QuantumPatch Output Files

QuantumPatch differentiates between Analysis Runtime and Error output files in the respective directories Analysis quantumpatch_runtime_files and quantumpatch_error_files. For most applications of QuantumPatch, the Analysis subdirectory will be the most informative and important subdirectory. The directory quantumpatch_runtime_files contains all files required to rerun or restart a QuantumPatch run at its respective state and the quantumpatch_error_files subdirectory is only generated in case of errors during a specific DFT computation and can be deleted after figuring out the possible convergence issues, e.g. by changing settings for a fallback engine. Unless quantumpatch_runtime_files was deleted, the Analysis folder can be regenerated using another one CPU run of QuantumPatch.

The QuantumPatch Analysis subdirectory

Depending on the setting in QuantumPatch.type, the QuantumPatch Analysis subdirectory has different outputs.

uncharged_equilibration computations

Uncharged_equilibration is used to compute most of all energetic disorder and optionally transfer integrals J. Information for pairs of $MOLTYPE1 and $MOLTYPE2 can be found in Analysis/energy/$MOLTYPE1_$MOLTYPE2_analysis_info.yml . The most important values in this file are

sigma-delta-homo: 0.022973691859927602
sigma-delta-lumo: 0.027603339354790243

It is very important to not that this is NOT the standard deviation of the delta HOMO array, but 1/sqrt(2) the standard deviation of the delta HOMO array. The reason is that the energetic disorder references the disorder of the absolute energies, but is calculated from the energy difference between adjacent pairs to increase accuracy and accounts for correlations of adjacent pairs.

An exemplary output file:

comdist: [7.400910560082673, 4.777731299148571, 6.244998836939266, 5.589848087296582,
  6.994684197142247, 6.4832027195637325, 5.168490728276876, 8.162138799786625, 6.626383280394988,
  5.048885631339176]
energies-delta-homo: [0.0023115354182765557, -0.04115199795327129, 0.04047320378288166,
  0.002990329588666185, 0.06362328250883298, 0.10409648629171464, 0.06593481792710953,
  0.06294448833844335, -0.038161668364605106, -0.0006787941703896294]
energies-delta-lumo: [-0.02546533798159545, -0.0857821643655099, 0.08437069961007948,
  -0.024053873226165035, -0.04927936796368737, 0.03509133164639211, -0.07474470594528282,
  -0.050690832719117784, -0.10983603759167493, -0.0014114647554304138]
energies-homo: [-5.365838066403557, -5.299903248476448, -5.363526530985281, -5.4039997347681625,
  -5.362847736814891]
energies-lumo: [-0.9989677223318854, -1.0737124282771682, -1.0244330603134808, -1.1088037599235603,
  -1.0230215955580504]
energies-total: [-8361.2991941, -8361.5568557, -8361.5705681, -8361.3324073, -8361.3562509]
mean-delta-homo: 0.02623816833676589
mean-delta-lumo: -0.03018017532919921
mindist: [3.517203576706927, 2.7287583256858783, 2.002145099636887, 3.2934494075361167,
  2.431741762605561, 1.9282740987733047, 2.431691797905318, 5.188619855028889, 3.267325817851657,
  2.7089123278541143]
molecule_ids: [35, 21, 22, 23, 30]
pairs:
- [22, 35]
- [23, 30]
- [22, 23]
- [30, 35]
- [21, 22]
- [21, 23]
- [21, 35]
- [21, 30]
- [23, 35]
- [22, 30]
sigma-delta-homo: 0.022973691859927602
sigma-delta-lumo: 0.027603339354790243

Here comdist are the center of mass distances of pairs of molecules, energies-delta-homo the energy delta between pairs of molecules, energies-homo the actual energies, mindist the minimum atom distance between a pair of molecules, pairs the ids of the pairs in the order of the other pair-wise values, molecule_ids the ids of the molecules in the non pair-wise values. The energies are also plot in the file Delta_E_$MOLTYPE1_$MOLTYPE2.png with its respective fit of the disorder.

If also Js were calculated the file mentioned above also contains:

j_homo: [0.00041403495667604305, -0.024932529513548674, 0.012075018623190853, 0.001221888230259073,
  0.0006487924129200816, -0.005491244889517493, 0.010354215346221229, 2.8145017070668093e-05,
  0.0003914093450712345, 0.01399380458321231]
j_lumo: [-1.3042755075433178e-05, 0.014736605529065945, 0.00034381045545732426, 0.00046493884830447346,
  -6.933968642889525e-05, 7.222570433784804e-05, 0.003353805255906561, 2.2255413361317983e-05,
  -7.444178095386454e-05, -0.06601044604833411]
dexter: [1.1459300762864084e-11, 3.2303658297827466e-06, -4.409182720941458e-09, -1.1598502835443854e-08,
  -4.1268887121548176e-10, 2.714147006498751e-09, 6.7780401608250165e-09, -5.443121231204768e-10,
  8.038515230640007e-10, 2.7323458546530613e-05]

Additionaly plots of the J distributions can be found in the Analysis/dimer/ folder.

matrix_eaip computations

The matrix_eaip computations main results are electron affinity and ionization potential of sites. In addition the reorganization energy can be calculated.

