mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3794 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
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commit
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@ -349,13 +349,13 @@ of each style or click on the style itself for a full description:
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each style or click on the style itself for a full description:
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_com_molecule.html">com/molecule</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_molecule.html">gyration/molecule</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_molecule.html">msd/molecule</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_property_molecule.html">property/molecule</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
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<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_com_molecule.html">com/molecule</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_molecule.html">gyration/molecule</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_molecule.html">msd/molecule</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_property_molecule.html">property/molecule</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
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</TD></TR></TABLE></DIV>
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<P>These are compute styles contributed by users, which can be used if
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@ -467,6 +467,7 @@ each style or click on the style itself for a full description:
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"angle/local"_compute_angle_local.html,
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"bond/local"_compute_bond_local.html,
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"centro/atom"_compute_centro_atom.html,
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"cna/atom"_compute_cna_atom.html,
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"com"_compute_com.html,
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"com/molecule"_compute_com_molecule.html,
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50
doc/prd.html
50
doc/prd.html
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@ -108,10 +108,10 @@ done by choosing a random set of velocities, based on the
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<I>random_seed</I> that is specified, and running <I>t_dephase</I> timesteps of
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dynamics. This is repeated <I>n_dephase</I> times. If the <I>temp</I> keyword
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is not specified, the target temperature for velocity randomization
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for each replica is the temperature at the timestep replication
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occured, otherwise, it is the specified <I>Tdephase</I> temperature. The
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style of velocity randomization is controlled using the keyword <I>vel</I>
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with arguments that have the same meaning as their counterparts in the
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for each replica is the current temperature of that replica.
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Otherwise, it is the specified <I>Tdephase</I> temperature. The style of
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velocity randomization is controlled using the keyword <I>vel</I> with
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arguments that have the same meaning as their counterparts in the
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<A HREF = "velocity.html">velocity</A> command.
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</P>
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<P>In the second stage, each replica runs dynamics continuously, stopping
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@ -135,17 +135,21 @@ event.
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PRD commmand, which is the <A HREF = "compute_event_displace.html">compute
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event/displace</A> command. Other
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event-checking computes may be added. <A HREF = "compute_event_displace.html">Compute
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event/displace</A> checks whether any atom in the
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compute group has moved further than a specified threshold distance.
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If so, an "event" has occurred.
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event/displace</A> checks whether any atom in
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the compute group has moved further than a specified threshold
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distance. If so, an "event" has occurred.
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</P>
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<P>In the third stage, the replica on which the event occurred continues
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to run dynamics to search for correlated events. This is done by
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running dynamics for <I>t_correlate</I> steps, quenching every <I>t_event</I>
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steps, and checking if another event has occurred. The first time no
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correlated event occurs, the final state of the system is shared with
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all replicas, the new basin reference coordinates are updated with the
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quenched state, and the outer loop begins again.
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<P>In the third stage, the replica on which the event occurred (event
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replica) continues to run dynamics to search for correlated events.
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This is done by running dynamics for <I>t_correlate</I> steps, quenching
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every <I>t_event</I> steps, and checking if another event has occurred.
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The first time no correlated event occurs, the final state of the
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event replica is shared with all replicas, the new basin reference
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coordinates are updated with the quenched state, and the outer loop
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begins again. While the replica event is searching for correlated
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events, all the other replicas also run dynamics and event checking
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with the same schedule, but the final states are always overwritten by
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the state of the event replica.
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</P>
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<HR>
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@ -160,7 +164,8 @@ only a single replica then the event statistics will be intermixed
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with the usual thermodynamic output discussed below.
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</P>
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<P>The quantities printed each time an event occurs are the timestep,
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clock, event number, a correlation flag, and the replica number.
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CPU time, clock, event number, a correlation flag,
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the number of coincident events, and the replica number of the chosen event.
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</P>
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<P>The timestep is the usual LAMMPS timestep, except that time does not
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advance during dephasing or quenches, but only during dynamics. Note
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@ -169,6 +174,9 @@ first is when all replicas are performing independent dynamics. The
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second is when correlated events are being searched for and only one
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replica is running dynamics.
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</P>
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<P>The CPU time is the total processor time since the start of the PRD
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run.
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</P>
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<P>The clock is the same as the timestep except that it advances by M
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steps every timestep during the first kind of dynamics when the M
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replicas are running independently. The clock represents the real
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@ -182,10 +190,16 @@ drawn from p(t).
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it is uncorrelated or correlated.
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</P>
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<P>The correlation flag will be 0 when an uncorrelated event occurs
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during the second stage of the loop listed above. I.e. when all
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during the second stage of the loop listed above, i.e. when all
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replicas are running independently. The correlation flag will be 1
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when a correlated event occurs during the third stage of the loop
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listed above. I.e. when only one replica is running dynamics.
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listed above, i.e. when only one replica is running dynamics.
