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9.11 Ab Initio Molecular Dynamics with Complex Absorbing Potentials

9.11.3 CAP-AIMD Job Control and Examples

(May 7, 2024)

The following three assignments are necessary in order to run a CAP-AIMD simulation:

  • JOBTYPE = AIMD in $rem,

  • COMPLEX_CCMAN = TRUE in $rem (see Section 7.10.9), and

  • CS_HF = 1 in $complex_ccman (see Section 7.10.9).

For now, CAP-AIMD simulations are possible only with the cuboid CAP type, so setting CAP_TYPE = 1 is also necessary in the $complex_ccman section (see Section 7.10.9).

With CAP-AIMD simulations, one gets two additional files in the AIMD directory (§9.9.2):

  • CAP_EComponents: Records for each step the total complex energy, the CAP-corrected total complex energy, and the real and imaginary parts of the CAP contribution to the total complex energy – all in atomic units (a.u.).

  • CAP_PositionAndWidth: Records for each step the total complex energy (in a.u.) and the resonance width (in electron-Volt).

CAP_AIMD_SWITCH

CAP_AIMD_SWITCH
       Sets CAP_ETA to zero during a CAP-AIMD simulation when the real part of the last alpha occupied orbital’s energy is negative
TYPE:
       LOGICAL
DEFAULT:
       TRUE
OPTIONS:
       TRUE Set CAP_ETA to zero when the real part of the last alpha occupied orbital’s becomes negative. FALSE Keep user’s CAP_ETA constant throughout simulation.
RECOMMENDATION:
       Use default.

CS_STRICT

CS_STRICT
       Determines Mulliken charges, multipole moments and complex orbital energies for CAP-HF calculations by reading, when applicable, complex density matrix or complex molecular orbital coefficient file
TYPE:
       LOGICAL
DEFAULT:
       FALSE
OPTIONS:
       TRUE determine Mulliken charges, multipole moments and complex orbital energies for CAP-HF calculations by reading – when applicable – the complex density matrix or complex molecular orbital coefficient file. FALSE Don’t read the complex density matrix or complex molecular orbital coefficient file when determining Mulliken charges, multipole moments and orbital energies for CAP-HF calculations.
RECOMMENDATION:
       Set to ‘TRUE’ for CAP-HF calculations.

SKIP_OLD_SCFMAN

SKIP_OLD_SCFMAN
       Skips only old SCF drivers
TYPE:
       LOGICAL
DEFAULT:
       FALSE
OPTIONS:
       TRUE Skip only old SCF drivers FALSE Do not skip old SCF drivers
RECOMMENDATION:
       When performing CAP calculations on temporary anions, it may help setting this variable to FALSE.

CS_SCF_FINAL_PRINT

CS_SCF_FINAL_PRINT
       Controls level of output from CAP-SCF procedure.
TYPE:
       INTEGER
DEFAULT:
       0 No extra print out.
OPTIONS:
       1 Print direct breakdown of CAP-SCF energy. 2 Print breakdown of CAP-SCF energy based on the complex coefficient matrix. Also required if the options below are requested. 3 Level 2 plus diagonal elements of complex orbital energy matrix, F. Triggered by Level 2. 4 Level 2 plus diagonal elements of complex kinetic energy matrix, T. Triggered by Level 2 5 Level 2 plus diagonal elements of complex electron-nuclear Coulomb potential energy matrix, V. Triggered by Level 2. 6 Level 2 plus diagonal elements of CAP matrix, W. Triggered by Level 2. 7 Level 2 plus diagonal elements of total complex one-electron energy matrix, 𝐓+𝐕+𝐖. Triggered by Level 2. 8 Level 2 plus diagonal elements of total complex electronic energy matrix, 𝐓+𝐕+𝐖+𝐅. Triggered by Level 2. 9 Level 2 to 8. Triggered by Level 2.
RECOMMENDATION:
       Level 1 is usually enough. Values for this $rem variable are transformed first into a set of distinct values; thus, for example, “1111” is equivalent to “1” and “28224” is equivalent to “248”. To request Levels 3–9, please remember to request Level 2 as well.

