├── .gitignore ├── .readthedocs.yml ├── LICENSE ├── Makefile ├── README.md ├── make.bat ├── requirements.txt └── source ├── Project_01 ├── Project_01.ipynb ├── assets │ └── acetaldehyde.png ├── input │ ├── acetaldehyde.dat │ ├── allene.dat │ └── benzene.dat └── solution_01.py ├── Project_02 ├── Project_02.ipynb ├── input │ ├── 3c1b_geom.txt │ ├── 3c1b_hessian.txt │ ├── benzene_geom.txt │ ├── benzene_hessian.txt │ ├── h2o_geom.txt │ └── h2o_hessian.txt └── solution_02.py ├── Project_03 ├── Project_03.ipynb ├── assets │ └── Duv.png ├── input │ ├── ch4 │ │ └── STO-3G │ │ │ ├── enuc.dat │ │ │ ├── eri.dat │ │ │ ├── geom.dat │ │ │ ├── input.dat │ │ │ ├── mux.dat │ │ │ ├── muy.dat │ │ │ ├── muz.dat │ │ │ ├── s.dat │ │ │ ├── t.dat │ │ │ └── v.dat │ └── h2o │ │ ├── DZ │ │ ├── enuc.dat │ │ ├── eri.dat │ │ ├── geom.dat │ │ ├── input.dat │ │ ├── mux.dat │ │ ├── muy.dat │ │ ├── muz.dat │ │ ├── s.dat │ │ ├── t.dat │ │ └── v.dat │ │ ├── DZP │ │ ├── enuc.dat │ │ ├── eri.dat │ │ ├── geom.dat │ │ ├── input.dat │ │ ├── mux.dat │ │ ├── muy.dat │ │ ├── muz.dat │ │ ├── s.dat │ │ ├── t.dat │ │ └── v.dat │ │ └── STO-3G │ │ ├── enuc.dat │ │ ├── eri.dat │ │ ├── geom.dat │ │ ├── input.dat │ │ ├── mux.dat │ │ ├── muy.dat │ │ ├── muz.dat │ │ ├── s.dat │ │ ├── t.dat │ │ └── v.dat └── solution_03.py ├── Project_04 ├── Project_04.ipynb ├── input │ ├── ch4 │ │ └── STO-3G │ │ │ ├── enuc.dat │ │ │ ├── eri.dat │ │ │ ├── geom.dat │ │ │ ├── input.dat │ │ │ ├── mux.dat │ │ │ ├── muy.dat │ │ │ ├── muz.dat │ │ │ ├── s.dat │ │ │ ├── t.dat │ │ │ └── v.dat │ └── h2o │ │ ├── DZ │ │ ├── enuc.dat │ │ ├── eri.dat │ │ ├── geom.dat │ │ ├── input.dat │ │ ├── mux.dat │ │ ├── muy.dat │ │ ├── muz.dat │ │ ├── s.dat │ │ ├── t.dat │ │ └── v.dat │ │ ├── DZP │ │ ├── enuc.dat │ │ ├── eri.dat │ │ ├── geom.dat │ │ ├── input.dat │ │ ├── mux.dat │ │ ├── muy.dat │ │ ├── muz.dat │ │ ├── s.dat │ │ ├── t.dat │ │ └── v.dat │ │ └── STO-3G │ │ ├── enuc.dat │ │ ├── eri.dat │ │ ├── geom.dat │ │ ├── input.dat │ │ ├── mux.dat │ │ ├── muy.dat │ │ ├── muz.dat │ │ ├── s.dat │ │ ├── t.dat │ │ └── v.dat └── solution_04.py ├── Project_05 ├── Project_05.ipynb ├── demo_data_h2o_sto3g.dat ├── input │ ├── ch4 │ │ └── STO-3G │ │ │ ├── enuc.dat │ │ │ ├── eri.dat │ │ │ ├── geom.dat │ │ │ ├── input.dat │ │ │ ├── mux.dat │ │ │ ├── muy.dat │ │ │ ├── muz.dat │ │ │ ├── s.dat │ │ │ ├── t.dat │ │ │ └── v.dat │ └── h2o │ │ ├── DZ │ │ ├── enuc.dat │ │ ├── eri.dat │ │ ├── geom.dat │ │ ├── input.dat │ │ ├── mux.dat │ │ ├── muy.dat │ │ ├── muz.dat │ │ ├── s.dat │ │ ├── t.dat │ │ └── v.dat │ │ ├── DZP │ │ ├── enuc.dat │ │ ├── eri.dat │ │ ├── geom.dat │ │ ├── input.dat │ │ ├── mux.dat │ │ ├── muy.dat │ │ ├── muz.dat │ │ ├── s.dat │ │ ├── t.dat │ │ └── v.dat │ │ └── STO-3G │ │ ├── enuc.dat │ │ ├── eri.dat │ │ ├── geom.dat │ │ ├── input.dat │ │ ├── mux.dat │ │ ├── muy.dat │ │ ├── muz.dat │ │ ├── s.dat │ │ ├── t.dat │ │ └── v.dat └── solution_05.py ├── conf.py └── index.rst /.gitignore: -------------------------------------------------------------------------------- 1 | # ajz34 2 | .idea 3 | 4 | # Byte-compiled / optimized / DLL files 5 | __pycache__/ 6 | *.py[cod] 7 | *$py.class 8 | 9 | # C extensions 10 | *.so 11 | 12 | # Distribution / packaging 13 | .Python 14 | build/ 15 | develop-eggs/ 16 | dist/ 17 | downloads/ 18 | eggs/ 19 | .eggs/ 20 | lib/ 21 | lib64/ 22 | parts/ 23 | sdist/ 24 | var/ 25 | wheels/ 26 | pip-wheel-metadata/ 27 | share/python-wheels/ 28 | *.egg-info/ 29 | .installed.cfg 30 | *.egg 31 | MANIFEST 32 | 33 | # PyInstaller 34 | # Usually these files are written by a python script from a template 35 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 36 | *.manifest 37 | *.spec 38 | 39 | # Installer logs 40 | pip-log.txt 41 | pip-delete-this-directory.txt 42 | 43 | # Unit test / coverage reports 44 | htmlcov/ 45 | .tox/ 46 | .nox/ 47 | .coverage 48 | .coverage.* 49 | .cache 50 | nosetests.xml 51 | coverage.xml 52 | *.cover 53 | *.py,cover 54 | .hypothesis/ 55 | .pytest_cache/ 56 | 57 | # Translations 58 | *.mo 59 | *.pot 60 | 61 | # Django stuff: 62 | *.log 63 | local_settings.py 64 | db.sqlite3 65 | db.sqlite3-journal 66 | 67 | # Flask stuff: 68 | instance/ 69 | .webassets-cache 70 | 71 | # Scrapy stuff: 72 | .scrapy 73 | 74 | # Sphinx documentation 75 | docs/_build/ 76 | 77 | # PyBuilder 78 | target/ 79 | 80 | # Jupyter Notebook 81 | .ipynb_checkpoints 82 | 83 | # IPython 84 | profile_default/ 85 | ipython_config.py 86 | 87 | # pyenv 88 | .python-version 89 | 90 | # pipenv 91 | # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. 92 | # However, in case of collaboration, if having platform-specific dependencies or dependencies 93 | # having no cross-platform support, pipenv may install dependencies that don't work, or not 94 | # install all needed dependencies. 95 | #Pipfile.lock 96 | 97 | # PEP 582; 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The text should be enclosed in the appropriate 184 | comment syntax for the file format. We also recommend that a 185 | file or class name and description of purpose be included on the 186 | same "printed page" as the copyright notice for easier 187 | identification within third-party archives. 188 | 189 | Copyright 2020 ajz34 (Zhenyu Zhu, Andrew J. Zhu, 祝震予) 190 | 191 | Licensed under the Apache License, Version 2.0 (the "License"); 192 | you may not use this file except in compliance with the License. 193 | You may obtain a copy of the License at 194 | 195 | http://www.apache.org/licenses/LICENSE-2.0 196 | 197 | Unless required by applicable law or agreed to in writing, software 198 | distributed under the License is distributed on an "AS IS" BASIS, 199 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 200 | See the License for the specific language governing permissions and 201 | limitations under the License. 202 | -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line, and also 5 | # from the environment for the first two. 6 | SPHINXOPTS ?= 7 | SPHINXBUILD ?