6.1 What is in our input file? 👀#
If you go to the repository program, you should see that a new folder with the name of the molecule was created. For the example that we ran, the folder should be called “water”. The following archives can be found:
COSMO_TZVPD folder
energy_TZVPD folder
6.1.2 What is TZVPD ❓#
TZVPD stands for Triple-Zeta Valence with Polarization and Diffuse functions. It is a type of basis set used in quantum chemistry calculations, in this case is used by the ORCA software. Basis sets are important in computational chemistry because they define the set of functions used to describe the electronic wave function of molecules. They are a collection of functions used to create and model the molecular orbitals of a system.
Triple-Zeta (TZ): it means that three functions are used to describe each valence orbital, providing a more accurate representation compared to single-zeta or double-zeta basis sets. The valence orbitals are the outermost orbitals of an atom that are involved in chemical bonding. The different types of valence orbitals are s, p, d and sometimes f.
Valence: it refers to the valence electrons
Polarization (P): adds extra features to account for how the electron cloud is distorted by the molecular environment, improving the accuracy of the calculations.
Think about a water molecule (H₂O). The oxygen atom has s and p orbitals that help it bond with hydrogen. When it forms bonds with hydrogen, the electron cloud around oxygen can become distorted. Adding polarization functions (e.g. d-type functions for oxygen) can help us model this distortion better.
Diffuse (D): includes extra functions that are more spread out in space. These are important for accurately describing anions and systems with weakly bound electrons.
Think about a chloride ion (Cl⁻). The extra electron in Cl⁻ is not as tightly bound as the electrons in a neutral chlorine atom. To describe this loosely bound electron correctly, we add special functions (e.g., additional s and p functions with larger exponents) to the basis set. This allows the basis set to capture the electron’s extended distribution.
You can find more about it in the Orca documentation
6.1.3 COSMO_TZVPD#
Opening the folder we see two files: water_c000 and log_output. The latter contains all details of the ORCA program and the steps taken to perform the necessary calculations to produce the .orcacosmo file.
Let’s analyze what the water_c000 file has:
ENERGY:
This is the energy obtained with the CPCM calculations i.e. as an ideal conductor in a.u. (atomic units).DIPOLE MOMENT:
The values represent the x, y, and z components of the dipole moment vector. The dipole moment is defined as a vector quantity that quantifies the separation between positive and negative charges within a molecule.XYZ_FILE:
Coordinates form the ORCA job. Here we can see the number of atoms (for water = 3) and the cartesian coordinates (x,y,z) in Angstroms.COSMO:
Molecule characteristics (no. of atoms, surface points), surface and epsilon function types (how the molecular surface is constructed for the COSMO calculations), the dielectric constant of the solvent, (measures the ability to reduce the electrostatic interactions between charged particles). Furthermore, we have the dielectric energy, (the total energy that we need to submerge our molecule from the gas phase to the CPCM phase)Cartesian Coordinates, RADII and Atomic Number:
Cartesian coordinates in atomic units (a.u.), atomic radii, and atomic numbers for each atom in the molecule.Surface points:
This section has the following columns3D coordinates of the center of the area.
the area of our segments
the chemical potential of the segment
w_leb, Switch_F and G_with are part of the ORCA algorithm to generate the position of the segments and its properties
the indices of the atoms (for water, three atoms ∴ 0, 1, 2 )
COSMO_corrected:
Corrected values for the dielectric energy and the CPCM charges after distributing the molecule’s charge between the cavities. A cavity is like a bubble surrounding the whole molecule. For some bigger atoms that have a higher charge, the electrons might be outside of the cavity, also known as outlying charge. To better represent how the molecule’s electron distribution looks, ORCA implemented a correction where they distributed the outlying charge throughout the whole cavity
Adjacency matrix:
The connections between atoms of the molecule. Node 0 represents the oxygen atom and nodes 1 and 2 the two hydrogen atoms.
