Here is how each line in the input script is parsed by LAMMPS:
-(1) If the line ends with a "&" character (with no trailing -whitespace), the command is assumed to continue on the next line. The -next line is concatenated to the previous line by removing the "&" -character and newline. This allows long commands to be continued -across two or more lines. +
(1) If the line ends with a "&" character (the "and" character which +is shift-7 on most keyboards) with no trailing whitespace (and no +surrounding quotes), the command is assumed to continue on the next +line. The next line is concatenated to the previous line by removing +the "&" character ("and" character) and newline. This allows long +commands to be continued across two or more lines.
(2) All characters from the first "#" character onward are treated as comment and discarded. diff -Naur lammps-3Nov09/doc/Section_commands.txt lammps-4Nov09/doc/Section_commands.txt --- lammps-3Nov09/doc/Section_commands.txt 2009-10-29 16:41:53.000000000 -0600 +++ lammps-4Nov09/doc/Section_commands.txt 2009-11-02 07:56:09.000000000 -0700 @@ -81,11 +81,12 @@ Here is how each line in the input script is parsed by LAMMPS: -(1) If the line ends with a "&" character (with no trailing -whitespace), the command is assumed to continue on the next line. The -next line is concatenated to the previous line by removing the "&" -character and newline. This allows long commands to be continued -across two or more lines. +(1) If the line ends with a "&" character (the "and" character which +is shift-7 on most keyboards) with no trailing whitespace (and no +surrounding quotes), the command is assumed to continue on the next +line. The next line is concatenated to the previous line by removing +the "&" character ("and" character) and newline. This allows long +commands to be continued across two or more lines. (2) All characters from the first "#" character onward are treated as comment and discarded. diff -Naur lammps-3Nov09/doc/compute_event_displace.html lammps-4Nov09/doc/compute_event_displace.html --- lammps-3Nov09/doc/compute_event_displace.html 2009-10-30 12:13:57.000000000 -0600 +++ lammps-4Nov09/doc/compute_event_displace.html 2009-11-02 10:41:54.000000000 -0700 @@ -41,7 +41,11 @@
The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation.
-Restrictions: none +
Restrictions: +
+This command can only be used if LAMMPS was built with the "prd" +package. See the Making LAMMPS section for +more info on packages.
Related commands:
diff -Naur lammps-3Nov09/doc/compute_event_displace.txt lammps-4Nov09/doc/compute_event_displace.txt --- lammps-3Nov09/doc/compute_event_displace.txt 2009-10-29 16:41:53.000000000 -0600 +++ lammps-4Nov09/doc/compute_event_displace.txt 2009-11-02 10:41:54.000000000 -0700 @@ -38,7 +38,11 @@ The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. -[Restrictions:] none +[Restrictions:] + +This command can only be used if LAMMPS was built with the "prd" +package. See the "Making LAMMPS"_Section_start.html#2_3 section for +more info on packages. [Related commands:] diff -Naur lammps-3Nov09/doc/pair_dpd.html lammps-4Nov09/doc/pair_dpd.html --- lammps-3Nov09/doc/pair_dpd.html 2008-06-24 13:47:40.000000000 -0600 +++ lammps-4Nov09/doc/pair_dpd.html 2009-11-02 11:25:19.000000000 -0700 @@ -38,8 +38,9 @@ the vector difference in velocities of the two atoms = Vi - Vj, alpha is a Gaussian random number with zero mean and unit variance, dt is the timestep size, and w(r) is a weighting factor that varies between -0 and 1. Rc is the cutoff. Sigma is set equal to sqrt(2 T gamma), -where T is a parameter in the pair_style command. +0 and 1. Rc is the cutoff. Sigma is set equal to sqrt(2 Kb T gamma), +where Kb is the Boltzmann constant and T is the temperature parameter +in the pair_style command.The pairwise energy associated with this potential is only due to the conservative force term Fc. diff -Naur lammps-3Nov09/doc/pair_dpd.txt lammps-4Nov09/doc/pair_dpd.txt --- lammps-3Nov09/doc/pair_dpd.txt 2008-06-24 13:47:40.000000000 -0600 +++ lammps-4Nov09/doc/pair_dpd.txt 2009-11-02 11:25:19.000000000 -0700 @@ -35,8 +35,9 @@ the vector difference in velocities of the two atoms = Vi - Vj, alpha is a Gaussian random number with zero mean and unit variance, dt is the timestep size, and w(r) is a weighting factor that varies between -0 and 1. Rc is the cutoff. Sigma is set equal to sqrt(2 T gamma), -where T is a parameter in the pair_style command. +0 and 1. Rc is the cutoff. Sigma is set equal to sqrt(2 Kb T gamma), +where Kb is the Boltzmann constant and T is the temperature parameter +in the pair_style command. The pairwise energy associated with this potential is only due to the conservative force term Fc. diff -Naur lammps-3Nov09/doc/pair_hybrid.html lammps-4Nov09/doc/pair_hybrid.html --- lammps-3Nov09/doc/pair_hybrid.html 2008-10-09 09:16:41.000000000 -0600 +++ lammps-4Nov09/doc/pair_hybrid.html 2009-10-30 16:56:44.000000000 -0600 @@ -91,11 +91,11 @@ to the list of potentials that will be calculated for two interactings atoms of those types.
