mcf file is not generating
- shub
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6 years 10 months ago #344
by shub
i am not able out find out why my mcf file is not generating .
Traceback (most recent call last):
File "./mcfgen.py", line 1558, in <module>
readNative(ffFile, atomParms)
File "./mcfgen.py", line 1020, in readNative
scaling_1_4 = float(line.split()[1])
IndexError: list index out of range
Traceback (most recent call last):
File "./mcfgen.py", line 1558, in <module>
readNative(ffFile, atomParms)
File "./mcfgen.py", line 1020, in readNative
scaling_1_4 = float(line.split()[1])
IndexError: list index out of range
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- emarin
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- shub
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6 years 10 months ago #347
by shub
thanks for your reply!the problem is sorted out ....the mcf file got generated.but now the the inputfile is showing some error.when i check the log file its showing Start type
********************************************************************************
************ERROR************
(Keyword read on line number 89 of the input file is not supported
Supported keywords are: make_config, read_config, add_to_config, checkpoint
This error occurred in subroutine Get_Start_Type on step 0.
Fatal Error. Stopping program.)
below is my input script!
! NPT simulation
! 100 [emim+][pf6-] ion pairs at 400 K at 1 bar
! start from an equilibrated config at 300K, 1 bar, with volume = (30.2 Ang)^3
# Run_Name
npt.out
!
# Sim_Type
NPT_MC
!
# Nbr_Species
2
!
# VDW_Style
LJ cut_tail 12.0
!
# Charge_Style
coul Ewald 12.0 0.00001
!
# Intra_Scaling
0.0 0.0 0.5 1.0
0.0 0.0 0.8333 1.0
0.0 0.0 0.5 1.0
0.0 0.0 0.8333 1.0
!
LJ and Coul lines for each species
# Mixing_Rule
LB
!
# Seed_Info
6092016 6092016
!
# Rcutoff_Low
1.0
!
# Molecule_Files
emim.mcf 100
pf6.mcf 100
!
# Box_Info
1
CUBIC
30.1692759218122
!
# Temperature_Info
300
!
# Pressure_Info
1.0
!
# Move_Probability_Info
# Prob_Translation
0.25
2.0 2.5
# Prob_Rotation
0.25
30.0 10.0
# Prob_Regrowth
# Prob_Volume
0.02
300
# Done_Probability_Info
!
# Start_Type
read config 300K.inp.xyz
!
# Run_Type
Equilibration 100 10
!
update max move size every N steps
# Average_Info
1
!
# Simulation_Length_Info
Units steps
Prop_Freq 100
Coord_Freq 10000
Run 50000
!
# Property_Info 1
Energy_Total
Volume
Pressure
Density
!
# Fragment_Files
species1/frag1/frag1.dat 1
species1/frag2/frag2.dat 2
species1/frag3/frag3.dat 3
species1/frag4/frag4.dat 4
species2/frag1/frag1.dat 5
!
one line per fragment
# CBMC_Info
kappa_ins 4
kappa_rot 0
kappa_dih 12
rcut_cbmc 6.5
!
END
********************************************************************************
************ERROR************
(Keyword read on line number 89 of the input file is not supported
Supported keywords are: make_config, read_config, add_to_config, checkpoint
This error occurred in subroutine Get_Start_Type on step 0.
Fatal Error. Stopping program.)
below is my input script!
! NPT simulation
! 100 [emim+][pf6-] ion pairs at 400 K at 1 bar
! start from an equilibrated config at 300K, 1 bar, with volume = (30.2 Ang)^3
# Run_Name
npt.out
!
# Sim_Type
NPT_MC
!
# Nbr_Species
2
!
# VDW_Style
LJ cut_tail 12.0
!
# Charge_Style
coul Ewald 12.0 0.00001
!
# Intra_Scaling
0.0 0.0 0.5 1.0
0.0 0.0 0.8333 1.0
0.0 0.0 0.5 1.0
0.0 0.0 0.8333 1.0
!
LJ and Coul lines for each species
# Mixing_Rule
LB
!
# Seed_Info
6092016 6092016
!
# Rcutoff_Low
1.0
!
# Molecule_Files
emim.mcf 100
pf6.mcf 100
!
# Box_Info
1
CUBIC
30.1692759218122
!
# Temperature_Info
300
!
# Pressure_Info
1.0
!
# Move_Probability_Info
# Prob_Translation
0.25
2.0 2.5
# Prob_Rotation
0.25
30.0 10.0
# Prob_Regrowth
# Prob_Volume
0.02
300
# Done_Probability_Info
!
# Start_Type
read config 300K.inp.xyz
!
# Run_Type
Equilibration 100 10
!
update max move size every N steps
# Average_Info
1
!
# Simulation_Length_Info
Units steps
Prop_Freq 100
Coord_Freq 10000
Run 50000
!
# Property_Info 1
Energy_Total
Volume
Pressure
Density
!
