diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 698ee45d7e..10e80e3078 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -349,13 +349,13 @@ of each style or click on the style itself for a full description: each style or click on the style itself for a full description:

- - - - - - - + + + + + +
angle/localbond/localcna/atomcomcom/moleculecoord/atom
damage/atomdihedral/localdisplace/atomerotate/asphereerotate/sphereevent/displace
group/groupgyrationgyration/moleculeheat/fluximproper/localke
ke/atommsdmsd/moleculepair/localpepe/atom
pressureproperty/atomproperty/localproperty/moleculerdfreduce
reduce/regionstress/atomtemptemp/aspheretemp/comtemp/deform
temp/partialtemp/profiletemp/ramptemp/regiontemp/sphere +
angle/localbond/localcentro/atomcna/atomcomcom/molecule
coord/atomdamage/atomdihedral/localdisplace/atomerotate/asphereerotate/sphere
event/displacegroup/groupgyrationgyration/moleculeheat/fluximproper/local
keke/atommsdmsd/moleculepair/localpe
pe/atompressureproperty/atomproperty/localproperty/moleculerdf
reducereduce/regionstress/atomtemptemp/aspheretemp/com
temp/deformtemp/partialtemp/profiletemp/ramptemp/regiontemp/sphere

These are compute styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index e37139e0c2..5eface305e 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -467,6 +467,7 @@ each style or click on the style itself for a full description: "angle/local"_compute_angle_local.html, "bond/local"_compute_bond_local.html, +"centro/atom"_compute_centro_atom.html, "cna/atom"_compute_cna_atom.html, "com"_compute_com.html, "com/molecule"_compute_com_molecule.html, diff --git a/doc/prd.html b/doc/prd.html index 3918f11c25..5659a519a4 100644 --- a/doc/prd.html +++ b/doc/prd.html @@ -108,10 +108,10 @@ done by choosing a random set of velocities, based on the random_seed that is specified, and running t_dephase timesteps of dynamics. This is repeated n_dephase times. If the temp keyword is not specified, the target temperature for velocity randomization -for each replica is the temperature at the timestep replication -occured, otherwise, it is the specified Tdephase temperature. The -style of velocity randomization is controlled using the keyword vel -with arguments that have the same meaning as their counterparts in the +for each replica is the current temperature of that replica. +Otherwise, it is the specified Tdephase temperature. The style of +velocity randomization is controlled using the keyword vel with +arguments that have the same meaning as their counterparts in the velocity command.

In the second stage, each replica runs dynamics continuously, stopping @@ -135,17 +135,21 @@ event. PRD commmand, which is the compute event/displace command. Other event-checking computes may be added. Compute -event/displace checks whether any atom in the -compute group has moved further than a specified threshold distance. -If so, an "event" has occurred. +event/displace checks whether any atom in +the compute group has moved further than a specified threshold +distance. If so, an "event" has occurred.

-

In the third stage, the replica on which the event occurred continues -to run dynamics to search for correlated events. This is done by -running dynamics for t_correlate steps, quenching every t_event -steps, and checking if another event has occurred. The first time no -correlated event occurs, the final state of the system is shared with -all replicas, the new basin reference coordinates are updated with the -quenched state, and the outer loop begins again. +

In the third stage, the replica on which the event occurred (event +replica) continues to run dynamics to search for correlated events. +This is done by running dynamics for t_correlate steps, quenching +every t_event steps, and checking if another event has occurred. +The first time no correlated event occurs, the final state of the +event replica is shared with all replicas, the new basin reference +coordinates are updated with the quenched state, and the outer loop +begins again. While the replica event is searching for correlated +events, all the other replicas also run dynamics and event checking +with the same schedule, but the final states are always overwritten by +the state of the event replica.

@@ -160,7 +164,8 @@ only a single replica then the event statistics will be intermixed with the usual thermodynamic output discussed below.

The quantities printed each time an event occurs are the timestep, -clock, event number, a correlation flag, and the replica number. +CPU time, clock, event number, a correlation flag, +the number of coincident events, and the replica number of the chosen event.

The timestep is the usual LAMMPS timestep, except that time does not advance during dephasing or quenches, but only during dynamics. Note @@ -169,6 +174,9 @@ first is when all replicas are performing independent dynamics. The second is when correlated events are being searched for and only one replica is running dynamics.

+

The CPU time is the total processor time since the start of the PRD +run. +

The clock is the same as the timestep except that it advances by M steps every timestep during the first kind of dynamics when the M replicas are running independently. The clock represents the real @@ -182,10 +190,16 @@ drawn from p(t). it is uncorrelated or correlated.

The correlation flag will be 0 when an uncorrelated event occurs -during the second stage of the loop listed above. I.e. when all +during the second stage of the loop listed above, i.e. when all replicas are running independently. The correlation flag will be 1 when a correlated event occurs during the third stage of the loop -listed above. I.e. when only one replica is running dynamics. +listed above, i.e. when only one replica is running dynamics. +

+

When more than one replica detects an event at the end of the second +stage, then one of them is chosen at random. The number of coincident +events is the number of replicas that detected an event. Normally, we +expect this value to be 1. If it is often greater than 1, then either +the number of replicas is too large, or t_event is too large.

