving a breakdown of how much CPU
time was spent in each stage (NEB, dynamics, quenching, etc). time was spent in each stage (NEB, dynamics, quenching, etc).
</P> </P>
<P>Any <A HREF = "dump.html">dump files</A> defined in the input script will be written <P>Any <A HREF = "dump.html">dump files</A> defined in the input script will be written
to during a TAD run at timesteps when an event is performed. This to during a TAD run at timesteps when an event is executed. This
means the the requested dump frequency in the <A HREF = "dump.html">dump</A> command means the the requested dump frequency in the <A HREF = "dump.html">dump</A> command
is ignored. There will be one dump file (per dump command) created is ignored. There will be one dump file (per dump command) created
for all partitions. The atom coordinates of the dump snapshot are for all partitions. The atom coordinates of the dump snapshot are
those of the minimum energy configuration resulting from quenching those of the minimum energy configuration resulting from quenching
following the performed event. The timesteps written into the dump following the executed event. The timesteps written into the dump
files correspond to the timestep at which the event occurred and NOT files correspond to the timestep at which the event occurred and NOT
the clock. A dump snapshot corresponding to the initial minimum state the clock. A dump snapshot corresponding to the initial minimum state
used for event detection is written to the dump file at the beginning used for event detection is written to the dump file at the beginning
@ -236,22 +234,22 @@ of each TAD run.
<P>If the <A HREF = "restart.html">restart</A> command is used, a single restart file <P>If the <A HREF = "restart.html">restart</A> command is used, a single restart file
for all the partitions is generated, which allows a TAD run to be for all the partitions is generated, which allows a TAD run to be
continued by a new input script in the usual manner. The restart file continued by a new input script in the usual manner. The restart file
is generated after an event is performed. The restart file contains a is generated after an event is executed. The restart file contains a
snapshot of the system in the new quenched state, including the event snapshot of the system in the new quenched state, including the event
number and the low-temperature time. The restart frequency specified number and the low-temperature time. The restart frequency specified
in the <A HREF = "restart.html">restart</A> command is interpreted differently when in the <A HREF = "restart.html">restart</A> command is interpreted differently when
performing a TAD run. It does not mean the timestep interval between performing a TAD run. It does not mean the timestep interval between
restart files. Instead it means an event interval for performed restart files. Instead it means an event interval for executed
events. Thus a frequency of 1 means write a restart file every time events. Thus a frequency of 1 means write a restart file every time
an event is performed. A frequency of 10 means write a restart file an event is executed. A frequency of 10 means write a restart file
every 10th performed event. When an input script reads a restart file every 10th executed event. When an input script reads a restart file
from a previous TAD run, the new script can be run on a different from a previous TAD run, the new script can be run on a different
number of replicas or processors. number of replicas or processors.
</P> </P>
<P>Note that within a single state, the dynamics will typically <P>Note that within a single state, the dynamics will typically
temporarily continue beyond the event that is ultimately chosen, until temporarily continue beyond the event that is ultimately chosen, until
the stopping criterionis satisfied. When the event is eventually the stopping criterionis satisfied. When the event is eventually
performed, the timestep counter is reset to the value when the event executed, the timestep counter is reset to the value when the event
was detected. Similarly, after each quench and NEB minimization, the was detected. Similarly, after each quench and NEB minimization, the
timestep counter is reset to the value at the start of the timestep counter is reset to the value at the start of the
minimization. This means that the timesteps listed in the replica log minimization. This means that the timesteps listed in the replica log

48
doc/tad.txt
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@ -109,7 +109,7 @@ while (time remains):
update earliest event update earliest event
update tstop update tstop
reflect back into current basin reflect back into current basin
perform earliest event :pre execute earliest event :pre
Before this outer loop begins, the initial potential energy basin is Before this outer loop begins, the initial potential energy basin is
identified by quenching (an energy minimization, see below) the identified by quenching (an energy minimization, see below) the
@ -145,7 +145,7 @@ and {neb_style} keywords.
A key aspect of the TAD method is setting the stopping criterion A key aspect of the TAD method is setting the stopping criterion
appropriately. If this criterion is too conservative, then many appropriately. If this criterion is too conservative, then many
events must be generated before one is finally performed. Conversely, events must be generated before one is finally executed. Conversely,
if this criterion is too aggressive, high-entropy high-barrier events if this criterion is too aggressive, high-entropy high-barrier events
will be over-sampled, while low-entropy low-barrier events will be will be over-sampled, while low-entropy low-barrier events will be
under-sampled. If the lowest pre-exponential factor is known fairly under-sampled. If the lowest pre-exponential factor is known fairly
@ -154,18 +154,7 @@ accurately, then it can be used to estimate {tmax}, and the value of
corresponds to 95% confidence. However, for systems where the dynamics corresponds to 95% confidence. However, for systems where the dynamics
are not well characterized (the most common case), it will be are not well characterized (the most common case), it will be
necessary to experiment with the values of {delta} and {tmax} to get a necessary to experiment with the values of {delta} and {tmax} to get a
good trade-off between accuracy and performance. To aid with this, for good trade-off between accuracy and performance.
each new event that is detected, a line is printed to the screen and
log output for the first partition, as follows:
New event: t_hi = 1950 ievent = 2 eb = 2.97066 dt_lo = 114049 dt_hi/t_stop = 0.610293 :pre
{t_hi} is the timestep on which the event occurrred. {ievent} is the
event index, zero for the first event in each basin. {eb} is the
energy barrier for the event. {dt_lo} is the low-temperature time
since entering the basin. {dt_hi/t_stop} is a measure of how close
the stopping criterion is to being met (if > 1.0, then the criterion
is met).