# Fragment_Files
species1/frag1/frag1.dat 1
species1/frag2/frag2.dat 2
species1/frag3/frag3.dat 3
species1/frag4/frag4.dat 4
species2/frag1/frag1.dat 5
!
one line per fragment
# CBMC_Info
kappa_ins 4
kappa_rot 0
kappa_dih 12
rcut_cbmc 6.5
!
END
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- ryangmullen
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6 years 10 months ago #348
by ryangmullen
You have 'read config' (with a space) under Start_Type in your input file. What you want is 'read_config' (with an underscore).
You will also need to tell Cassandra how many molecules of each species are in your starting xyz file. For example,
read_config 100 100 300K.inp.xyz
You will also need to tell Cassandra how many molecules of each species are in your starting xyz file. For example,
read_config 100 100 300K.inp.xyz
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- shub
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6 years 10 months ago #349
by shub
thanks for ur suggestion,but a new problem arise
Error attempting to parse line 69 of input file:
into at least 1 entries
This error occurred in subroutine Parse_String on step 0.
Fatal Error. Stopping program
! NPT simulation
! 100 [emim+][pf6-] ion pairs at 400 K at 1 bar
! start from an equilibrated config at 300K, 1 bar, with volume = (30.2 Ang)^3
# Run_Name
npt.out
!
# Sim_Type
NPT_MC
!
# Nbr_Species
2
!
# VDW_Style
LJ cut_tail 12.0
!
# Charge_Style
coul Ewald 12.0 0.00001
!
# Intra_Scaling
0.0 0.0 0.5 1.0
0.0 0.0 0.8333 1.0
0.0 0.0 0.5 1.0
0.0 0.0 0.8333 1.0
!
LJ and Coul lines for each species
# Mixing_Rule
LB
!
# Seed_Info
6092016 6092016
!
# Rcutoff_Low
1.0
!
# Molecule_Files
emim.mcf 100
pf6.mcf 100
!
# Box_Info
1
CUBIC
300
!
# Temperature_Info
400
!
# Pressure_Info
1.0
!
# Move_Probability_Info
# Prob_Translation
0.25
2.0 2.5
# Prob_Rotation
0.25
30.0 10.0
# Prob_Regrowth
# Prob_Volume
0.02
400
# Done_Probability_Info
!
# Start_Type
make config 50 50
!
# Run_Type
production 300 10
!
update max move size every N steps
# Average_Info
1
!
# Simulation_Length_Info
units sweeps
prop_freq 10
coord_freq 10
run 100
!
# Property_Info 1
Energy_Total
Volume
Pressure
Density
!
# Fragment_Files
species1/frag1/frag1.dat 1
species1/frag2/frag2.dat 2
species1/frag3/frag3.dat 3
species1/frag4/frag4.dat 4
species2/frag1/frag1.dat 5
!
one line per fragment
# CBMC_Info
kappa_ins 4
kappa_rot 0
kappa_dih 12
rcut_cbmc 6.5
!
END
Error attempting to parse line 69 of input file:
into at least 1 entries
This error occurred in subroutine Parse_String on step 0.
Fatal Error. Stopping program
! NPT simulation
! 100 [emim+][pf6-] ion pairs at 400 K at 1 bar
! start from an equilibrated config at 300K, 1 bar, with volume = (30.2 Ang)^3
# Run_Name
npt.out
!
# Sim_Type
NPT_MC
!
# Nbr_Species
2
!
# VDW_Style
LJ cut_tail 12.0
!
# Charge_Style
coul Ewald 12.0 0.00001
!
# Intra_Scaling
0.0 0.0 0.5 1.0
0.0 0.0 0.8333 1.0
0.0 0.0 0.5 1.0
0.0 0.0 0.8333 1.0
!
LJ and Coul lines for each species
# Mixing_Rule
LB
!
# Seed_Info
6092016 6092016
!
# Rcutoff_Low
1.0
!
# Molecule_Files
emim.mcf 100
pf6.mcf 100
!
# Box_Info
1
CUBIC
300
!
# Temperature_Info
400
!
# Pressure_Info
1.0
!
# Move_Probability_Info
# Prob_Translation
0.25
2.0 2.5
# Prob_Rotation
0.25
30.0 10.0
# Prob_Regrowth
# Prob_Volume
0.02
400
# Done_Probability_Info
!
# Start_Type
make config 50 50
!
# Run_Type
production 300 10
!
update max move size every N steps
# Average_Info
1
!
# Simulation_Length_Info
units sweeps
prop_freq 10
coord_freq 10
run 100
!
# Property_Info 1
Energy_Total
Volume
Pressure
Density
!
# Fragment_Files
species1/frag1/frag1.dat 1
species1/frag2/frag2.dat 2
species1/frag3/frag3.dat 3
species1/frag4/frag4.dat 4
species2/frag1/frag1.dat 5
!
one line per fragment
# CBMC_Info
kappa_ins 4
kappa_rot 0
kappa_dih 12
rcut_cbmc 6.5
!
END
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- jshah46545
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