= sphinx-build 8 | SOURCEDIR = source 9 | BUILDDIR = build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 21 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | Crawford’s Programming Exercises by Python (under-construction) 2 | ========================================== 3 | 4 | For documents on web-page, refer to https://pycrawfordprogproj.readthedocs.io/en/latest/index.html. 5 | 6 | ## Important message 7 | 8 | This is an ongoing project which uses awesome [Crawford’s Programming Projects](https://github.com/CrawfordGroup/ProgrammingProjects) as original materials, so in many cases, several sentences may be shamelessly ctrl-c/ctrl-v’ed with little or a little modification. The author of this repository really thanks original authors of the origin of this tutorial. 9 | 10 | The author also regards [PySCF](https://github.com/pyscf/pyscf) as one of the magnificent quantum packages. In this tutorial, [PySCF](https://github.com/pyscf/pyscf) may become the default SCF and orbital integral engine/interface. 11 | 12 | ## Preface 13 | 14 | This tutorial is intended to touch on many, but certainly not all, of the fundamentals of Python/PySCF programming with an emphasis on quantum chemistry. 15 | 16 | Currently, the author is not going to write fundamentals of python. So, before heading to the first project, the reader is suggested to review his/hers comprehension of python. Knowledge of other languages with OOP (object-oriented programming), and scientific calculation/simulation softwares (e.g., `MATLAB` and `Wolfram Mathematica`) is also appreciated. 17 | 18 | To begin work on the projects, you can create a clone of this repository. First, navigate to the directory where you would like to keep your programming projects. Then create the clone by this command 19 | 20 | ```bash 21 | git clone https://github.com/ajz34/PyCrawfordProgProj.git 22 | ``` 23 | 24 | Now you should see a directory called `PyCrawfordProgProj/source` inside. You will find all the files that you can see on github. 25 | 26 | 27 | -------------------------------------------------------------------------------- /make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | pushd %~dp0 4 | 5 | REM Command file for Sphinx documentation 6 | 7 | if "%SPHINXBUILD%" == "" ( 8 | set SPHINXBUILD=sphinx-build 9 | ) 10 | set SOURCEDIR=source 11 | set BUILDDIR=build 12 | 13 | if "%1" == "" goto help 14 | 15 | %SPHINXBUILD% >NUL 2>NUL 16 | if errorlevel 9009 ( 17 | echo. 18 | echo.The 'sphinx-build' command was not found. Make sure you have Sphinx 19 | echo.installed, then set the SPHINXBUILD environment variable to point 20 | echo.to the full path of the 'sphinx-build' executable. Alternatively you 21 | echo.may add the Sphinx directory to PATH. 22 | echo. 23 | echo.If you don't have Sphinx installed, grab it from 24 | echo.http://sphinx-doc.org/ 25 | exit /b 1 26 | ) 27 | 28 | %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 29 | goto end 30 | 31 | :help 32 | %SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 33 | 34 | :end 35 | popd 36 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | sphinx_book_theme 2 | sphinx>=2,<3 3 | myst_nb 4 | sphinxcontrib-bibtex 5 | sphinx_copybutton 6 | sphinx_thebe 7 | jupyter 8 | jupyterlab 9 | pyscf 10 | numpy 11 | scipy<1.5 12 | matplotlib 13 | 14 | molmass 15 | -------------------------------------------------------------------------------- /source/Project_01/assets/acetaldehyde.