Example: partial charges and total charge

This example shows you some ways to use partial atomic charges for ions. The atomic charges should add up to the total charge.

Download ChargedMolecules.run

#!/bin/sh

# Here we consider a Butane molecule with the C in the end groups changed to N
# The ion has a charge of plus two.
# The (partial) atomic charges used in the forcefield need to add up to the total charge


# There is explicit specification via the inut, Loading charges, and guessing charges


# Charges taken "manually" from a DFTB calc., specified via the System%Atoms block

export AMS_JOBNAME=C2H10N2++

rm -rf $AMS_JOBNAME.results

"$AMSBIN/ams" << eor

Task GeometryOptimization

Properties Charges=yes

GeometryOptimization
  Convergence Gradients=1.0e-6
End

System
    Atoms
        N -0.005073166519502884 0.008770355996886468   1.060120635725228   ForceField.Charge=-0.224106970135964811E+000
      	C -0.003379615065181385 0.005774705419397744 -0.4323726711546611   ForceField.Charge=0.481803346892513140E-001
      	C 0.7147029862216027 -1.238161594687982      -0.9787933548287219   ForceField.Charge=0.481357488383262755E-001
      	N 0.7166487936613554 -1.241183181538415       -2.471469363728673   ForceField.Charge=-0.224111043229265006E+000
      	H -0.489254727061788 0.8470579056083724        1.393322418122902   ForceField.Charge=0.327048167700910608E+000
      	H 0.9419603270459358 0.02859511576851682       1.443864570589139   ForceField.Charge=0.312019677649949589E+000
      	H -0.4954439060007188 -0.801643243084588       1.443905390218997   ForceField.Charge=0.312016700963803795E+000
      	H 0.497012567535054 0.9247340386709353       -0.7538297483507286   ForceField.Charge=0.112420754799849087E+000
      	H -1.049427360359161 0.0320094307806696      -0.7537906795101232   ForceField.Charge=0.112425859786873958E+000
      	H 1.760678843023289 -1.264262738726653       -0.6572703272452628   ForceField.Charge=0.112415997624231642E+000
      	H 0.2140471968077103 -2.156981931600252      -0.6574882069415752   ForceField.Charge=0.112419970108937881E+000
      	H 1.207324110469442 -0.4308282262683778       -2.854859298860555   ForceField.Charge=0.312043881750391661E+000
      	H -0.2304034502578771 -1.260970512043685      -2.855040966499596   ForceField.Charge=0.312048243703216099E+000
      	H 1.200917269444972 -2.079821003490794        -2.803581935602674   ForceField.Charge=0.327042675749500744E+000
    End

    GuessBonds True
    Charge 2.0
End

    
Engine ForceField
EndEngine

eor


# Now the neutral molecule, to show it behaves differently

export AMS_JOBNAME=C2H10N2

rm -rf $AMS_JOBNAME.results

"$AMSBIN/ams" << eor

Task GeometryOptimization

Properties Charges=yes

GeometryOptimization
  Convergence Gradients=1.0e-6
End

System
    Atoms
        N -0.005073166519502884 0.008770355996886468   1.060120635725228   ForceField.Charge=-0.571011278205044492E+000
       	C -0.003379615065181385 0.005774705419397744 -0.4323726711546611   ForceField.Charge=-0.628203646719944775E-001
       	C 0.7147029862216027 -1.238161594687982      -0.9787933548287219   ForceField.Charge=-0.628837746183146251E-001
       	N 0.7166487936613554 -1.241183181538415       -2.471469363728673   ForceField.Charge=-0.571125568500377101E+000
       	H -0.489254727061788 0.8470579056083724        1.393322418122902   ForceField.Charge=0.194366247283714433E+000
       	H 0.9419603270459358 0.02859511576851682       1.443864570589139   ForceField.Charge=0.194416030458134853E+000
       	H -0.4954439060007188 -0.801643243084588       1.443905390218997   ForceField.Charge=0.194415295916033237E+000
       	H 0.497012567535054 0.9247340386709353       -0.7538297483507286   ForceField.Charge=0.253223131130085044E-001
       	H -1.049427360359161 0.0320094307806696      -0.7537906795101232   ForceField.Charge=0.253801306729796901E-001
       	H 1.760678843023289 -1.264262738726653       -0.6572703272452628   ForceField.Charge=0.253595653793994673E-001
       	H 0.2140471968077103 -2.156981931600252      -0.6574882069415752   ForceField.Charge=0.254060553518517668E-001
       	H 1.207324110469442 -0.4308282262683778       -2.854859298860555   ForceField.Charge=0.194371032691725371E+000
       	H -0.2304034502578771 -1.260970512043685      -2.855040966499596   ForceField.Charge=0.194368207022870332E+000
       	H 1.200917269444972 -2.079821003490794        -2.803581935602674   ForceField.Charge=0.194436108106012751E+000
    End

