added respa compatability, and simplified examples

.gitignore

@@ -43,3 +43,6 @@ Thumbs.db
 /Makefile
 /cmake_install.cmake
 /lmp
+
+#python example
+/example/python/gjf_python

examples/gjf/README.md

@@ -7,7 +7,7 @@ This directory contains the ingredients to run an NVT simulation using the GJF-2
 Example:
 ```
 NP=4 #number of processors
-mpirun -np $NP lmp_mpi -in.argon -out.argon
+mpirun -np $NP lmp_mpi -in.gjf.vhalf
 ```
 
 ## Required LAMMPS packages: MOLECULE package

examples/gjf/in.argon

@@ -1,162 +0,0 @@
-###############################mm
-# Atom style - charge/vdw/bonded#
-#################################
-atom_style full
-
-##############################################
-#Units Metal : eV       - ps - angstrom - bar#
-#      Real  : kcal/mol - fs - angstrom - atm#
-##############################################
-units   	metal
-
-############
-#Run number#
-############
-variable run_no   equal   0             # is it a restart?
-variable res_no   equal   ${run_no}-1   # restart file number 
-
-#######################################
-#Random Seeds and Domain Decomposition#
-#######################################
-variable iseed0 equal 2357  
-variable iseed1 equal 26488 
-variable iseed2 equal 10669 
-processors      * * *
-
-###########
-#Data File#
-###########
-variable inpfile   string   argon.lmp
-variable resfile   string   final_restart.${res_no}
-variable ff_file   string   ff-argon.lmp
-
-##########
-#Run Type#
-##########
-variable minimise equal    0   #Energy Minimization
-variable md       equal    1   #Plain MD
-
-###############################
-#Molecular Dynamics Parameters#
-###############################
-variable run_no   equal        0       # is it a restart?
-
-variable ens      equal        9       # ensemble (0=nve, 1=nvt, 2=npt, 3=ber, 4=lang, 5=stoc, 6=vres, 7=stoch, 8=gjf)
-variable ts       equal        0.120   # simulation timestep (time units)
-variable nequil   equal        0       # number of equilibration steps
-variable nsteps   equal   200000       # number of MD steps
-#variable nsteps   equal   20       # number of MD steps
-
-variable temp_s   equal       10       # starting temperature
-variable temp_f   equal       10       # final simulation temperature
-variable trel     equal        1       # thermostat relaxation time
-variable tscale   equal        1       # thermostat relaxation freq - vel rescaling only
-variable deltat   equal        1       # maximum temperature change - vel rescaling only
-
-variable npttype  string       iso     # type of NPT (iso, aniso, tri, z...)
-variable pres     equal        1.01325 # pressure (NPT runs only)
-variable prel     equal        1.0     # barostat relaxation time
-
-neighbor 1 bin
-
-###################
-#Output Parameters#
-###################
-variable ntraj    equal     1000       # trajectory output frequency - all system
-variable ntraj_s  equal     -100       # trajectory output frequency - solute only
-variable nthermo  equal      200       # thermodynamic data output frequency
-
-################################
-#Energy Minimization Parameters#
-################################
-variable mtraj    equal        1       # trajectory output frequency - all system
-variable etol     equal     1e-5       # % change in energy
-variable ftol     equal     1e-5       # max force threshold (force units)
-variable maxiter  equal    10000       # max # of iterations
-
-########################
-#3D Periodic Simulation#
-########################
-boundary 	p p p
-
-#############################
-#Reading the input structure#
-#############################
-if "${run_no} == 0" then "read_data ${inpfile}" else "read_restart ${resfile}"
-
-#############
-#Force Field#
