mirror of https://github.com/lammps/lammps.git
added respa compatability, and simplified examples
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casievers
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14d3859605
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cc96ea1ded
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@ -43,3 +43,6 @@ Thumbs.db
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/Makefile
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/cmake_install.cmake
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/lmp
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#python example
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/example/python/gjf_python
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@ -7,7 +7,7 @@ This directory contains the ingredients to run an NVT simulation using the GJF-2
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Example:
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```
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NP=4 #number of processors
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mpirun -np $NP lmp_mpi -in.argon -out.argon
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mpirun -np $NP lmp_mpi -in.gjf.vhalf
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```
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## Required LAMMPS packages: MOLECULE package
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@ -1,162 +0,0 @@
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###############################mm
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# Atom style - charge/vdw/bonded#
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#################################
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atom_style full
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##############################################
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#Units Metal : eV - ps - angstrom - bar#
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# Real : kcal/mol - fs - angstrom - atm#
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##############################################
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units metal
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############
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#Run number#
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############
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variable run_no equal 0 # is it a restart?
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variable res_no equal ${run_no}-1 # restart file number
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#######################################
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#Random Seeds and Domain Decomposition#
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#######################################
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variable iseed0 equal 2357
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variable iseed1 equal 26488
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variable iseed2 equal 10669
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processors * * *
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###########
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#Data File#
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###########
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variable inpfile string argon.lmp
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variable resfile string final_restart.${res_no}
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variable ff_file string ff-argon.lmp
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##########
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#Run Type#
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##########
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variable minimise equal 0 #Energy Minimization
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variable md equal 1 #Plain MD
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###############################
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#Molecular Dynamics Parameters#
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###############################
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variable run_no equal 0 # is it a restart?
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variable ens equal 9 # ensemble (0=nve, 1=nvt, 2=npt, 3=ber, 4=lang, 5=stoc, 6=vres, 7=stoch, 8=gjf)
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variable ts equal 0.120 # simulation timestep (time units)
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variable nequil equal 0 # number of equilibration steps
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variable nsteps equal 200000 # number of MD steps
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#variable nsteps equal 20 # number of MD steps
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variable temp_s equal 10 # starting temperature
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variable temp_f equal 10 # final simulation temperature
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variable trel equal 1 # thermostat relaxation time
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variable tscale equal 1 # thermostat relaxation freq - vel rescaling only
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variable deltat equal 1 # maximum temperature change - vel rescaling only
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variable npttype string iso # type of NPT (iso, aniso, tri, z...)
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variable pres equal 1.01325 # pressure (NPT runs only)
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variable prel equal 1.0 # barostat relaxation time
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neighbor 1 bin
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###################
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#Output Parameters#
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###################
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variable ntraj equal 1000 # trajectory output frequency - all system
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variable ntraj_s equal -100 # trajectory output frequency - solute only
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variable nthermo equal 200 # thermodynamic data output frequency
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################################
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#Energy Minimization Parameters#
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################################
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variable mtraj equal 1 # trajectory output frequency - all system
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variable etol equal 1e-5 # % change in energy
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variable ftol equal 1e-5 # max force threshold (force units)
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variable maxiter equal 10000 # max # of iterations
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########################
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#3D Periodic Simulation#
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########################
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boundary p p p
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#############################
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#Reading the input structure#
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#############################
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if "${run_no} == 0" then "read_data ${inpfile}" else "read_restart ${resfile}"
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#############
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#Force Field#
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#############