#⚠️⚠️⚠️
water_c000 = r"orcacosmo_files\water\COSMO_TZVPD\water_c000.orcacosmo"
# Open and read the .orcacosmo file
with open(water_c000, 'r') as file:
contents = file.read()
# Print the contents
print(contents)
water_c000 : DFT_CPCM_BP86_def2-TZVP+def2-TZVPD_SP
##################################################
#ENERGY
FINAL SINGLE POINT ENERGY -76.479237520247
##################################################
#DIPOLE MOMENT (Debye)
0.000045 -2.302726 0.000000
##################################################
#XYZ_FILE
3
Coordinates from ORCA-job geo_opt_tzvp E -76.476432672917
O -0.00079486659693 0.40142783814538 0.00000000000000
H -0.76479998168973 -0.20221738824042 0.00000000000000
H 0.76559484828666 -0.19921044990496 0.00000000000000
##################################################
#COSMO
3 # Number of atoms
252 # Number of surface points
2 # Surface type
0 # Epsilon function type
1 # Print level
0 # FEps X flag
110 # Number of Leb. points (used if Isodens = 0)
1 # Isodensity discr. scheme
5.000000000 # Threshold for H atoms (Ncharges/Angstroem^2) for Isodens = 1
5.000000000 # Threshold for non-H atoms (Ncharges/Angstroem^2) for Isodens = 1
0.000000000 # FEps X parameter
0.035710648 # cutoff segment area (a.u.)
0.00000010000000 # cutoff switching function
171.174913270 # Volume
153.190631794 # Area
-0.012548950 # CPCM dielectric energy
-0.015758673 # One-electron operator energy
#------------------------------------------------------------
# CARTESIAN COORDINATES (A.U.) + RADII (A.U.) + ATOMIC NUMBER
#------------------------------------------------------------
-0.001502080 0.758588677 0.000000000 3.250328950 8
-1.445262513 -0.382135483 0.000000000 2.456643974 1
1.446764593 -0.376453193 0.000000000 2.456643974 1
#------------------------------------------------------------
# SURFACE POINTS (A.U.) (Hint - charge NOT scaled by FEps)
#------------------------------------------------------------
X Y Z area potential charge w_leb Switch_F G_width atom
-0.001502080 4.008917627 0.000000000 0.236622021 -0.066172204 0.001061458 0.022397551 1.00000000000000 10.07939148879902 0
-0.001502080 -2.491740274 0.000000000 0.204342317 0.069751051 -0.000806324 0.022397551 0.86358115176696 10.07939148879902 0
-0.001502080 0.758588677 3.250328950 0.236622021 -0.042026343 0.001188527 0.022397551 1.00000000000000 10.07939148879902 0
-0.001502080 0.758588677 -3.250328950 0.236622021 -0.042026343 0.001188527 0.022397551 1.00000000000000 10.07939148879902 0
-0.001502080 3.056918319 2.298329642 0.758971632 -0.064577408 0.003723818 0.071840759 1.00000000000000 5.62793562792147 0
-0.001502080 -1.539740965 2.298329642 0.758912205 0.020218897 0.000480553 0.071840759 0.99992170058670 5.62793562792147 0
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2.296827562 0.758588677 2.298329642 0.739171626 -0.005514008 0.000568259 0.071840759 0.97391206079688 5.62793562792147 0
-2.299831722 0.758588677 2.298329642 0.740526419 -0.005758323 0.000585497 0.071840759 0.97569709814880 5.62793562792147 0
2.296827562 0.758588677 -2.298329642 0.739171626 -0.005514008 0.000568259 0.071840759 0.97391206079688 5.62793562792147 0
-2.299831722 0.758588677 -2.298329642 0.740526419 -0.005758323 0.000585497 0.071840759 0.97569709814880 5.62793562792147 0
2.296827562 3.056918319 0.000000000 0.758971632 -0.040318381 0.001920492 0.071840759 1.00000000000000 5.62793562792147 0
-2.299831722 3.056918319 0.000000000 0.758971632 -0.040569389 0.001933170 0.071840759 1.00000000000000 5.62793562792147 0
1.875076214 2.635166971 1.876578294 0.739917670 -0.045843443 0.002561179 0.070037199 1.00000000000000 5.69993881575195 0
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2.180435112 2.940525869 1.021243586 0.744606843 -0.042051157 0.002092070 0.070481054 1.00000000000000 5.68196274193532 0