Example 9.9.45  CAP-HF single point job for N-2, with energy decomposition of the complex energy. Basis set is cc-PVTZ+3p.

$molecule
-1 2
N
N   1  1.098
$end

$rem
¯JOBTYPE¯¯SP
¯METHOD¯¯¯hf
¯BASIS¯¯¯general
¯GEN_SCFMAN¯¯TRUE
¯SKIP_OLD_SCFMAN¯true¯! skip old scfman drivers
¯SCF_CONVERGENCE¯8
¯SCF_GUESS¯¯CORE
¯COMPLEX_CCMAN¯¯TRUE
¯UNRESTRICTED¯¯TRUE
¯CS_STRICT¯¯TRUE¯! Determine orbital energies and props. using the complex density matrix/complex MO coefficients
¯CS_SCF_FINAL_PRINT¯1111¯! Print summary of energy decomposition
$end

$complex_ccman
¯CS_HF ¯¯¯1
¯CAP_TYPE ¯¯1
¯CAP_ETA ¯¯420
¯CAP_X ¯¯¯3535
¯CAP_Y ¯¯¯3535
¯CAP_Z ¯¯¯8102
$end

$basis
N     0
S    7   1.00
  11420.                     0.00052898
   1712.                     0.00409115
    389.3                    0.02101161
    110.0                    0.08163835
     35.57                   0.23564992
     12.54                   0.43792615
      4.644                  0.35006007
S    7   1.00
  11420.                     0.00000185
   1712.                     0.00000699
    110.0                   -0.00073647
     35.57                  -0.00718168
     12.54                  -0.04679022
      4.644                 -0.12512392
      0.5118                 0.78627029
S    1   1.00
      1.293                  1.000000
S    1   1.00
      0.1787                 1.000000
P    3   1.00
     26.63                   0.014670
      5.948                  0.091764
      1.742                  0.298683
P    1   1.00
      0.5550                 1.000000
P    1   1.00
      0.1725                 1.000000
D    1   1.00
      1.654                  1.000000
D    1   1.00
      0.469                  1.000000
F    1   1.00
      1.093                  1.000000
¯P    1   1.00
¯¯0.08625       1.000000
      ¯P    1   1.00
      ¯¯0.043125      1.000000
      ¯P    1   1.00
      ¯¯0.0215625     1.000000
****
$end

Example 9.9.46  CAP-AIMD simulation for N-2. Basis set is cc-PVTZ+3p.

$molecule
-1 2
N
N   1  1.098
$end


$rem
 JOBTYPE¯¯AIMD
 METHOD¯¯¯HF
 BASIS¯¯¯GENERAL
 GEN_SCFMAN¯¯TRUE
 SKIP_OLD_SCFMAN¯TRUE¯¯! Skip old scfman drivers
 SCF_CONVERGENCE¯8
 MAX_SCF_CYCLES¯¯200
 SCF_GUESS¯¯CORE
 COMPLEX_CCMAN¯¯TRUE¯¯! Activate Complex CCMAN. Necessary for CAP calculations.
 UNRESTRICTED¯¯TRUE
 TIME_STEP¯¯10
 AIMD_STEPS¯¯200
 FOCK_EXTRAP_ORDER      0
 FOCK_EXTRAP_POINTS     0
 AIMD_MOMENTS¯¯1
 AIMD_TEMP¯¯300
 AIMD_INIT_VELOC¯THERMAL
 CAP_AIMD_SWITCH¯TRUE¯¯! Set CAP_ETA=0 when extra electron is bound
 CS_STRICT¯¯TRUE¯¯! Determine orbital energies and props. using the complex density. matrix/complex MO coefficients
 INTEGRAL_SYMMETRY      FALSE
 POINT_GROUP_SYMMETRY   FALSE
$end

$complex_ccman
¯CS_HF ¯¯¯1¯¯! Do complex HF
¯CAP_TYPE ¯¯1¯¯! CAP type is cuboid.
¯CAP_ETA ¯¯420
¯CAP_X ¯¯¯3535
¯CAP_Y ¯¯¯3535
¯CAP_Z ¯¯¯8102
$end