The replica number is the ID of the replica (from 0 to M-1) that found the event. @@ -277,7 +291,7 @@ dt/reset and fix deposit.

Default:

-

The option defaults are min = 40 50 0.1 0.1, no temp setting, and +

The option defaults are min = 0.1 0.1 40 50, no temp setting, and vel = geom gaussian.

diff --git a/doc/prd.txt b/doc/prd.txt index 2a3c32a33e..f126afae5b 100644 --- a/doc/prd.txt +++ b/doc/prd.txt @@ -96,9 +96,9 @@ done by choosing a random set of velocities, based on the dynamics. This is repeated {n_dephase} times. If the {temp} keyword is not specified, the target temperature for velocity randomization for each replica is the current temperature of that replica. -Otherwise, it is the specified {Tdephase} temperature. The -style of velocity randomization is controlled using the keyword {vel} -with arguments that have the same meaning as their counterparts in the +Otherwise, it is the specified {Tdephase} temperature. The style of +velocity randomization is controlled using the keyword {vel} with +arguments that have the same meaning as their counterparts in the "velocity"_velocity.html command. In the second stage, each replica runs dynamics continuously, stopping @@ -122,21 +122,21 @@ The event check is performed by a compute with the specified PRD commmand, which is the "compute event/displace"_compute_event_displace.html command. Other event-checking computes may be added. "Compute -event/displace"_compute_event_displace.html checks whether any atom in the -compute group has moved further than a specified threshold distance. -If so, an "event" has occurred. +event/displace"_compute_event_displace.html checks whether any atom in +the compute group has moved further than a specified threshold +distance. If so, an "event" has occurred. -In the third stage, the replica on which the event occurred -(event replica) continues -to run dynamics to search for correlated events. This is done by -running dynamics for {t_correlate} steps, quenching every {t_event} -steps, and checking if another event has occurred. The first time no -correlated event occurs, the final state of the event replica is shared with -all replicas, the new basin reference coordinates are updated with the -quenched state, and the outer loop begins again. While the replica event is -searching for correlated events, all the other replicas also run -dynamics and event checking with the same schedule, but the final states -are always overwritten by the state of the event replica. +In the third stage, the replica on which the event occurred (event +replica) continues to run dynamics to search for correlated events. +This is done by running dynamics for {t_correlate} steps, quenching +every {t_event} steps, and checking if another event has occurred. +The first time no correlated event occurs, the final state of the +event replica is shared with all replicas, the new basin reference +coordinates are updated with the quenched state, and the outer loop +begins again. While the replica event is searching for correlated +events, all the other replicas also run dynamics and event checking +with the same schedule, but the final states are always overwritten by +the state of the event replica. :line @@ -278,7 +278,7 @@ dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposity.html. [Default:] -The option defaults are {min} = 40 50 0.1 0.1, no {temp} setting, and +The option defaults are {min} = 0.1 0.1 40 50, no {temp} setting, and {vel} = {geom} {gaussian}. :line diff --git a/doc/thermo_style.html b/doc/thermo_style.html index 6adfad029e..887b7b6021 100644 --- a/doc/thermo_style.html +++ b/doc/thermo_style.html @@ -27,7 +27,7 @@ evdwl, ecoul, epair, ebond, eangle, edihed, eimp, emol, elong, etail, vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi, - xy, xz, yz, + xy, xz, yz, xlat, ylat, zlat, pxx, pyy, pzz, pxy, pxz, pyz, c_ID, c_ID[I], c_ID[I][J], f_ID, f_ID[I], f_ID[I][J], @@ -55,6 +55,7 @@ lx,ly,lz = box lengths in x,y,z xlo,xhi,ylo,yhi,zlo,zhi = box boundaries xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes + xlat,ylat,zlat = lattice spacings as calculated by lattice command pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor c_ID = global scalar value calculated by a compute with ID c_ID[I] = Ith component of global vector calculated by a compute with ID diff --git a/doc/thermo_style.txt b/doc/thermo_style.txt index 75883361f2..09051ab15d 100644 --- a/doc/thermo_style.txt +++ b/doc/thermo_style.txt @@ -22,7 +22,7 @@ args = list of arguments for a particular style :l evdwl, ecoul, epair, ebond, eangle, edihed, eimp, emol, elong, etail, vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi, - xy, xz, yz, + xy, xz, yz, xlat, ylat, zlat, pxx, pyy, pzz, pxy, pxz, pyz, c_ID, c_ID\[I\], c_ID\[I\]\[J\], f_ID, f_ID\[I\], f_ID\[I\]\[J\], @@ -50,6 +50,7 @@ args = list of arguments for a particular style :l lx,ly,lz = box lengths in x,y,z xlo,xhi,ylo,yhi,zlo,zhi = box boundaries xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes + xlat,ylat,zlat = lattice spacings as calculated by "lattice"_lattice.html command pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor c_ID = global scalar value calculated by a compute with ID c_ID\[I\] = Ith component of global vector calculated by a compute with ID