EAIP

For all centers in the EAIP computation EAIP is evaluated. The files Analysis/EAIP/eaip_$MOLTYPE_EA_summary contain a per molecule analysis of the EAIP together with a summary of all a mean EAIP and its standard deviation:

The example file shows the EA with full environment double counting correction as "mean_full_env" and the result without double counting correction as mean_single_delta:

30: [1.6815448499983177, 1.5224298000011913]
22: [1.4106706000020495, 1.1529618999993545]
23: [1.4254134000002523, 1.1109109000008175]
35: [1.6748924999992596, 1.6823855000002368]
21: [1.2937219499999628, 0.9927271000015025]
mean_full_env: 1.4972486599999684
mean_single_delta: 1.2922830400006204
std_full_env: 0.15466195800729918
std_single_delta: 0.26350994472491096

Also for each core molecule setup in the QuantumPatch.core specification a file called Matrix_EAIPMatrix-EAIP-analysis-$MOLTYPE-$MOLSTATE.yml, which gives access to the raw data used in the summary calculation. This contains all information about the energies of the molecule referenced in $MOLSTATE, i.e. the total energies of the charged and uncharged states with and without its respective electrostatic contribution (_vacuum) and the same info for all its environment molecules in yaml format:

30 <- molecule id of the center molecule:
  environment_molecules: 
    23: {total_e_charged: -8361.5279858, total_e_charged_vacuum: -8360.9310895, total_e_uncharged: -8361.3324073,
      total_e_uncharged_vacuum: -8361.0280059} <- identical information for all center molecules
    48: {total_e_charged: -8361.3555424, total_e_charged_vacuum: -8361.0066579, total_e_uncharged: -8361.1623782,
      total_e_uncharged_vacuum: -8361.0539987}
  total_e_charged: -8353.60123
  total_e_charged_vacuum: -8352.806788
  total_e_uncharged: -8361.3562509
  total_e_uncharged_vacuum: -8361.0359951

Lambda - reorganization energies

If the option Analysis.MatrixEAIP.do_lambda is set to true, also an analysis of the reorganization energies for the charge centers (System.Core) is carried out. The files of interest are called: lambda_environment_$MOLTYPE_hole.yml and contain a per molecule id rundown of the specific reorganization energies and the mean and sigma of all values:

30: {ene_c_geom_c_env: -8353.60123, ene_c_geom_uc_env: -8361.3710979, ene_uc_geom_c_env: -8353.4843464,
  ene_uc_geom_uc_env: -8361.3562509, lambda: 0.10203659999933734, lambda_1: 7.8719044999998005,
  lambda_2: -7.769867900000463}
22: {ene_c_geom_c_env: -8353.4699858, ene_c_geom_uc_env: -8361.6023433, ene_uc_geom_c_env: -8353.2221212,
  ene_uc_geom_uc_env: -8361.5705681, lambda: 0.21608940000078292, lambda_1: 8.348446899999544,
  lambda_2: -8.132357499998761}
23: {ene_c_geom_c_env: -8353.2103818, ene_c_geom_uc_env: -8361.3396639, ene_uc_geom_c_env: -8353.093841,
  ene_uc_geom_uc_env: -8361.3324073, lambda: 0.10928419999981998, lambda_1: 8.238566300000457,
  lambda_2: -8.129282100000637}
35: {ene_c_geom_c_env: -8353.145215, ene_c_geom_uc_env: -8361.3080508, ene_uc_geom_c_env: -8352.8624715,
  ene_uc_geom_uc_env: -8361.2991941, lambda: 0.2738867999996728, lambda_1: 8.436722599999484,
  lambda_2: -8.162835799999812}
21: {ene_c_geom_c_env: -8352.9384726, ene_c_geom_uc_env: -8361.6050412, ene_uc_geom_c_env: -8352.5156918,
  ene_uc_geom_uc_env: -8361.5568557, lambda: 0.37459530000160157, lambda_1: 9.041163900001266,
  lambda_2: -8.666568599999664}
mean: 0.21517846000024293
std: 0.10283569677762068

excitonic_preprocessing computations

Comment on output files here.

Next: DFT Engines