74 lines
2.4 KiB
Plaintext
74 lines
2.4 KiB
Plaintext
units real
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dimension 3
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boundary p p p
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atom_style atomic
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newton on
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timestep 1.0
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read_data methanol.data
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velocity all create 300.0 16802 dist gaussian
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pair_style table spline 15000
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pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
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neigh_modify delay 0 every 1 check yes one 10000
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neighbor 12.0 bin
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thermo 500
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thermo_style custom step temp pe etotal press vol
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variable STEP equal step
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variable TEMP equal temp
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## volume from cubic angstroms to cubic nm
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variable VOL equal vol/1000.0
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## pressure from atm to bar
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variable PRESS equal press*1.01325
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variable PXX equal pxx*1.01325
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variable PYY equal pyy*1.01325
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variable PZZ equal pzz*1.01325
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variable PXY equal pxy*1.01325
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variable PXZ equal pxz*1.01325
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variable PYZ equal pyz*1.01325
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## energy from kcal/mol to kJ/mol
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variable KE equal ke*4.184
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variable PE equal pe*4.184
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variable UVDW equal evdwl*4.184
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##### SPECIAL COMMANDS FOR FIX_BOCS #####
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# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
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fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
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# Compute the modified pressure
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compute bocsPress all pressureBocs thermo_temp
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# Report the modified pressure
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thermo_modify press bocsPress
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# Use the modified pressure for fix bocs instead of thermo_press
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fix_modify 1 press bocsPress
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## Save some data from simulation to files
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fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
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fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
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fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
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fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
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fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
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fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
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fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
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fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
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## Prints a configuration to dump.txt every 500 steps
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dump 1 all custom 500 dump.txt id type x y z fx fy fz
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# Write restart files to continue simulations
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restart 10000 state1.restart state2.restart
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## Run for this many steps
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run_style verlet
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run 10000
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