$basis
N     0
S    7   1.00
  11420.                     0.00052898
   1712.                     0.00409115
    389.3                    0.02101161
    110.0                    0.08163835
     35.57                   0.23564992
     12.54                   0.43792615
      4.644                  0.35006007
S    7   1.00
  11420.                     0.00000185
   1712.                     0.00000699
    110.0                   -0.00073647
     35.57                  -0.00718168
     12.54                  -0.04679022
      4.644                 -0.12512392
      0.5118                 0.78627029
S    1   1.00
      1.293                  1.000000
S    1   1.00
      0.1787                 1.000000
P    3   1.00
     26.63                   0.014670
      5.948                  0.091764
      1.742                  0.298683
P    1   1.00
      0.5550                 1.000000
P    1   1.00
      0.1725                 1.000000
D    1   1.00
      1.654                  1.000000
D    1   1.00
      0.469                  1.000000
F    1   1.00
      1.093                  1.000000
¯P    1   1.00
¯¯0.08625       1.000000
      ¯P    1   1.00
      ¯¯0.043125      1.000000
      ¯P    1   1.00
      ¯¯0.0215625     1.000000
****
$end

Example 9.9.47  CAP-AIMD simulation for C2H-4. Basis set is cc-PVTZ+3p(C).
A CAP single point calculation is first done. The CAP-SCF solution is then read as the initial guess for the CAP-AIMD part. This procedure is useful, for example, when one wants to use the MOM_START option (§4.5.13) to preserve orbital occupation in the course of the simulation.

$molecule
-1 2
C    0.0000   0.0000   0.0000
H    0.0000   0.0000   1.0742
H    0.9596   0.0000  -0.4829
C   -1.1191   0.0000  -0.6897
H   -2.0787   0.0000  -0.2068
H   -1.1191   0.0000  -1.7639
$end


$rem
 METHOD¯¯¯HF
 BASIS¯¯¯GENERAL
 GEN_SCFMAN¯¯TRUE
 SKIP_OLD_SCFMAN¯TRUE¯! skip old scfman drivers
 SCF_CONVERGENCE¯8
 SCF_GUESS¯¯CORE
 COMPLEX_CCMAN¯¯TRUE
 UNRESTRICTED¯¯TRUE
 CS_STRICT¯¯TRUE¯! Determine orbital energies and props. using the complex density matrix/complex MO coefficients
 CS_SCF_FINAL_PRINT¯1111¯! Print summary of energy decomposition
 INTEGRAL_SYMMETRY ¯FALSE
 POINT_GROUP_SYMMETRY¯FALSE
$end

$complex_ccman
 CS_HF ¯¯¯1
 CAP_TYPE ¯¯1
 CAP_ETA ¯¯230
 CAP_X ¯¯¯4360
 CAP_Y ¯¯¯2680
 CAP_Z ¯¯¯4360
$end

$basis
H¯0
cc-pvtz
****
C     0
S    8   1.00
   8236.0000000              0.0005310
   1235.0000000              0.0041080
    280.8000000              0.0210870
     79.2700000              0.0818530
     25.5900000              0.2348170
      8.9970000              0.4344010
      3.3190000              0.3461290
      0.3643000             -0.0089830
S    8   1.00
   8236.0000000             -0.0001130
   1235.0000000             -0.0008780
    280.8000000             -0.0045400
     79.2700000             -0.0181330
     25.5900000             -0.0557600
      8.9970000             -0.1268950
      3.3190000             -0.1703520
      0.3643000              0.5986840
S    1   1.00
     11.8760000              1.0000000
S    1   1.00
      4.2920000              1.0000000
S    1   1.00
      0.9059000              1.0000000
S    1   1.00
      0.1285000              1.0000000
P    3   1.00
     18.7100000              0.0140310
      4.1330000              0.0868660
      1.2000000              0.2902160
P    1   1.00
     33.1900000              1.0000000
P    1   1.00
      8.7780000              1.0000000
P    1   1.00
      0.3827000              1.0000000
P    1   1.00
      0.1209000              1.0000000
D    1   1.00
     14.8390000              1.0000000
D    1   1.00
      1.0970000              1.0000000
D    1   1.00
      0.3180000              1.0000000
F    1   1.00
      0.7610000              1.0000000
      P¯1¯¯1.00
      ¯¯0.06045¯1.00
      P¯1¯¯1.00
      ¯¯0.030225¯1.00
      P¯1¯¯1.00
      ¯¯0.0151125¯1.00
****
$end