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2.180435112 1.779832263 2.181937192 0.744606836 -0.029894588 0.002015054 0.070481054 0.99999998957825 5.68196274193532 0
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1.019741506 2.940525869 2.181937192 0.744606843 -0.059374847 0.003351460 0.070481054 1.00000000000000 5.68196274193532 0
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1.019741506 -1.423348516 2.181937192 0.374289518 0.030826345 -0.000420515 0.070481054 0.50266730916957 5.68196274193532 0
-1.022745666 -1.423348516 2.181937192 0.366663245 0.030915017 -0.000419784 0.070481054 0.49242529508130 5.68196274193532 0
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1.122364875 3.808434796 0.000000000 0.670678841 -0.060826142 0.002612389 0.063483370 1.00000000000000 5.98693565867642 0
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3.048344039 1.882455632 0.000000000 0.667941166 -0.003265532 -0.000320575 0.063483370 0.99591805444115 5.98693565867642 0
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1.122364875 0.758588677 3.049846119 0.670678840 -0.034175930 0.002713523 0.063483370 0.99999999999720 5.98693565867642 0
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-0.001502080 -0.365278279 3.049846119 0.670678841 -0.018360449 0.002369249 0.063483370 0.99999999999999 5.98693565867642 0
-0.001502080 1.882455632 -3.049846119 0.670678841 -0.056735485 0.003466744 0.063483370 1.00000000000000 5.98693565867642 0
-0.001502080 -0.365278279 -3.049846119 0.670678841 -0.018360449 0.002369249 0.063483370 0.99999999999999 5.98693565867642 0
-0.001502080 3.808434796 1.123866955 0.670678841 -0.066160784 0.002971058 0.063483370 1.00000000000000 5.98693565867642 0
-0.001502080 -2.291257443 1.123866955 0.601394772 0.057249560 -0.001707975 0.063483370 0.89669561016068 5.98693565867642 0
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2.621946985 -2.533776989 0.000000000 0.735261723 0.068558687 -0.003479594 0.121830917 1.00000000000000 5.71562495585747 2
0.271582201 -2.533776989 0.000000000 0.486194261 0.069160087 -0.001863724 0.121830917 0.66125332825795 5.71562495585747 2
3.604088389 0.798729199 0.000000000 0.733768969 0.034728350 -0.003031834 0.121830917 0.99796976585344 5.71562495585747 2
3.604088389 -1.551635585 0.000000000 0.735261723 0.065652922 -0.003671929 0.121830917 1.00000000000000 5.71562495585747 2
2.621946985 -0.376453193 2.157323796 0.732508767 0.031590642 -0.002176271 0.121830917 0.99625581541340 5.71562495585747 2
2.621946985 -0.376453193 -2.157323796 0.732508767 0.031590642 -0.002176271 0.121830917 0.99625581541340 5.71562495585747 2
3.604088389 -0.376453193 1.175182392 0.735261719 0.050024841 -0.003206084 0.121830917 0.99999999480267 5.71562495585747 2
3.604088389 -0.376453193 -1.175182392 0.735261719 0.050024841 -0.003206084 0.121830917 0.99999999480267 5.71562495585747 2
1.446764593 -1.551635585 2.157323796 0.710604251 0.037930169 -0.001671579 0.121830917 0.96646436068642 5.71562495585747 2
1.446764593 -1.551635585 -2.157323796 0.710604251 0.037930169 -0.001671579 0.121830917 0.96646436068642 5.71562495585747 2
1.446764593 -2.533776989 1.175182392 0.735255808 0.060158601 -0.002786999 0.121830917 0.99999195599340 5.71562495585747 2
1.446764593 -2.533776989 -1.175182392 0.735255808 0.060158601 -0.002786999 0.121830917 0.99999195599340 5.71562495585747 2
##################################################
#COSMO_corrected
Corrected dielectric energy = -0.012505722
Total C-PCM charge = 0.000000000
C-PCM corrected charges:
0.001091047
-0.000798400
0.001217204
0.001217204
0.003813498
0.000565417
0.003813498
0.000565417
0.000644188
0.000661863
0.000644188
0.000661863
0.002008922
0.002021630
0.002647543
0.002656423
0.002647543
0.002656423
