diff --git a/examples/USER/misc/grem/README b/examples/USER/misc/grem/README new file mode 100644 index 0000000000000000000000000000000000000000..a9d37ea8692792378d89063380d0b8ff62f623c3 --- /dev/null +++ b/examples/USER/misc/grem/README @@ -0,0 +1,81 @@ +Generalized Replica Exchange Method (gREM) examples +=================================================== + +Examples: +--------------------------------------------------- + + lj-single: + This example is the simplest case scenario utilizing the generalized + ensemble defined by fix_grem. It utilizes only 1 replica and requires + the LAMMPS executable to be run as usual: + + mpirun -np 4 lmp_mpi -in in.gREM-npt + ./lmp_serial -in in.gREM-nvt + + While this does not obtain any information about Ts(H), it is most similar to + a microcanonical simulation and "single-replica gREM" can be useful for + studying non-equilibrium processes as well. + + lj-6rep: + This example utilizes an external python script to handle swaps between + replicas. Included is run.sh, which requires the path to your LAMMPS + executable. The python script is fragile as it relies on parsing output files + from the LAMMPS run and moving LAMMPS data files between directories. Use + caution if modifying this example further. If complied with mpi, multiple + processors can be used as: + + ./run.sh $NUM_PROCS + + a serial run is completed simply as + + ./run.sh 1 + + where the executable provided must be serial if "1" is provided as the number + of procs. While this external replica exchange module is quite slow and + inefficient, it allows for many replicas to be used on a single processor. + While here there are only 6 replicas, this example could be extended to >100 + replicas while still using a serial compilation. This is also beneficial for + running on high performance nodes with few cores to complete a full-scale gREM + simulation with a large number of replicas. + + A quick note on efficiency: frequent exchanges slow down this script + substantially because LAMMPS is restarted every exchange attempt. The script + works best for large systems with infrequent exchanges. + + lj-temper: + This is an example using the internal replica exchange module. While fast + in comparison to the python version, it requires substantial resources + (at least 1 proc per replica). Instead of stopping LAMMPS every exchange + attempt, all replicas are run concurrently, and exchanges take place + internally. This requires use of LAMMPS partition mode, via the command + line using the -p flag. Input files require world type variables defining + the parameters of each replica. The included example with 4 replicas must + run on at least 4 procs, in that case LAMMPS could be initiated as: + + mpirun -np 4 lmp_mpi -p 4x1 -in in.gREM-temper + + spawning 4 partitions with 1 replica each. Multiple procs per replica could + be used. In the case of a 16 system with 4 replicas, the + following logic could be used: + + mpirun -np 16 lmp_mpi -p 4x4 -in in.gREM-temper + + Once started, a universe log file will be created as well as log files for + each replica. The universe (log.lammps) contains exchange information, while + the replicas (*/log.lammps.*) contains the thermo_output as usual. In this + example, in.gREM-temper moves the log files to their respective folders. + + +Closing Notes: +--------------------------------------------------- + + Of significant difference between lj-6rep and lj-temper is the format of data. + In lj-6rep, data is stored as 'replicas' meaning discontinuous trajectories, as + files are moved between directories labeled by the 'lambda' of the replica. In + lj-temper, data is stored as 'walkers' with continuous trajectories, but + discontinuous parameters. The later is significantly more efficient, but + requires post-processing to obtain per-replica information. + + +Any problems/questions should be directed to <dstelter@bu.edu>. + diff --git a/examples/USER/misc/grem/lj-6rep/double-re-short.py b/examples/USER/misc/grem/lj-6rep/double-re-short.py index f04636c8fb5d54287d3cfbf9b23f26d449a81725..36705fe7b50c648c85fb8ed212717f2700930d7e 100755 --- a/examples/USER/misc/grem/lj-6rep/double-re-short.py +++ b/examples/USER/misc/grem/lj-6rep/double-re-short.py @@ -51,7 +51,7 @@ for exchange in arange(starting_ex,max_exchange): os.chdir(path+"/%s" % lambdas[l]) #os.system("cp restart_file restart_file%d" % exchange) if (nproc > 1): - os.system("mpirun -np %d " + lmp + " -in ../" + inp + " -var lambda %g -var eta %g -var enthalpy %g > output" % (nproc, lambdas[l], eta, H)) + os.system("mpirun -np %d " % (nproc) + lmp + " -in ../" + inp + " -var lambda %g -var eta %g -var enthalpy %g > output" % (lambdas[l], eta, H)) if (nproc == 1): os.system(lmp + " -in ../" + inp + " -var lambda %g -var eta %g -var enthalpy %g > output" % (lambdas[l], eta, H)) os.system("grep -v '[a-zA-Z]' output | awk '{if(NF==6 && NR>19)print $0}' | awk '{print $3}' >ent") @@ -60,7 +60,6 @@ for exchange in arange(starting_ex,max_exchange): aver_enthalpy[l] = mean(ee[-1]) # os.system("mv dump.dcd dump%d.dcd" % exchange) os.system("mv log.lammps log%d.lammps" % exchange) -# os.system("rm output") os.system("mv final_restart_file final_restart_file%d" % exchange) os.system("mv ent ent%d" % exchange) os.system("bzip2 log%d.lammps ent%d" % (exchange,exchange))