    GuessBonds True
End

    
Engine ForceField
EndEngine

eor

# The remaining calculations are again on the +2 ion

# Charges obtained with GuessCharges, using by default dftb.

export AMS_JOBNAME=C2H10N2++.guessed

rm -rf $AMS_JOBNAME.results

"$AMSBIN/ams" << eor

Task GeometryOptimization

Properties Charges=yes

GeometryOptimization
  Convergence Gradients=1.0e-6
End

System
    Atoms
        N -0.005073166519502884 0.008770355996886468   1.060120635725228
       	C -0.003379615065181385 0.005774705419397744 -0.4323726711546611
       	C 0.7147029862216027 -1.238161594687982      -0.9787933548287219
       	N 0.7166487936613554 -1.241183181538415       -2.471469363728673
       	H -0.489254727061788 0.8470579056083724        1.393322418122902
       	H 0.9419603270459358 0.02859511576851682       1.443864570589139
       	H -0.4954439060007188 -0.801643243084588       1.443905390218997
       	H 0.497012567535054 0.9247340386709353       -0.7538297483507286
       	H -1.049427360359161 0.0320094307806696      -0.7537906795101232
       	H 1.760678843023289 -1.264262738726653       -0.6572703272452628
       	H 0.2140471968077103 -2.156981931600252      -0.6574882069415752
       	H 1.207324110469442 -0.4308282262683778       -2.854859298860555
       	H -0.2304034502578771 -1.260970512043685      -2.855040966499596
       	H 1.200917269444972 -2.079821003490794        -2.803581935602674
    End

    GuessBonds True
    Charge 2.0
End

    
Engine ForceField
   GuessCharges True
EndEngine

eor


# Charges are now both specified on input and also Guessed
# The values on the input (ForceField.Charge) are on purpose unreasonable
# The Guessed charges have a higher priority and the input values are ignored
# The output is a bit confusing as unused ForceField.Charge is printed

export AMS_JOBNAME=C2H10N2++.inputandguessed

rm -rf $AMS_JOBNAME.results

"$AMSBIN/ams" << eor

Task GeometryOptimization

Properties Charges=yes

GeometryOptimization
  Convergence Gradients=1.0e-6
End

System
    Atoms
        N -0.005073166519502884 0.008770355996886468   1.060120635725228   ForceField.Charge=-1.224106970135964811E+000
       	C -0.003379615065181385 0.005774705419397744 -0.4323726711546611   ForceField.Charge=0.481803346892513140E-001
       	C 0.7147029862216027 -1.238161594687982      -0.9787933548287219   ForceField.Charge=0.481357488383262755E-001
       	N 0.7166487936613554 -1.241183181538415       -2.471469363728673   ForceField.Charge=-0.224111043229265006E+000
       	H -0.489254727061788 0.8470579056083724        1.393322418122902   ForceField.Charge=1.327048167700910608E+000
       	H 0.9419603270459358 0.02859511576851682       1.443864570589139   ForceField.Charge=0.312019677649949589E+000
       	H -0.4954439060007188 -0.801643243084588       1.443905390218997   ForceField.Charge=0.312016700963803795E+000
       	H 0.497012567535054 0.9247340386709353       -0.7538297483507286   ForceField.Charge=0.112420754799849087E+000
       	H -1.049427360359161 0.0320094307806696      -0.7537906795101232   ForceField.Charge=0.112425859786873958E+000
       	H 1.760678843023289 -1.264262738726653       -0.6572703272452628   ForceField.Charge=0.112415997624231642E+000
       	H 0.2140471968077103 -2.156981931600252      -0.6574882069415752   ForceField.Charge=0.112419970108937881E+000
       	H 1.207324110469442 -0.4308282262683778       -2.854859298860555   ForceField.Charge=0.312043881750391661E+000
       	H -0.2304034502578771 -1.260970512043685      -2.855040966499596   ForceField.Charge=0.312048243703216099E+000
       	H 1.200917269444972 -2.079821003490794        -2.803581935602674   ForceField.Charge=0.327042675749500744E+000
    End