A second key aspect is the choice of {t_hi}. A larger value greatly A second key aspect is the choice of {t_hi}. A larger value greatly
increases the rate at which new events are generated. However, too increases the rate at which new events are generated. However, too
@ -180,16 +169,25 @@ statistics, NEB statistics, thermodynamic output by each replica, dump
files, and restart files. files, and restart files.
Event statistics are printed to the screen and master log.lammps file Event statistics are printed to the screen and master log.lammps file
each time an event is performed. The quantities are the timestep, CPU each time an event is executed. The quantities are the timestep, CPU
time, clock, and event number. The timestep is the usual LAMMPS time, global event number N, local event number M,
event status, energy barrier, time margin, and clock.
The timestep is the usual LAMMPS
timestep, which corresponds to the high-temperature time at which the timestep, which corresponds to the high-temperature time at which the
event was detected, in units of timestep. The CPU time is the total event was detected, in units of timestep. The CPU time is the total
processor time since the start of the TAD run. The clock is the processor time since the start of the TAD run. The clock is the
low-temperature event time, in units of timestep. Each clock interval low-temperature event time, in units of timestep. Each clock interval
is equal to the timestep interval between events scaled by an is equal to the timestep interval between events scaled by an
exponential factor that depends on the hi/lo temperature ratio and the exponential factor that depends on the hi/lo temperature ratio and the
energy barrier for that event. The event number is a counter that energy barrier for that event. The global event number N is a counter
increments with each performed event. that increments with each executed event. The local event number
is a counter that resets to zero upon entering each new basin.
The event status is {E} when an event is executed, and
is {D} for an event that is detected, while {DF} is for a detected
event that is also the earliest (first) event at the low temperature.
The time margin is the ratio of the high temperature time in the current
basin to the stopping time. This last number can be used to judge
whether the stopping time is too short or too long (see above).
The NEB statistics are written to the file specified by the {neb_log} The NEB statistics are written to the file specified by the {neb_log}
keyword. If the keyword value is "none", then no NEB statistics are keyword. If the keyword value is "none", then no NEB statistics are
@ -212,12 +210,12 @@ printed in each replica's log file, giving a breakdown of how much CPU
time was spent in each stage (NEB, dynamics, quenching, etc). time was spent in each stage (NEB, dynamics, quenching, etc).
Any "dump files"_dump.html defined in the input script will be written Any "dump files"_dump.html defined in the input script will be written
to during a TAD run at timesteps when an event is performed. This to during a TAD run at timesteps when an event is executed. This
means the the requested dump frequency in the "dump"_dump.html command means the the requested dump frequency in the "dump"_dump.html command
is ignored. There will be one dump file (per dump command) created is ignored. There will be one dump file (per dump command) created
for all partitions. The atom coordinates of the dump snapshot are for all partitions. The atom coordinates of the dump snapshot are
those of the minimum energy configuration resulting from quenching those of the minimum energy configuration resulting from quenching
following the performed event. The timesteps written into the dump following the executed event. The timesteps written into the dump
files correspond to the timestep at which the event occurred and NOT files correspond to the timestep at which the event occurred and NOT
the clock. A dump snapshot corresponding to the initial minimum state the clock. A dump snapshot corresponding to the initial minimum state
used for event detection is written to the dump file at the beginning used for event detection is written to the dump file at the beginning
@ -226,22 +224,22 @@ of each TAD run.
If the "restart"_restart.html command is used, a single restart file If the "restart"_restart.html command is used, a single restart file
for all the partitions is generated, which allows a TAD run to be for all the partitions is generated, which allows a TAD run to be
continued by a new input script in the usual manner. The restart file continued by a new input script in the usual manner. The restart file
is generated after an event is performed. The restart file contains a is generated after an event is executed. The restart file contains a
snapshot of the system in the new quenched state, including the event snapshot of the system in the new quenched state, including the event
number and the low-temperature time. The restart frequency specified number and the low-temperature time. The restart frequency specified
in the "restart"_restart.html command is interpreted differently when in the "restart"_restart.html command is interpreted differently when
performing a TAD run. It does not mean the timestep interval between performing a TAD run. It does not mean the timestep interval between
restart files. Instead it means an event interval for performed restart files. Instead it means an event interval for executed
events. Thus a frequency of 1 means write a restart file every time events. Thus a frequency of 1 means write a restart file every time
an event is performed. A frequency of 10 means write a restart file an event is executed. A frequency of 10 means write a restart file
every 10th performed event. When an input script reads a restart file every 10th executed event. When an input script reads a restart file
from a previous TAD run, the new script can be run on a different from a previous TAD run, the new script can be run on a different
number of replicas or processors. number of replicas or processors.
Note that within a single state, the dynamics will typically Note that within a single state, the dynamics will typically
temporarily continue beyond the event that is ultimately chosen, until temporarily continue beyond the event that is ultimately chosen, until
the stopping criterionis satisfied. When the event is eventually the stopping criterionis satisfied. When the event is eventually
performed, the timestep counter is reset to the value when the event executed, the timestep counter is reset to the value when the event
was detected. Similarly, after each quench and NEB minimization, the was detected. Similarly, after each quench and NEB minimization, the
timestep counter is reset to the value at the start of the timestep counter is reset to the value at the start of the
minimization. This means that the timesteps listed in the replica log minimization. This means that the timesteps listed in the replica log