Dear all

During my simulation, I got an error, “Variable ID in variable formula does not exist”. Here are the details of my simulation.

I have to print dump files of atom style at timesteps that could be decided only during the course of simulation (there are intermediate minimizations, but dump has to be after certain runs), and therefore I dynamically create file that contains timesteps, at which I should create the dump. And then using variable next(), dump_modify every, etc I change the dump frequency. The error above mentioned started after implementing this dynamic frequency of dumping in the source code.

The error looks so bizarre for me since I was unable to find out the error, even after many checks. I would be grateful to you if anybody could point out even if its a care-less petty mistake.

Here are my source code and log_restart files

**Source code:**

*# VARIABLES*

*variable fname index data.susigrapheneminimlammps*

*variable simname index datarestart_susigrapheneminimlammps*

*# Initialization*

*units real*

*boundary p p p*

*atom_style molecular*

*log log.{simname}.txt*
*read_data {fname}*

*neighbor 3 bin*

*neigh_modify page 10000000 one 1000000 every 1 delay 0 check no*

*# dielectric 1.0*

*# potentials*

*pair_style lj/cut 20.045 # global cut off 5*sigma sigma for rminij 4.5*

*pair_coeff 1 1 0.0936 4.009 9.2207 # 2.3 sigma as suggested by doxasrakis*

*pair_coeff 1 2 0.1015 3.7925 8.72278 #*

*pair_coeff 1 3 0.1015 3.7925 8.72278 #*

*pair_coeff 1 4 0.0936 4.009 9.2207 #*

*pair_coeff 1 5 0.1456 4.009 9.2207 #*

*pair_coeff 1 6 0.1456 4.009 9.2207 #*

*pair_coeff 1 7 0.1456 4.009 9.2207 #*

*pair_coeff 1 8 0.0892 3.8398 8.8315 #*

*pair_coeff 2 2 0.1 3.3854 7.78642 #*

*pair_coeff 2 3 0.1 3.3854 7.78642 #*

*pair_coeff 2 4 0.1015 3.7925 8.72278 #*

*pair_coeff 2 5 0.1505 3.7925 8.72278 #*

*pair_coeff 2 6 0.1505 3.7925 8.72278 #*

*pair_coeff 2 7 0.1505 3.7925 8.72278 #*

*pair_coeff 2 8 0.0922 3.5279 8.1142 #*

*pair_coeff 3 3 0.1 3.3854 7.78642 #*

*pair_coeff 3 4 0.1015 3.7925 8.72278 #*

*pair_coeff 3 5 0.1505 3.7925 8.72278 #*

*pair_coeff 3 6 0.1505 3.7925 8.72278 #*

*pair_coeff 3 7 0.1505 3.7925 8.72278 #*

*pair_coeff 3 8 0.0922 3.5279 8.1142 #*

*pair_coeff 4 4 0.0936 4.009 9.2207 #*

*pair_coeff 4 5 0.1456 4.009 9.2207 #*

*pair_coeff 4 6 0.1456 4.009 9.2207 #*

*pair_coeff 4 7 0.1456 4.009 9.2207 #*

*pair_coeff 4 8 0.0892 3.8398 8.8315 #*

*pair_coeff 5 5 0.2264 4.009 9.2207 #*

*pair_coeff 5 6 0.2264 4.009 9.2207 #*

*pair_coeff 5 7 0.2264 4.009 9.2207 #*

*pair_coeff 5 8 0.1387 3.8398 8.8315 #*

*pair_coeff 6 6 0.2264 4.009 9.2207 #*

*pair_coeff 6 7 0.2264 4.009 9.2207 #*

*pair_coeff 6 8 0.1387 3.8398 8.8315 #*

*pair_coeff 7 7 0.2264 4.009 9.2207 #*

*pair_coeff 7 8 0.1387 3.8398 8.8315 #*

*pair_coeff 8 8 0.085 3.6705 8.4421 #*

*bond_style harmonic # CVFF http://redmine.scorec.rpi.edu/anonsvn/lammps-cuda/tools/msi2lmp/biosym_frc_files/cvff.frc*