0.002178909
0.002190355
0.002178909
0.002190355
0.002100080
0.002111285
-0.000202102
-0.000204871
0.002100080
0.002111285
-0.000202102
-0.000204871
0.003439236
0.003443828
-0.000402915
-0.000402790
0.003439236
0.003443828
-0.000402915
-0.000402790
0.003303246
0.003306113
0.002217979
0.002218197
0.003303246
0.003306113
0.002217979
0.002218197
0.002895865
0.002900357
0.002895865
0.002900357
-0.000179570
-0.000145584
-0.000179570
-0.000145584
0.003146720
0.003152510
0.000078192
0.000076369
0.003146720
0.003152510
0.000078192
0.000076369
0.002926792
0.002933850
0.002926792
0.002933850
0.001532890
0.001547946
0.001532890
0.001547946
0.002720321
0.002721127
0.002388866
0.002389316
0.002720321
0.002721127
0.002388866
0.002389316
0.002358271
0.002359929
-0.000344465
-0.000312737
0.002358271
0.002359929
-0.000344465
-0.000312737
-0.000389773
-0.000416722
-0.000389773
-0.000416722
0.002691935
0.002697320
-0.000247299
-0.000215330
0.002789946
0.002792472
0.002789946
0.002792472
-0.000150071
-0.000150071
0.003545277
0.002444380
0.003545277
0.002444380
0.003050755
-0.001669108
0.003050755
-0.001669108
0.003428703
0.003431198
-0.000782100
-0.000771634
0.003428703
0.003431198
-0.000782100
-0.000771634
0.003753190
0.003755189
0.001610077
0.001605330
0.003753190
0.003755189
0.001610077
0.001605330
0.000094171
0.000122702
0.000094171
0.000122702
0.001191897
0.001208697
0.001191897
0.001208697
0.002629951
0.002636370
0.001522328
0.001529108
0.002629951
0.002636370
0.001522328
0.001529108
0.002588160
0.002596982
0.002588160
0.002596982
-0.001385146
-0.001197129
-0.000562204
-0.003187309
-0.000562204
-0.003187309
-0.000058565
-0.001205653
-0.000058565
-0.001205653
-0.002371786
-0.002582613
-0.002371786
-0.002582613
-0.002643900
-0.002897079
-0.002643900
-0.002897079
-0.000779570
-0.003573776
-0.000779570
-0.003573776
-0.002619507
-0.002992435
-0.002619507
-0.002992435
-0.001768406
-0.002720668
-0.001768406
-0.002720668
-0.000260533
-0.002479377
-0.000260533
-0.002479377
-0.001996672
-0.003147021
-0.001996672
-0.003147021
-0.002786774
-0.003361116
-0.002786774
-0.003361116
-0.001878965
-0.003380972
-0.002923923
-0.003567785
-0.002080143
-0.002080143
-0.003101627
-0.003101627
-0.001603874
-0.001603874
-0.002696530
-0.002696530
-0.001387007
-0.001195473
-0.000602999
-0.003186341
-0.000602999
-0.003186341
-0.000060627
-0.001205762
-0.000060627
-0.001205762
-0.002579214
-0.002372765
-0.002579214
-0.002372765
-0.002648901
-0.002899498
-0.002648901
-0.002899498
-0.000830504
-0.003572666
-0.000830504
-0.003572666
-0.002638504
-0.002994706
-0.002638504
-0.002994706
-0.002717683
-0.001756887
-0.002717683
-0.001756887
-0.000271919
-0.002478798
-0.000271919
-0.002478798
-0.003144118
-0.001973864
-0.003144118
-0.001973864
-0.002840435
-0.003362195
-0.002840435
-0.003362195
-0.003378260
-0.001836545
-0.002938574
-0.003568434
-0.002087000
-0.002087000
-0.003107186
-0.003107186
-0.001598653
-0.001598653
-0.002694567
-0.002694567
##################################################
#ADJACENCY_MATRIX
0 1 1
1 0 0
1 0 0
6.1.4 energy_TZVPD 📂#
The folder contains an xyz file with the same name: water_c000:
Number of Atoms: The first line 3 indicates that the number of atoms in our molecule
Energy: The energy of the molecule in the gas phase
Atomic Coordinates: atomic symbols and their Cartesian coordinates in space. Each line corresponds to an atom.
# ⚠️⚠️⚠️
energy = r"orcacosmo_files\water\energy_TZVPD\water_c000.xyz"
# Open and read the .orcacosmo file
with open(energy, 'r') as file:
contents = file.read()
# Print the contents
print(contents)
3
energy: -76.4684885136930035
O -0.0007809143160200 0.3969563993601200 0.0000000000000000
H -0.7671274283801700 -0.1999882198486500 0.0000000000000000
H 0.7679083426961900 -0.1969681795114700 0.0000000000000000