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</P>
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<P>When more than one replica detects an event at the end of the second
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stage, then one of them is chosen at random. The number of coincident
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events is the number of replicas that detected an event. Normally, we
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expect this value to be 1. If it is often greater than 1, then either
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the number of replicas is too large, or <I>t_event</I> is too large.
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</P>
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<P>The replica number is the ID of the replica (from 0 to M-1) that
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found the event.
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@ -277,7 +291,7 @@ dt/reset</A> and <A HREF = "fix_deposity.html">fix deposit</A>.
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are <I>min</I> = 40 50 0.1 0.1, no <I>temp</I> setting, and
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<P>The option defaults are <I>min</I> = 0.1 0.1 40 50, no <I>temp</I> setting, and
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<I>vel</I> = <I>geom</I> <I>gaussian</I>.
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</P>
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<HR>
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36
doc/prd.txt
36
doc/prd.txt
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@ -96,9 +96,9 @@ done by choosing a random set of velocities, based on the
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dynamics. This is repeated {n_dephase} times. If the {temp} keyword
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is not specified, the target temperature for velocity randomization
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for each replica is the current temperature of that replica.
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Otherwise, it is the specified {Tdephase} temperature. The
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style of velocity randomization is controlled using the keyword {vel}
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with arguments that have the same meaning as their counterparts in the
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Otherwise, it is the specified {Tdephase} temperature. The style of
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velocity randomization is controlled using the keyword {vel} with
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arguments that have the same meaning as their counterparts in the
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"velocity"_velocity.html command.
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In the second stage, each replica runs dynamics continuously, stopping
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@ -122,21 +122,21 @@ The event check is performed by a compute with the specified
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PRD commmand, which is the "compute
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event/displace"_compute_event_displace.html command. Other
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event-checking computes may be added. "Compute
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event/displace"_compute_event_displace.html checks whether any atom in the
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compute group has moved further than a specified threshold distance.
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If so, an "event" has occurred.
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event/displace"_compute_event_displace.html checks whether any atom in
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the compute group has moved further than a specified threshold
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distance. If so, an "event" has occurred.
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In the third stage, the replica on which the event occurred
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(event replica) continues
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to run dynamics to search for correlated events. This is done by
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running dynamics for {t_correlate} steps, quenching every {t_event}
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steps, and checking if another event has occurred. The first time no
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correlated event occurs, the final state of the event replica is shared with
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all replicas, the new basin reference coordinates are updated with the
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quenched state, and the outer loop begins again. While the replica event is
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searching for correlated events, all the other replicas also run
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dynamics and event checking with the same schedule, but the final states
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are always overwritten by the state of the event replica.
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In the third stage, the replica on which the event occurred (event
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replica) continues to run dynamics to search for correlated events.
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This is done by running dynamics for {t_correlate} steps, quenching
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every {t_event} steps, and checking if another event has occurred.
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The first time no correlated event occurs, the final state of the
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event replica is shared with all replicas, the new basin reference
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coordinates are updated with the quenched state, and the outer loop
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begins again. While the replica event is searching for correlated
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events, all the other replicas also run dynamics and event checking
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with the same schedule, but the final states are always overwritten by
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the state of the event replica.
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:line
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@ -278,7 +278,7 @@ dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposity.html.
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[Default:]
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The option defaults are {min} = 40 50 0.1 0.1, no {temp} setting, and
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The option defaults are {min} = 0.1 0.1 40 50, no {temp} setting, and
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{vel} = {geom} {gaussian}.
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:line
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@ -27,7 +27,7 @@
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evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
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emol, elong, etail,
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vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
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xy, xz, yz,
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xy, xz, yz, xlat, ylat, zlat,
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pxx, pyy, pzz, pxy, pxz, pyz,
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c_ID, c_ID[I], c_ID[I][J],
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f_ID, f_ID[I], f_ID[I][J],
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lx,ly,lz = box lengths in x,y,z
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xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
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xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes
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xlat,ylat,zlat = lattice spacings as calculated by <A HREF = "lattice.html">lattice</A> command
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pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
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c_ID = global scalar value calculated by a compute with ID
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c_ID[I] = Ith component of global vector calculated by a compute with ID
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evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
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emol, elong, etail,
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vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
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xy, xz, yz,
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xy, xz, yz, xlat, ylat, zlat,
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pxx, pyy, pzz, pxy, pxz, pyz,
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c_ID, c_ID\[I\], c_ID\[I\]\[J\],
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f_ID, f_ID\[I\], f_ID\[I\]\[J\],
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lx,ly,lz = box lengths in x,y,z
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xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
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xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes
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xlat,ylat,zlat = lattice spacings as calculated by "lattice"_lattice.html command
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pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
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c_ID = global scalar value calculated by a compute with ID
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c_ID\[I\] = Ith component of global vector calculated by a compute with ID
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Reference in New Issue