-The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: +
Coefficients must be defined for each pair of atoms types via the +pair_coeff command as described above, or in the +data file or restart files read by the read_data or +read_restart commands, or by mixing as described +below.
For both the hybrid and hybrid/overlay styles, every atom type pair I,J (where I <= J) must be assigned to at least one sub-style via diff -Naur lammps-3Nov09/doc/pair_hybrid.txt lammps-4Nov09/doc/pair_hybrid.txt --- lammps-3Nov09/doc/pair_hybrid.txt 2008-10-09 09:16:41.000000000 -0600 +++ lammps-4Nov09/doc/pair_hybrid.txt 2009-10-30 16:56:44.000000000 -0600 @@ -87,11 +87,11 @@ to the list of potentials that will be calculated for two interactings atoms of those types. -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: +Coefficients must be defined for each pair of atoms types via the +"pair_coeff"_pair_coeff.html command as described above, or in the +data file or restart files read by the "read_data"_read_data.html or +"read_restart"_read_restart.html commands, or by mixing as described +below. For both the {hybrid} and {hybrid/overlay} styles, every atom type pair I,J (where I <= J) must be assigned to at least one sub-style via diff -Naur lammps-3Nov09/doc/prd.html lammps-4Nov09/doc/prd.html --- lammps-3Nov09/doc/prd.html 2009-10-30 13:28:00.000000000 -0600 +++ lammps-4Nov09/doc/prd.html 2009-11-02 10:41:54.000000000 -0700 @@ -53,27 +53,30 @@
Description:
-Run Parallel Replica Dynamics (PRD) as described in (Voter). -PRD is a method for performing accelerated dynamics that is suitable -for infrequent-event systems that obey first-order kinetics. To quote -from the paper: "The dynamical evolution is characterized by -vibrational excursions within a potential basin, punctuated by -occasional transitions between basins." The transition probability is -characterized by p(t) = k*exp(-kt) where k is the rate constant. +
Run Parallel Replica Dynamics (PRD) as described in Art Voter's +paper. PRD is a method for performing accelerated dynamics +that is suitable for infrequent-event systems that obey first-order +kinetics. To quote from the paper: "The dynamical evolution is +characterized by vibrational excursions within a potential basin, +punctuated by occasional transitions between basins." The transition +probability is characterized by p(t) = k*exp(-kt) where k is the rate +constant.
A PRD run is performed by running independent simulations on multiple -replicas of the same system. To run with M replicas, you must launch -LAMMPS on M partitions, where a partition is one or more processors. -This is done by using the "-partition" command-line argument when -LAMMPS is launched. See this section of the -manual for details. A PRD run can be performed on a single partition, -though this offers no effective parallel speed-up in searching for -infrequent events. +replicas of the same system, which gives an effective enhancement in +the timescale spanned by the multiple simulations, waiting for an +event to occur. To run with M replicas, you must launch LAMMPS on M +partitions, where a partition is one or more processors. This is done +by using the "-partition" command-line argument when LAMMPS is +launched. See this section of the manual for +details. A PRD run can be performed on a single partition, though +this offers no effective parallel speed-up in searching for infrequent +events.
When a PRD run is performed, it is assumed that each replica is -running the same model, though LAMMPS does not check that this is the -case. I.e. the simulation domain, the number of atoms, the -interaction potentials, etc are the same for every replica. +running the same model, though LAMMPS does not check for this. +I.e. the simulation domain, the number of atoms, the interaction +potentials, etc are the same for every replica.
A PRD run has several stages, which are repeated each time an "event" occurs in one of the replicas, as defined below. The logic for a PRD @@ -93,9 +96,9 @@
Before this loop begins, the state of the system on replica 0 is shared with all replicas, so that all replicas begin from the same -initial state. The first basin is identified by quenching (an energy -minimization, see below) the initial state and storing the resulting -coordinates for reference. +initial state. The first potential energy basin is identified by +quenching (an energy minimization, see below) the initial state and +storing the resulting coordinates for reference.
