sbin/bdf_extractor.py
A tool for extracting useful information from BDF output. It is to be used for preparation interface for geometry optimization, nonadiabatic dynamics
An example of a single step for nonadiabatic dynamics involving different spin states
To perform nonadiabatic dynamics involving different spins for CH2O, we need the following information:
1. two TD-DFT calculations for singlet and triplet calculations, respectively
2. a TD-DFT/SOC calculation for generating SOC matrix elements (isoc=3)
3. one RESP calculations for gradients of spin-free states,
4. one RESP calculations for nonadiabatic couplings (NAC) between spin-free states
Input:
$COMPASS Title nh3 Basis sto-3g Geometry C 0.000000 0.000000 -0.526806 O 0.000000 0.000000 0.677133 H 0.000000 0.945218 -1.128115 H 0.000000 -0.945218 -1.128115 End geometry $END $xuanyuan scalar heff 0 soint hsoc 0 $end $scf RHF charge 0 spin 1 THRESHCONV 1.d-12 1.d-10 OPTSCR 1 $end $traint tddft orbi hforb $end $tddft imethod 1 isf 0 idiag 1 iexit 1 itda 1 istore 1 crit_e 1.d-10 crit_vec 1.d-6 $end $tddft imethod 1 isf 1 itda 1 idiag 1 iexit 1 istore 2 crit_e 1.d-10 crit_vec 1.d-6 $end # print all SOC mat $tddft isoc 3 nfiles 2 ifgs 1 imatsoc -1 $end # gs & Excited-state gradients $resp iprt 0 geom norder 1 method 2 nfiles 2 $end # NAC calculations $resp iprt 0 quad fnac method 2 nfiles 2 $end
After running the job, useful information for dynamics can be generated using bdf_extractor.py and extractor.py:
./run.sh taskname.inp > taskname.out ./bdf_extractor.py taskname
Output:
SUMMARY via Extractors:
=======================
job type = ['SCF', 'TDDFT_ENE', 'TDDFT_ENE', 'TDDFT_SOC', 'RESP_EXGRAD', 'RESP_FNAC']
### JOB TYPE = SCF ###
E_tot= -112.35347426
### JOB TYPE = TDDFT_ENE ###
nsym = 4
nstate = 4
nexit = [1, 1, 1, 1]
info =
sym = 1
[{'No.': 1, 'f': 0.3008, 'energy': -111.8973417521, 'Ova': 0.9169, 'weV': 12.412, 'DPab': 0.0}]
sym = 2
[{'No.': 1, 'f': 88.8888, 'energy': -112.1933869555, 'Ova': 0.5112, 'weV': 4.3562, 'DPab': 0.0}]
sym = 3
[{'No.': 1, 'f': 0.3017, 'energy': -111.6950889318, 'Ova': 0.563, 'weV': 17.9156, 'DPab': 0.0}]
sym = 4
[{'No.': 1, 'f': 0.0114, 'energy': -112.0012697504, 'Ova': 0.5931, 'weV': 9.584, 'DPab': 0.0}]
### JOB TYPE = TDDFT_ENE ###
nsym = 4
nstate = 4
nexit = [1, 1, 1, 1]
info =
sym = 1
[{'No.': 1, 'f': 0.0, 'energy': -112.1987475668, 'Ova': 0.947, 'weV': 4.2103, 'DPab': 2.0}]
sym = 2
[{'No.': 1, 'f': 0.0, 'energy': -112.2334312783, 'Ova': 0.5115, 'weV': 3.2665, 'DPab': 2.0}]
sym = 3