-#############
-include ${ff_file}
-
-######################
-#Thermodynamic Output#
-######################
-variable str_basic string 'step time pe temp press'
-
-#MD ensemble (0=nve, 1=nvt, 2=npt, 3=ber, 4=lang, 5=stoc, 6=vres)
-variable str_ens string ' '
-if "${ens} == 0" then "variable str_ens string 'etotal'"
-if "${ens} == 2" then "variable str_ens string 'vol pxx pyy pzz cella cellb cellc cellakpha cellbeta cellgamma'"
-
-#Variable for a gulp friend output
-if "${ens} >= 0" then "thermo_style custom time temp  pe  etotal press vol  cpu" &
-        "thermo ${nthermo}" &
-        "thermo_modify flush yes" 
-
-#####################
-#Energy Minimization#
-#####################
-if "${minimise} <= 0 || ${run_no} > 0" then "jump SELF end_minimise"
-  print "Doing CG minimisation"
-  dump mdcd all dcd ${mtraj} min.dcd
-  dump_modify mdcd unwrap yes
-  min_style cg
-  min_modify line quadratic
-  minimize ${etol} ${ftol} ${maxiter} ${maxiter}
-  reset_timestep 0
-  undump mdcd
-label end_minimise
-
-################
-#Timestep in ps#
-################
-timestep ${ts}
-
-##############
-#Restart file#
-##############
-restart 100000 restart.1 restart.2
-
-###################
-#Trajectory output#
-###################
-#dump  xyz all atom 1000 silicon.lammpstrj
-
-if "${ntraj} > 0" then &
-  "dump 1 all dcd ${ntraj} trajectory.${run_no}.dcd" &
-  "dump_modify 1 unwrap yes"
-
-fix mom all momentum 1 linear 1 1 1
-
-###############################################################
-#Ensembles (0=nve,1=nvt, 2=npt, 3=ber, 4=lang, 5=stoc, 6=vres)#
-###############################################################
-if "${md} > 0" then 'print "Setting up the ensembles"' &
-  'if "${run_no} == 0" then "velocity all create ${temp_s} ${iseed0} mom yes dist gaussian"' &
-  'if "${ens} == 0" then "fix nve all nve"' &
-  'if "${ens} == 1" then "fix nvt all nvt temp ${temp_s} ${temp_f} ${trel} tchain 5"' &
-  'if "${ens} == 2" then "fix npt all npt temp ${temp_s} ${temp_f} ${trel} ${npttype} ${pres} ${pres} ${prel} tchain 5 pchain 5 mtk yes"' &
-  'if "${ens} == 3" then "fix nve all nve" "fix ber all temp/berendsen ${temp_s} ${temp_f} ${trel}"' &
-  'if "${ens} == 4" then "fix nve all nve" "fix lang all langevin ${temp_s} ${temp_f} ${trel} ${iseed1} tally yes zero yes"' &
-  'if "${ens} == 5" then "fix nve all nve" "fix stoch all temp/csvr ${temp_s} ${temp_f} ${trel} ${iseed1}"' &
-  'if "${ens} == 6" then "fix nve all nve" "fix stoch all temp/csld ${temp_s} ${temp_f} ${trel} ${iseed1}"' &
-  'if "${ens} == 7" then "fix nve all nve" "fix vres all temp/rescale ${tscale} ${temp_s} ${temp_f} ${tmin} ${tmax}"' &
-  'if "${ens} == 8" then "fix nve all nve" "fix lang all langevin ${temp_s} ${temp_f} ${trel} ${iseed1} gjf yes"' &
-  'if "${ens} == 9" then "fix nve all nve" "fix lang all langevin ${temp_s} ${temp_f} ${trel} ${iseed1} gjf yes halfstep yes"'
-
-if "${md} > 0" then "print 'Doing Molecular dynamics'" &
-        "run ${nsteps}" &
-        "write_restart final_restart.${run_no}"
-
-

examples/gjf/in.gjf.vfull

@@ -0,0 +1,23 @@
+# GJF-2GJ thermostat
+
+units   	metal
+atom_style      full
+
+boundary 	p p p
+read_data argon.lmp
+
+include ff-argon.lmp
+
+velocity all create 10 2357 mom yes dist gaussian
+
+neighbor 1 bin
+
+timestep 0.1
+
+fix nve all nve
+fix lang all langevin 10 10 1 26488 gjf vfull
+
+thermo 200
+run 50000
+
+

examples/gjf/in.gjf.vhalf

@@ -0,0 +1,23 @@
+# GJF-2GJ thermostat
+
+units   	metal
+atom_style      full
+
+boundary 	p p p
+read_data argon.lmp
+
+include ff-argon.lmp
+
+velocity all create 10 2357 mom yes dist gaussian
+
+neighbor 1 bin
+
+timestep 0.1
+
+fix nve all nve
+fix lang all langevin 10 10 1 26488 gjf vhalf
+
+thermo 200
+run 50000
+
+