In the first stage, dephasing is performed by each replica independently to eliminate correlations between replicas. This is @@ -246,6 +249,10 @@
Restrictions:
+This command can only be used if LAMMPS was built with the "prd" +package. See the Making LAMMPS section for +more info on packages. +
N and t_correlate settings must be integer multiples of t_event.
diff -Naur lammps-3Nov09/doc/prd.txt lammps-4Nov09/doc/prd.txt --- lammps-3Nov09/doc/prd.txt 2009-10-30 13:28:00.000000000 -0600 +++ lammps-4Nov09/doc/prd.txt 2009-11-02 10:41:54.000000000 -0700 @@ -40,27 +40,30 @@ [Description:] -Run Parallel Replica Dynamics (PRD) as described in "(Voter)"_#Voter. -PRD is a method for performing accelerated dynamics that is suitable -for infrequent-event systems that obey first-order kinetics. To quote -from the paper: "The dynamical evolution is characterized by -vibrational excursions within a potential basin, punctuated by -occasional transitions between basins." The transition probability is -characterized by p(t) = k*exp(-kt) where k is the rate constant. +Run Parallel Replica Dynamics (PRD) as described in "Art Voter's +paper"_#Voter. PRD is a method for performing accelerated dynamics +that is suitable for infrequent-event systems that obey first-order +kinetics. To quote from the paper: "The dynamical evolution is +characterized by vibrational excursions within a potential basin, +punctuated by occasional transitions between basins." The transition +probability is characterized by p(t) = k*exp(-kt) where k is the rate +constant. A PRD run is performed by running independent simulations on multiple -replicas of the same system. To run with M replicas, you must launch -LAMMPS on M partitions, where a partition is one or more processors. -This is done by using the "-partition" command-line argument when -LAMMPS is launched. See "this section"_Section_start.html#2_6 of the -manual for details. A PRD run can be performed on a single partition, -though this offers no effective parallel speed-up in searching for -infrequent events. +replicas of the same system, which gives an effective enhancement in +the timescale spanned by the multiple simulations, waiting for an +event to occur. To run with M replicas, you must launch LAMMPS on M +partitions, where a partition is one or more processors. This is done +by using the "-partition" command-line argument when LAMMPS is +launched. See "this section"_Section_start.html#2_6 of the manual for +details. A PRD run can be performed on a single partition, though +this offers no effective parallel speed-up in searching for infrequent +events. When a PRD run is performed, it is assumed that each replica is -running the same model, though LAMMPS does not check that this is the -case. I.e. the simulation domain, the number of atoms, the -interaction potentials, etc are the same for every replica. +running the same model, though LAMMPS does not check for this. +I.e. the simulation domain, the number of atoms, the interaction +potentials, etc are the same for every replica. A PRD run has several stages, which are repeated each time an "event" occurs in one of the replicas, as defined below. The logic for a PRD @@ -80,9 +83,9 @@ Before this loop begins, the state of the system on replica 0 is shared with all replicas, so that all replicas begin from the same -initial state. The first basin is identified by quenching (an energy -minimization, see below) the initial state and storing the resulting -coordinates for reference. +initial state. The first potential energy basin is identified by +quenching (an energy minimization, see below) the initial state and +storing the resulting coordinates for reference. In the first stage, dephasing is performed by each replica independently to eliminate correlations between replicas. This is @@ -233,6 +236,10 @@ [Restrictions:] +This command can only be used if LAMMPS was built with the "prd" +package. See the "Making LAMMPS"_Section_start.html#2_3 section for +more info on packages. + {N} and {t_correlate} settings must be integer multiples of {t_event}. diff -Naur lammps-3Nov09/src/DPD/pair_dpd.cpp lammps-4Nov09/src/DPD/pair_dpd.cpp --- lammps-3Nov09/src/DPD/pair_dpd.cpp 2009-08-08 14:06:53.000000000 -0600 +++ lammps-4Nov09/src/DPD/pair_dpd.cpp 2009-11-02 11:25:41.000000000 -0700 @@ -271,7 +271,7 @@ { if (setflag[i][j] == 0) error->all("All pair coeffs are not set"); - sigma[i][j] = sqrt(2.0*temperature*gamma[i][j]); + sigma[i][j] = sqrt(2.0*force->boltz*temperature*gamma[i][j]); cut[j][i] = cut[i][j]; a0[j][i] = a0[i][j];