[{'No.': 1, 'f': 0.0, 'energy': -111.8335424533, 'Ova': 0.5869, 'weV': 14.1481, 'DPab': 2.0}]
sym = 4
[{'No.': 1, 'f': 0.0, 'energy': -112.0639429411, 'Ova': 0.5941, 'weV': 7.8786, 'DPab': 2.0}]
### JOB TYPE = TDDFT_SOC ###
npair= 45
ipair = 1
pairs = [0, 0, 0, 0, 0, 0, 1, 1]
socmat= [[0.0, 0.0]]
ipair = 2
pairs = [0, 0, 0, 1, 1, 1, 1, 1]
socmat= [[0.0, 0.0]]
ipair = 3
pairs = [0, 0, 0, 1, 2, 1, 1, 1]
socmat= [[0.0, 0.0]]
ipair = 4
pairs = [0, 0, 0, 1, 3, 1, 1, 1]
socmat= [[0.0, 0.0]]
ipair = 5
pairs = [0, 0, 0, 1, 4, 1, 1, 1]
socmat= [[0.0, 0.0]]
ipair = 6
pairs = [0, 0, 0, 2, 1, 1, 1, 3]
socmat= [[0.0, 0.0], [0.0, 0.0], [0.0, 0.0]]
ipair = 7
pairs = [0, 0, 0, 2, 2, 1, 1, 3]
socmat= [[0.0, -0.0], [0.0, 0.0003859934], [0.0, 0.0]]
ipair = 8
pairs = [0, 0, 0, 2, 3, 1, 1, 3]
socmat= [[9.63651e-05, -0.0], [0.0, -0.0], [9.63651e-05, 0.0]]
ipair = 9
pairs = [0, 0, 0, 2, 4, 1, 1, 3]
socmat= [[-0.0, -0.0002505808], [0.0, 0.0], [-0.0, 0.0002505808]]
ipair = 10
pairs = [1, 1, 1, 1, 1, 1, 1, 1]
socmat= [[0.0, 0.0]]
ipair = 11
pairs = [1, 1, 1, 1, 2, 1, 1, 1]
socmat= [[0.0, 0.0]]
ipair = 12
pairs = [1, 1, 1, 1, 3, 1, 1, 1]
socmat= [[0.0, 0.0]]
ipair = 13
pairs = [1, 1, 1, 1, 4, 1, 1, 1]
socmat= [[0.0, 0.0]]
ipair = 14
pairs = [1, 1, 1, 2, 1, 1, 1, 3]
socmat= [[0.0, 0.0], [0.0, 0.0], [0.0, 0.0]]
ipair = 15
pairs = [1, 1, 1, 2, 2, 1, 1, 3]
socmat= [[0.0, -0.0], [0.0, -0.000267303], [0.0, 0.0]]
ipair = 16
pairs = [1, 1, 1, 2, 3, 1, 1, 3]
socmat= [[9.9813e-06, -0.0], [0.0, 0.0], [9.9813e-06, 0.0]]
ipair = 17
pairs = [1, 1, 1, 2, 4, 1, 1, 3]
socmat= [[-0.0, 0.0001380162], [0.0, -0.0], [-0.0, -0.0001380162]]
ipair = 18
pairs = [1, 2, 1, 1, 2, 1, 1, 1]
socmat= [[0.0, 0.0]]
ipair = 19
pairs = [1, 2, 1, 1, 3, 1, 1, 1]
socmat= [[0.0, 0.0]]
ipair = 20
pairs = [1, 2, 1, 1, 4, 1, 1, 1]
socmat= [[0.0, 0.0]]
ipair = 21
pairs = [1, 2, 1, 2, 1, 1, 1, 3]
socmat= [[-0.0, 0.0], [0.0, 0.0002395748], [-0.0, -0.0]]
ipair = 22
pairs = [1, 2, 1, 2, 2, 1, 1, 3]
socmat= [[0.0, 0.0], [0.0, 0.0], [0.0, 0.0]]
ipair = 23
pairs = [1, 2, 1, 2, 3, 1, 1, 3]
socmat= [[-0.0, 6.71293e-05], [0.0, 0.0], [-0.0, -6.71293e-05]]
ipair = 24
pairs = [1, 2, 1, 2, 4, 1, 1, 3]
socmat= [[0.0001918886, -0.0], [0.0, 0.0], [0.0001918886, 0.0]]
ipair = 25
pairs = [1, 3, 1, 1, 3, 1, 1, 1]
socmat= [[0.0, 0.0]]
ipair = 26
pairs = [1, 3, 1, 1, 4, 1, 1, 1]
socmat= [[0.0, 0.0]]
ipair = 27
pairs = [1, 3, 1, 2, 1, 1, 1, 3]
socmat= [[5.3791e-06, 0.0], [0.0, 0.0], [5.3791e-06, -0.0]]
ipair = 28
pairs = [1, 3, 1, 2, 2, 1, 1, 3]
socmat= [[0.0, -9.33422e-05], [0.0, -0.0], [0.0, 9.33422e-05]]
ipair = 29
pairs = [1, 3, 1, 2, 3, 1, 1, 3]