*bond_coeff 1 322.8 1.51*

*bond_coeff 2 655.2 1.34*

*bond_coeff 3 322.8 1.51*

*bond_coeff 4 322.8 1.51*

*bond_coeff 5 322.8 1.51*

*bond_coeff 6 322.7 1.53*

*bond_coeff 7 322.8 1.51*

*bond_coeff 8 480.0 1.42*

*angle_style harmonic # CVFF, smith paul paper*

*angle_coeff 1 45 125.0*

*angle_coeff 2 45 125.0*

*angle_coeff 3 45 126.0*

*angle_coeff 4 45 125.0*

*angle_coeff 5 57 112.0*

*angle_coeff 6 57 112.0*

*angle_coeff 7 45 125.0*

*angle_coeff 8 100 120.0*

*dihedral_style table spline 10000*

*dihedral_coeff 1 dihedrallistminimisationsusi.table TORSION13*

*dihedral_coeff 2 dihedrallistminimisationsusi.table TORSION2*

*dihedral_coeff 3 dihedrallistminimisationsusi.table TORSION13*

*improper_style harmonic # a high value*

*improper_coeff 1 500 0.0*

*improper_coeff 2 500 0.0*

*improper_coeff 3 500 0.0*

*improper_coeff 4 500 0.0*

*improper_coeff 5 500 0.0*

*improper_coeff 6 500 0.0*

*special_bonds lj 0.0 0.0 0.05*

*compute 1 all reduce max z*

*compute 2 all reduce min z*

*thermo 400*

*thermo_style custom step temp etotal pe ke evdwl eangle ebond edihed eimp lx ly lz density vol press c_1 c_2 # c_inter c_inter[1] c_inter[2] c_inter[3] c_poly[1] c_poly[2] c_poly[3] c_grap[1] c_grap[2] c_grap[3]*

*min_style cg*

*minimize 0.0 0.0 5000000 1000000*

*variable 1 equal c_1*

*variable 2 equal c_2*

*variable networkfixed atom “z > (v_2 + (v_1 - v_2)*(5/7))”*

*group fixednetwork variable networkfixed*

*group fixedgraphene type 8*

*group timeintegrable subtract all fixednetwork fixedgraphene*

*group timeintnetfixed union timeintegrable fixednetwork*

*# compute load fixedgraphene reduce ave fx fy fz*

*compute load fixedgraphene group/group timeintnetfixed*

*variable displacement equal 0*

*dump 2 all atom 100000000000 dump.*.opening #*

*dump_modify 2 first yes*

*dump 1 all dcd 1000000 susiminimlammps.dcd #*

*dump_modify 1 first yes*

*variable tm equal step+10*

*print {tm} file time.txt*
*print 100000000000 append time.txt #*
*variable filassign file time.txt*
*variable timeselect equal next(filassign)*
*dump_modify 2 every v_timeselect*
*# equilibration to 305 K 1 atm*
*timestep 0.05*
*velocity all create 305.0 123456 rot yes dist gaussian*
*fix 1 all npt temp 305.0 305.0 100.0 iso 1.0 1.0 20000.0 tchain 1 pchain 14 # drag 4*
*velocity all scale 305.0*
*fix 2 all momentum 1 linear 1 1 1*
*thermo_style custom step temp etotal pe ke evdwl eangle ebond edihed eimp xlo xhi ylo yhi zlo zhi c_load[1] c_load[2] c_load density press v_displacement c_load[3]*
*thermo 100*
*run 10*
*unfix 1*
*unfix 2*
*variable displacement delete*
*undump 1 #*
*write_dump all custom dump.intermediatesusigrapheneopen id type x y z ix iy iz modify sort id*
*variable n4 equal 5*
*variable a loop {n4}*

*label loop4*

_variable displacement equal .125*{a}_
*timestep 0.05*
*fix 1 fixednetwork move linear 0.0 0.0 0.0 units box*
*fix 2 fixedgraphene move linear 0.0 0.0 -0.0025 units box*
*fix 3 timeintegrable nve*
*thermo_style custom step temp etotal pe ke evdwl eangle ebond edihed eimp xlo xhi ylo yhi zlo zhi density press*
*thermo 200*
*run 1000*
*unfix 1*
*unfix 2*
*unfix 3*
*# Minimization*
*fix 1 fixednetwork setforce 0.0 0.0 0.0*
*fix 2 fixedgraphene setforce 0.0 0.0 0.0*
*thermo 400*
*thermo_style custom step temp etotal pe ke evdwl eangle ebond edihed eimp xlo xhi ylo yhi zlo zhi density press*
*min_style cg*
*minimize 0.0 0.0 5000000 1000000*
*unfix 1*
*unfix 2*
*variable tm equal step+35*
*print {tm} file time.txt*

*print 100000000000 append time.txt*

*variable filassign file time.txt*

*variable timeselect equal next(filassign)*

*dump_modify 2 every v_timeselect*

*timestep 0.05*

*fix 1 fixednetwork setforce 0.0 0.0 0.0*

*fix 2 fixedgraphene setforce 0.0 0.0 0.0*

*velocity fixednetwork set 0.0 0.0 0.0 units box*

*velocity fixedgraphene set 0.0 0.0 0.0 units box*

*fix 3 timeintegrable npt temp 305.0 305.0 100.0 iso 1.0 1.0 2000.0 tchain 1 pchain 14 # drag 4*

*thermo 100*

*thermo_style custom step temp etotal pe ke evdwl eangle ebond edihed eimp xlo xhi ylo yhi zlo zhi c_load[1] c_load[2] c_load density press v_displacement c_load[3]*

*run 35*

*unfix 1*

*unfix 2*

*unfix 3*