@@@


$molecule
 READ
$end

$velocity
3.6095e-05   4.1623e-06   2.3754e-05
-9.7386e-04  -1.4552e-05  -1.2310e-03
-2.8737e-04   1.2165e-04   2.9068e-04
3.3619e-05  -1.3939e-04   1.0849e-04
6.4312e-04   2.0187e-04  -4.2066e-04
-2.1196e-04   1.3012e-03  -2.1364e-04
$end

$rem
¯JOBTYPE¯¯AIMD
¯METHOD¯¯¯HF
¯BASIS¯¯¯GENERAL
¯GEN_SCFMAN¯¯TRUE
¯SKIP_OLD_SCFMAN¯TRUE
¯SCF_CONVERGENCE¯8
¯MAX_SCF_CYCLES¯¯3000
integral_symmetry FALSE
point_group_symmetry False
¯SCF_GUESS¯¯READ
¯COMPLEX_CCMAN¯¯TRUE
¯UNRESTRICTED¯¯TRUE
¯MOM_START¯¯1
¯MOM_METHOD¯¯MOM
¯TIME_STEP¯¯2
¯AIMD_STEPS¯¯200
   ¯FOCK_EXTRAP_ORDER      0
   ¯FOCK_EXTRAP_POINTS     0
  ¯AIMD_MOMENTS¯¯1
  ¯AIMD_PRINT¯¯2¯! Print Mulliken charges and dipole moments at each step
¯CS_STRICT¯¯TRUE
$end

$complex_ccman
¯CS_HF ¯¯¯1
¯CAP_TYPE ¯¯1
¯CAP_ETA ¯¯230
¯CAP_X ¯¯¯4360
¯CAP_Y ¯¯¯2680
¯CAP_Z ¯¯¯4360
$end

$basis
H¯0
cc-pvtz
****
C     0
S    8   1.00
   8236.0000000              0.0005310
   1235.0000000              0.0041080
    280.8000000              0.0210870
     79.2700000              0.0818530
     25.5900000              0.2348170
      8.9970000              0.4344010
      3.3190000              0.3461290
      0.3643000             -0.0089830
S    8   1.00
   8236.0000000             -0.0001130
   1235.0000000             -0.0008780
    280.8000000             -0.0045400
     79.2700000             -0.0181330
     25.5900000             -0.0557600
      8.9970000             -0.1268950
      3.3190000             -0.1703520
      0.3643000              0.5986840
S    1   1.00
     11.8760000              1.0000000
S    1   1.00
      4.2920000              1.0000000
S    1   1.00
      0.9059000              1.0000000
S    1   1.00
      0.1285000              1.0000000
P    3   1.00
     18.7100000              0.0140310
      4.1330000              0.0868660
      1.2000000              0.2902160
P    1   1.00
     33.1900000              1.0000000
P    1   1.00
      8.7780000              1.0000000
P    1   1.00
      0.3827000              1.0000000
P    1   1.00
      0.1209000              1.0000000
D    1   1.00
     14.8390000              1.0000000
D    1   1.00
      1.0970000              1.0000000
D    1   1.00
      0.3180000              1.0000000
F    1   1.00
      0.7610000              1.0000000
      P¯1¯¯1.00
      ¯¯0.06045¯1.00
      P¯1¯¯1.00
      ¯¯0.030225¯1.00
      P¯1¯¯1.00
      ¯¯0.0151125¯1.00
****
$end