socmat= [[0.0, 0.0], [0.0, 0.0], [0.0, 0.0]]
ipair = 30
pairs = [1, 3, 1, 2, 4, 1, 1, 3]
socmat= [[-0.0, 0.0], [0.0, 3.9987e-06], [-0.0, -0.0]]
ipair = 31
pairs = [1, 4, 1, 1, 4, 1, 1, 1]
socmat= [[0.0, 0.0]]
ipair = 32
pairs = [1, 4, 1, 2, 1, 1, 1, 3]
socmat= [[0.0, -0.0001082041], [0.0, 0.0], [0.0, 0.0001082041]]
ipair = 33
pairs = [1, 4, 1, 2, 2, 1, 1, 3]
socmat= [[-0.0001922613, 0.0], [0.0, -0.0], [-0.0001922613, -0.0]]
ipair = 34
pairs = [1, 4, 1, 2, 3, 1, 1, 3]
socmat= [[-0.0, 0.0], [0.0, -2.31593e-05], [-0.0, -0.0]]
ipair = 35
pairs = [1, 4, 1, 2, 4, 1, 1, 3]
socmat= [[0.0, 0.0], [0.0, 0.0], [0.0, 0.0]]
ipair = 36
pairs = [2, 1, 1, 2, 1, 1, 3, 3]
socmat= [[0.0, 0.0], [0.0, 0.0], [0.0, 0.0], [0.0, -0.0], [0.0, 0.0], [0.0, 0.0], [0.0, -0.0], [0.0, -0.0], [0.0, 0.0]]
ipair = 37
pairs = [2, 1, 1, 2, 2, 1, 3, 3]
socmat= [[0.0, -0.0002418587], [0.0, 0.0], [0.0, 0.0], [-0.0, 0.0], [0.0, 0.0], [0.0, 0.0], [0.0, 0.0], [-0.0, 0.0], [0.0, 0.0002418587]]
ipair = 38
pairs = [2, 1, 1, 2, 3, 1, 3, 3]
socmat= [[0.0, -0.0], [-2.7796e-06, 0.0], [0.0, 0.0], [2.7796e-06, 0.0], [0.0, 0.0], [-2.7796e-06, 0.0], [0.0, 0.0], [2.7796e-06, 0.0], [0.0, 0.0]]
ipair = 39
pairs = [2, 1, 1, 2, 4, 1, 3, 3]
socmat= [[0.0, -0.0], [-0.0, -0.0001122211], [0.0, 0.0], [0.0, -0.0001122211], [0.0, 0.0], [-0.0, -0.0001122211], [0.0, 0.0], [0.0, -0.0001122211], [0.0, 0.0]]
ipair = 40
pairs = [2, 2, 1, 2, 2, 1, 3, 3]
socmat= [[0.0, 0.0], [0.0, 0.0], [0.0, 0.0], [0.0, -0.0], [0.0, 0.0], [0.0, 0.0], [0.0, -0.0], [0.0, -0.0], [0.0, 0.0]]
ipair = 41
pairs = [2, 2, 1, 2, 3, 1, 3, 3]
socmat= [[0.0, -0.0], [0.0, 6.64953e-05], [0.0, 0.0], [-0.0, 6.64953e-05], [0.0, 0.0], [0.0, 6.64953e-05], [0.0, 0.0], [-0.0, 6.64953e-05], [0.0, 0.0]]
ipair = 42
pairs = [2, 2, 1, 2, 4, 1, 3, 3]
socmat= [[0.0, 0.0], [0.000192495, 0.0], [0.0, 0.0], [-0.000192495, 0.0], [0.0, 0.0], [0.000192495, 0.0], [0.0, 0.0], [-0.000192495, 0.0], [0.0, -0.0]]
ipair = 43
pairs = [2, 3, 1, 2, 3, 1, 3, 3]
socmat= [[0.0, 0.0], [0.0, 0.0], [0.0, 0.0], [0.0, -0.0], [0.0, 0.0], [0.0, 0.0], [0.0, -0.0], [0.0, -0.0], [0.0, 0.0]]
ipair = 44
pairs = [2, 3, 1, 2, 4, 1, 3, 3]
socmat= [[0.0, -1.55095e-05], [-0.0, -0.0], [0.0, 0.0], [0.0, -0.0], [0.0, 0.0], [-0.0, -0.0], [0.0, 0.0], [0.0, -0.0], [0.0, 1.55095e-05]]
ipair = 45
pairs = [2, 4, 1, 2, 4, 1, 3, 3]
socmat= [[0.0, 0.0], [0.0, 0.0], [0.0, 0.0], [0.0, -0.0], [0.0, 0.0], [0.0, 0.0], [0.0, -0.0], [0.0, -0.0], [0.0, 0.0]]
### JOB TYPE = RESP_EXGRAD ###
nstate/natom= 8 4
istate= 1
state = [1, 1, 1]
energy= -111.897341752
egrad =