    GuessBonds True
    Charge 2.0
End

    
Engine ForceField
   GuessCharges True
EndEngine

eor






# Charges obtained with Load Charges from a DFTB calc.

export AMS_JOBNAME=C2H10N2++.dftb

rm -rf $AMS_JOBNAME.results

"$AMSBIN/ams" << eor

Task SinglePoint

Properties Charges=yes

GeometryOptimization
  Convergence Gradients=1.0e-6
End

System
    Atoms
        N -0.005073166519502884 0.008770355996886468   1.060120635725228
       	C -0.003379615065181385 0.005774705419397744 -0.4323726711546611
       	C 0.7147029862216027 -1.238161594687982      -0.9787933548287219
       	N 0.7166487936613554 -1.241183181538415       -2.471469363728673
       	H -0.489254727061788 0.8470579056083724        1.393322418122902
       	H 0.9419603270459358 0.02859511576851682       1.443864570589139
       	H -0.4954439060007188 -0.801643243084588       1.443905390218997
       	H 0.497012567535054 0.9247340386709353       -0.7538297483507286
       	H -1.049427360359161 0.0320094307806696      -0.7537906795101232
       	H 1.760678843023289 -1.264262738726653       -0.6572703272452628
       	H 0.2140471968077103 -2.156981931600252      -0.6574882069415752
       	H 1.207324110469442 -0.4308282262683778       -2.854859298860555
       	H -0.2304034502578771 -1.260970512043685      -2.855040966499596
       	H 1.200917269444972 -2.079821003490794        -2.803581935602674
    End

    Charge 2.0
End

    
Engine DFTB
EndEngine

eor

loadChargeFile='C2H10N2++.dftb.results/dftb.rkf'

export AMS_JOBNAME=C2H10N2++.loaded

rm -rf $AMS_JOBNAME.results

"$AMSBIN/ams" << eor

Task GeometryOptimization

Properties Charges=yes

GeometryOptimization
  Convergence Gradients=1.0e-6
End

System
    Atoms
        N -0.005073166519502884 0.008770355996886468   1.060120635725228
       	C -0.003379615065181385 0.005774705419397744 -0.4323726711546611
       	C 0.7147029862216027 -1.238161594687982      -0.9787933548287219
       	N 0.7166487936613554 -1.241183181538415       -2.471469363728673
       	H -0.489254727061788 0.8470579056083724        1.393322418122902
       	H 0.9419603270459358 0.02859511576851682       1.443864570589139
       	H -0.4954439060007188 -0.801643243084588       1.443905390218997
       	H 0.497012567535054 0.9247340386709353       -0.7538297483507286
       	H -1.049427360359161 0.0320094307806696      -0.7537906795101232
       	H 1.760678843023289 -1.264262738726653       -0.6572703272452628
       	H 0.2140471968077103 -2.156981931600252      -0.6574882069415752
       	H 1.207324110469442 -0.4308282262683778       -2.854859298860555
       	H -0.2304034502578771 -1.260970512043685      -2.855040966499596
       	H 1.200917269444972 -2.079821003490794        -2.803581935602674
    End

    GuessBonds True
    Charge 2.0
End

    
Engine ForceField
   LoadCharges
      File $loadChargeFile
   End
EndEngine

eor


# Charges are now both specified on input and also Guessed
# The values on the input (ForceField.Charge) are on purpose unreasonable
# The Guessed charges have a higher priority and the input values are ignored
# The output is a bit confusing as unused ForceField.Charge is printed