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include ${ff_file}
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######################
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#Thermodynamic Output#
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######################
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variable str_basic string 'step time pe temp press'
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#MD ensemble (0=nve, 1=nvt, 2=npt, 3=ber, 4=lang, 5=stoc, 6=vres)
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variable str_ens string ' '
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if "${ens} == 0" then "variable str_ens string 'etotal'"
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if "${ens} == 2" then "variable str_ens string 'vol pxx pyy pzz cella cellb cellc cellakpha cellbeta cellgamma'"
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#Variable for a gulp friend output
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if "${ens} >= 0" then "thermo_style custom time temp pe etotal press vol cpu" &
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"thermo ${nthermo}" &
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"thermo_modify flush yes"
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#####################
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#Energy Minimization#
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#####################
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if "${minimise} <= 0 || ${run_no} > 0" then "jump SELF end_minimise"
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print "Doing CG minimisation"
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dump mdcd all dcd ${mtraj} min.dcd
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dump_modify mdcd unwrap yes
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min_style cg
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min_modify line quadratic
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minimize ${etol} ${ftol} ${maxiter} ${maxiter}
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reset_timestep 0
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undump mdcd
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label end_minimise
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################
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#Timestep in ps#
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################
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timestep ${ts}
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##############
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#Restart file#
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##############
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restart 100000 restart.1 restart.2
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###################
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#Trajectory output#
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###################
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#dump xyz all atom 1000 silicon.lammpstrj
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if "${ntraj} > 0" then &
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"dump 1 all dcd ${ntraj} trajectory.${run_no}.dcd" &
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"dump_modify 1 unwrap yes"
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fix mom all momentum 1 linear 1 1 1
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###############################################################
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#Ensembles (0=nve,1=nvt, 2=npt, 3=ber, 4=lang, 5=stoc, 6=vres)#
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###############################################################
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if "${md} > 0" then 'print "Setting up the ensembles"' &
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'if "${run_no} == 0" then "velocity all create ${temp_s} ${iseed0} mom yes dist gaussian"' &
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'if "${ens} == 0" then "fix nve all nve"' &
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'if "${ens} == 1" then "fix nvt all nvt temp ${temp_s} ${temp_f} ${trel} tchain 5"' &
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'if "${ens} == 2" then "fix npt all npt temp ${temp_s} ${temp_f} ${trel} ${npttype} ${pres} ${pres} ${prel} tchain 5 pchain 5 mtk yes"' &
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'if "${ens} == 3" then "fix nve all nve" "fix ber all temp/berendsen ${temp_s} ${temp_f} ${trel}"' &
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'if "${ens} == 4" then "fix nve all nve" "fix lang all langevin ${temp_s} ${temp_f} ${trel} ${iseed1} tally yes zero yes"' &
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'if "${ens} == 5" then "fix nve all nve" "fix stoch all temp/csvr ${temp_s} ${temp_f} ${trel} ${iseed1}"' &
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'if "${ens} == 6" then "fix nve all nve" "fix stoch all temp/csld ${temp_s} ${temp_f} ${trel} ${iseed1}"' &
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'if "${ens} == 7" then "fix nve all nve" "fix vres all temp/rescale ${tscale} ${temp_s} ${temp_f} ${tmin} ${tmax}"' &
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'if "${ens} == 8" then "fix nve all nve" "fix lang all langevin ${temp_s} ${temp_f} ${trel} ${iseed1} gjf yes"' &
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'if "${ens} == 9" then "fix nve all nve" "fix lang all langevin ${temp_s} ${temp_f} ${trel} ${iseed1} gjf yes halfstep yes"'
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if "${md} > 0" then "print 'Doing Molecular dynamics'" &
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"run ${nsteps}" &
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"write_restart final_restart.${run_no}"
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@ -0,0 +1,23 @@
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# GJF-2GJ thermostat
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units metal
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atom_style full
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boundary p p p
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read_data argon.lmp
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include ff-argon.lmp
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velocity all create 10 2357 mom yes dist gaussian
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neighbor 1 bin
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timestep 0.1
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fix nve all nve
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fix lang all langevin 10 10 1 26488 gjf vfull
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thermo 200
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run 50000
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@ -0,0 +1,23 @@
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# GJF-2GJ thermostat
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units metal
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atom_style full
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boundary p p p
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read_data argon.lmp
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include ff-argon.lmp
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velocity all create 10 2357 mom yes dist gaussian
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neighbor 1 bin
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timestep 0.1
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fix nve all nve
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fix lang all langevin 10 10 1 26488 gjf vhalf
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thermo 200
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run 50000
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