1 -0.0000000000 -0.0000000000 0.4136839017
2 0.0000000000 -0.0000000000 -0.4346071844
3 -0.0030391817 0.0000000000 0.0104616413
4 0.0030391817 0.0000000000 0.0104616413
istate= 2
state = [1, 2, 1]
energy= -112.193386955
egrad =
1 -0.0000000000 -0.0000000000 0.2425215017
2 0.0000000000 -0.0000000000 -0.2013989026
3 -0.0229461214 0.0000000000 -0.0205612996
4 0.0229461214 0.0000000000 -0.0205612996
istate= 3
state = [1, 3, 1]
energy= -111.695088932
egrad =
1 -0.0000000000 0.0000000000 -0.0010564203
2 0.0000000000 -0.0000000000 -0.2697570388
3 0.1631768518 0.0000000000 0.1354067295
4 -0.1631768518 0.0000000000 0.1354067295
istate= 4
state = [1, 4, 1]
energy= -112.00126975
egrad =
1 -0.0000000000 -0.0000000000 0.3767555079
2 0.0000000000 -0.0000000000 -0.3221802249
3 -0.0071175389 0.0000000000 -0.0272876415
4 0.0071175389 0.0000000000 -0.0272876415
istate= 5
state = [2, 1, 1]
energy= -112.198747567
egrad =
1 -0.0000000000 -0.0000000000 0.4885322307
2 0.0000000000 -0.0000000000 -0.4641017184
3 -0.0191644721 0.0000000000 -0.0122152562
4 0.0191644721 0.0000000000 -0.0122152562
istate= 6
state = [2, 2, 1]
energy= -112.233431278
egrad =
1 -0.0000000000 -0.0000000000 0.2631090310
2 0.0000000000 -0.0000000000 -0.2100776374
3 -0.0264667592 0.0000000000 -0.0265156968
4 0.0264667592 0.0000000000 -0.0265156968
istate= 7
state = [2, 3, 1]
energy= -111.833542453
egrad =
1 -0.0000000000 0.0000000000 -0.2969301734
2 0.0000000000 -0.0000000000 -0.0134824551
3 0.2561475309 -0.0000000000 0.1552063142
4 -0.2561475309 -0.0000000000 0.1552063142
istate= 8
state = [2, 4, 1]
energy= -112.063942941
egrad =
1 -0.0000000000 -0.0000000000 0.3514891824
2 0.0000000000 -0.0000000000 -0.2943029219
3 -0.0149237261 0.0000000000 -0.0285931303
4 0.0149237261 0.0000000000 -0.0285931303
### JOB TYPE = RESP_FNAC ###
npair/natom= 16 4
ipair = 1
pairs = [0, 0, 0, 1, 1, 1]
epair = [-112.35347426254684, -111.89734175213182]
nacmat=
[-0.0, 0.0, -0.1642594137]
[0.0, 0.0, 0.0619337655]
[0.0249537306, -0.0, 0.0741276177]
[-0.0249537306, -0.0, 0.0741276177]
ipair = 2
pairs = [0, 0, 0, 1, 2, 1]
epair = [-112.35347426254684, -112.19338695546372]
nacmat=
[0.0, -0.0, -0.0]
[-0.0, 0.0, -0.0]
[-0.0, -0.3084825076, -0.0]
[-0.0, 0.3084825076, 0.0]
ipair = 3
pairs = [0, 0, 0, 1, 3, 1]
epair = [-112.35347426254684, -111.69508893176938]
nacmat=
[-0.2395755087, 0.0, 0.0]
[0.1091754128, -0.0, -0.0]
[-0.1355182046, 0.0, -0.0972633809]
[-0.1355182046, -0.0, 0.0972633809]
ipair = 4
pairs = [0, 0, 0, 1, 4, 1]
epair = [-112.35347426254684, -112.00126975036943]
nacmat=