export AMS_JOBNAME=C2H10N2++.inputandloaded

rm -rf $AMS_JOBNAME.results

"$AMSBIN/ams" << eor

Task GeometryOptimization

Properties Charges=yes

GeometryOptimization
  Convergence Gradients=1.0e-6
End

System
    Atoms
        N -0.005073166519502884 0.008770355996886468   1.060120635725228   ForceField.Charge=-1.224106970135964811E+000
       	C -0.003379615065181385 0.005774705419397744 -0.4323726711546611   ForceField.Charge=0.481803346892513140E-001
       	C 0.7147029862216027 -1.238161594687982      -0.9787933548287219   ForceField.Charge=0.481357488383262755E-001
       	N 0.7166487936613554 -1.241183181538415       -2.471469363728673   ForceField.Charge=-0.224111043229265006E+000
       	H -0.489254727061788 0.8470579056083724        1.393322418122902   ForceField.Charge=1.327048167700910608E+000
       	H 0.9419603270459358 0.02859511576851682       1.443864570589139   ForceField.Charge=0.312019677649949589E+000
       	H -0.4954439060007188 -0.801643243084588       1.443905390218997   ForceField.Charge=0.312016700963803795E+000
       	H 0.497012567535054 0.9247340386709353       -0.7538297483507286   ForceField.Charge=0.112420754799849087E+000
       	H -1.049427360359161 0.0320094307806696      -0.7537906795101232   ForceField.Charge=0.112425859786873958E+000
       	H 1.760678843023289 -1.264262738726653       -0.6572703272452628   ForceField.Charge=0.112415997624231642E+000
       	H 0.2140471968077103 -2.156981931600252      -0.6574882069415752   ForceField.Charge=0.112419970108937881E+000
       	H 1.207324110469442 -0.4308282262683778       -2.854859298860555   ForceField.Charge=0.312043881750391661E+000
       	H -0.2304034502578771 -1.260970512043685      -2.855040966499596   ForceField.Charge=0.312048243703216099E+000
       	H 1.200917269444972 -2.079821003490794        -2.803581935602674   ForceField.Charge=0.327042675749500744E+000
    End

    GuessBonds True
    Charge 2.0
End

    
Engine ForceField
   LoadCharges
      File $loadChargeFile
   End
EndEngine

eor



# finally let us make on purpose an error (total charge incorrect), this calculation is supposed to fail, and not print an energy

echo "The following error is intended"

export AMS_JOBNAME=C2H10N2++.inputerror

rm -rf $AMS_JOBNAME.results

"$AMSBIN/ams" << eor

Task GeometryOptimization

Properties Charges=yes

GeometryOptimization
  Convergence Gradients=1.0e-6
End

System
    Atoms
        N -0.005073166519502884 0.008770355996886468   1.060120635725228   ForceField.Charge=-0.224106970135964811E+000
       	C -0.003379615065181385 0.005774705419397744 -0.4323726711546611   ForceField.Charge=0.481803346892513140E-001
       	C 0.7147029862216027 -1.238161594687982      -0.9787933548287219   ForceField.Charge=0.481357488383262755E-001
       	N 0.7166487936613554 -1.241183181538415       -2.471469363728673   ForceField.Charge=-0.224111043229265006E+000
       	H -0.489254727061788 0.8470579056083724        1.393322418122902   ForceField.Charge=0.327048167700910608E+000
       	H 0.9419603270459358 0.02859511576851682       1.443864570589139   ForceField.Charge=0.312019677649949589E+000
       	H -0.4954439060007188 -0.801643243084588       1.443905390218997   ForceField.Charge=0.312016700963803795E+000
       	H 0.497012567535054 0.9247340386709353       -0.7538297483507286   ForceField.Charge=0.112420754799849087E+000
       	H -1.049427360359161 0.0320094307806696      -0.7537906795101232   ForceField.Charge=0.112425859786873958E+000
       	H 1.760678843023289 -1.264262738726653       -0.6572703272452628   ForceField.Charge=0.112415997624231642E+000
       	H 0.2140471968077103 -2.156981931600252      -0.6574882069415752   ForceField.Charge=0.112419970108937881E+000
       	H 1.207324110469442 -0.4308282262683778       -2.854859298860555   ForceField.Charge=0.312043881750391661E+000
       	H -0.2304034502578771 -1.260970512043685      -2.855040966499596   ForceField.Charge=0.312048243703216099E+000
       	H 1.200917269444972 -2.079821003490794        -2.803581935602674   ForceField.Charge=0.327042675749500744E+000
    End

    GuessBonds True
End

    
Engine ForceField
EndEngine

eor