[-0.0, -0.3757009746, -0.0]
[-0.0, 0.7088608799, 0.0]
[-0.0, -0.0870383529, -0.0]
[0.0, -0.0870383529, -0.0]
ipair = 5
pairs = [1, 1, 1, 1, 2, 1]
epair = [-111.89734175213182, -112.19338695546372]
nacmat=
[-0.0, 0.0, -0.0]
[0.0, 0.0, 0.0]
[0.0, 0.0781656512, 0.0]
[0.0, -0.0781656512, -0.0]
ipair = 6
pairs = [1, 1, 1, 1, 3, 1]
epair = [-111.89734175213182, -111.69508893176938]
nacmat=
[0.0592465847, 0.0, 0.0]
[0.285626323, -0.0, -0.0]
[-0.1797565656, 0.0, -0.2123344574]
[-0.1797565857, -0.0, 0.2123344574]
ipair = 7
pairs = [1, 2, 1, 1, 3, 1]
epair = [-112.19338695546372, -111.69508893176938]
nacmat=
[0.0, -0.3931299931, -0.0]
[0.0, 0.1477346234, -0.0]
[0.0, 0.1640143348, 0.0]
[-0.0, 0.1640143348, 0.0]
ipair = 8
pairs = [1, 1, 1, 1, 4, 1]
epair = [-111.89734175213182, -112.00126975036943]
nacmat=
[0.0, -0.3416632221, -0.0]
[0.0, 0.0175298544, 0.0]
[0.0, 0.1474282182, 0.0]
[-0.0, 0.1474282182, 0.0]
ipair = 9
pairs = [1, 2, 1, 1, 4, 1]
epair = [-112.19338695546372, -112.00126975036943]
nacmat=
[-0.71061252, -0.0, 0.0]
[0.6594135245, 0.0, -0.0]
[0.0594083452, -0.0, -0.0454566405]
[0.0594083452, 0.0, 0.0454566405]
ipair = 10
pairs = [1, 3, 1, 1, 4, 1]
epair = [-111.69508893176938, -112.00126975036943]
nacmat=
[0.0, -0.0, -0.0]
[-0.0, 0.0, 0.0]
[-0.0, 0.0025202585, -0.0]
[0.0, -0.0025202585, -0.0]
ipair = 11
pairs = [2, 1, 1, 2, 2, 1]
epair = [-112.19874756677972, -112.23343127829399]
nacmat=
[-0.0, 0.0, 0.0]
[-0.0, -0.0, 0.0]
[0.0, 0.2926613968, 0.0]
[0.0, -0.2926613968, -0.0]
ipair = 12
pairs = [2, 1, 1, 2, 3, 1]
epair = [-112.19874756677972, -111.83354245330469]
nacmat=
[0.0501232837, 0.0, -0.0]
[-0.0169144001, -0.0, 0.0]
[-0.0040500362, -0.0, 0.0005938735]
[-0.0040499994, 0.0, -0.0005938735]
ipair = 13
pairs = [2, 2, 1, 2, 3, 1]
epair = [-112.23343127829399, -111.83354245330469]
nacmat=
[0.0, -0.3814255489, -0.0]
[-0.0, 0.0951559803, -0.0]
[0.0, 0.1687002906, 0.0]
[-0.0, 0.1687002906, 0.0]
ipair = 14
pairs = [2, 1, 1, 2, 4, 1]
epair = [-112.19874756677972, -112.06394294114064]
nacmat=
[-0.0, 0.490738486, 0.0]
[-0.0, -0.5361069059, -0.0]
[-0.0, -0.0483178262, -0.0]
[0.0, -0.0483178262, -0.0]
ipair = 15
pairs = [2, 2, 1, 2, 4, 1]
epair = [-112.23343127829399, -112.06394294114064]
nacmat=
[-0.6691857117, -0.0, 0.0]
[0.6764960763, 0.0, -0.0]
[0.0467607902, -0.0, -0.0522083054]
[0.0467607902, 0.0, 0.0522083054]
ipair = 16
pairs = [2, 3, 1, 2, 4, 1]
epair = [-111.83354245330469, -112.06394294114064]
nacmat=
[-0.0, 0.0, 0.0]
[0.0, -0.0, -0.0]
[-0.0, -0.0002096409, -0.0]
[-0.0, 0.0002096409, 0.0]
Final status: ierror= 0