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajz34/PyCrawfordProgProj/a3c5670d1d3b9f5271208884594435b58398bf63/source/Project_01/assets/acetaldehyde.png -------------------------------------------------------------------------------- /source/Project_01/input/acetaldehyde.dat: -------------------------------------------------------------------------------- 1 | 7 2 | 6 0.000000000000 0.000000000000 0.000000000000 3 | 6 0.000000000000 0.000000000000 2.845112131228 4 | 8 1.899115961744 0.000000000000 4.139062527233 5 | 1 -1.894048308506 0.000000000000 3.747688672216 6 | 1 1.942500819960 0.000000000000 -0.701145981971 7 | 1 -1.007295466862 -1.669971842687 -0.705916966833 8 | 1 -1.007295466862 1.669971842687 -0.705916966833 9 | -------------------------------------------------------------------------------- /source/Project_01/input/allene.dat: -------------------------------------------------------------------------------- 1 | 7 2 | 6 0.000000000000 0.000000000000 1.889725988579 3 | 6 2.551130084582 0.000000000000 1.889725988579 4 | 6 -2.551130084582 0.000000000000 1.889725988579 5 | 1 3.495993078871 1.157216106424 0.732509882155 6 | 1 3.495993078871 -1.157216106424 3.046942095003 7 | 1 -3.495993078871 -1.157216106424 0.732509882155 8 | 1 -3.495993078871 1.157216106424 3.046942095003 9 | -------------------------------------------------------------------------------- /source/Project_01/input/benzene.dat: -------------------------------------------------------------------------------- 1 | 12 2 | 6 0.000000000000 0.000000000000 0.000000000000 3 | 6 0.000000000000 0.000000000000 2.616448463377 4 | 6 2.265910476936 0.000000000000 3.924672487195 5 | 6 4.531821084796 0.000000000000 2.616448387788 6 | 6 4.531821084796 0.000000000000 -0.000000132281 7 | 6 2.265910689687 0.000000000000 -1.308224146651 8 | 1 2.265910689687 -0.000000000000 -3.334218200677 9 | 1 6.286383272575 0.000000000000 -1.012997083705 10 | 1 6.286383239844 0.000000000000 3.629445320315 11 | 1 2.265910476936 0.000000000000 5.950666541222 12 | 1 -1.754562187779 0.000000000000 3.629445414801 13 | 1 -1.754562155048 -0.000000000000 -1.012996932527 14 | -------------------------------------------------------------------------------- /source/Project_01/solution_01.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | from molmass import ELEMENTS 3 | from scipy import constants 4 | from scipy.constants import physical_constants 5 | 6 | E_h = physical_constants["Hartree energy"][0] 7 | a_0 = physical_constants["Bohr radius"][0] 8 | amu = physical_constants["atomic mass constant"][0] 9 | c_0 = physical_constants["speed of light in vacuum"][0] 10 | h = physical_constants["Planck constant"][0] 11 | kilo = constants.kilo 12 | centi = constants.centi 13 | angstrom = constants.angstrom 14 | mega = constants.mega 15 | 16 | 17 | class Molecule: 18 | 19 | def __init__(self): 20 | self.atom_charges = NotImplemented # type: np.ndarray 21 | self.atom_coords = NotImplemented # type: np.ndarray 22 | self.natm = NotImplemented # type: int 23 | 24 | def construct_from_dat_file(self, file_path: str): 25 | # Input: Read file from `file_path` 26 | # Attribute modification: Obtain atom charges to `self.atom_charges` 27 | # Attribute modification: Obtain coordinates to `self.atom_coords` 28 | # Attribute modification: Obtain atom numbers in molecule to `self.natm` 29 | with open(file_path, "r") as f: 30 | # Ignore the redundant first line 31 | dat = np.array([line.split() for line in f.readlines()][1:]) 32 | self.atom_charges = np.array(dat[:, 0], dtype=int) 33 | self.atom_coords = np.array(dat[:, 1:4], dtype=float) 34 | self.natm = self.atom_charges.shape[0] 35 | 36 | def bond_length(self, i: int, j: int) -> float: 37 | # Input: `i`, `j` index of molecule's atom 38 | # Output: Bond length from atom `i` to atom `j` 39 | return np.linalg.norm(self.atom_coords[i] - self.atom_coords[j]) 40 | 41 | def print_bond_length(self): 42 | # Usage: Print all bond length 43 | print("=== Bond Length ===") 44 | for i in range(self.natm): 45 | for j in range(i + 1, self.natm): 46 | print("{:3d} - {:3d}: {:10.5f} Bohr".format(i, j, self.bond_length(i, j))) 47 | 48 | def bond_unit_vector(self, i: int, j: int) -> np.ndarray: 49 | # Input: `i`, `j` index of molecule's atom 50 | # Output: Unit vector of bond from atom `i` to atom `j` 51 | vec = self.atom_coords[j] - self.atom_coords[i] 52 | return vec / np.linalg.norm(vec) 53 | 54 | def bond_angle(self, i: int, j: int, k: int) -> float: 55 | # Input: `i`, `j`, `k` index of molecule's atom; where `j` is the central atom 56 | # Output: Bond angle for atoms `i`-`j`-`k` 57 | e_ji = self.bond_unit_vector(j, i) 58 | e_jk = self.bond_unit_vector(j, k) 59 | return np.arccos(e_ji.dot(e_jk)) * 180 / np.pi 60 | 61 | def is_valid_bond_angle(self, i: int, j: int, k: int) -> bool: 62 | # Input: `i`, `j`, `k` index of molecule's atom; where `j` is the central atom 63 | # Output: Test if `i`-`j`-`k` is a valid bond angle 64 | # if i != j != k 65 | # and if i-j and j-k bond length smaller than 3 Angstrom, 66 | # and if angle i-j-k > 90 degree 67 | return len({i, j, k}) == 3 and self.bond_length(i, j) < 3 and self.bond_length(j, k) < 3 and self.bond_angle(i, j, k) > 90 68 | 69 | def print_bond_angle(self): 70 | # Usage: Print all bond angle i-j-k which is considered as valid angle 71 | print("=== Bond Angle ===") 72 | for i in range(self.natm): 73 | for j in range(i + 1, self.natm): 74 | for k in range(j + 1, self.natm): 75 | for tup in [(i, j, k), (j, i, k), (i, k, j)]: 76 | if self.is_valid_bond_angle(*tup): 77 | print("{:3d} - {:3d} - {:3d}: {:10.5f} Degree".format(*tup, self.bond_angle(*tup))) 78 | break 79 | 80 | def out_of_plane_angle(self, i: int, j: int, k: int, l: int) -> float: 81 | # Input: `i`, `j`, `k`, `l` index of molecule's atom; where `k` is the central atom, and angle is i - j-k-l 82 | # Output: Out-of-plane bond angle for atoms `i`-`j`-`k`-`l` 83 | res = np.cross(self.bond_unit_vector(k, j), self.bond_unit_vector(k, l)).dot(self.bond_unit_vector(k, i)) 84 | res /= np.sin(self.bond_angle(j, k, l) / 180 * np.pi) 85 | assert(np.abs(res) < 1 + 1e-7) 86 | res = np.sign(res) if np.abs(res) > 1 else res 87 | return np.arcsin(res) * 180 / np.pi 88 | 89 | def is_valid_out_of_plane_angle(self, i: int, j: int, k: int, l: int) -> bool: 90 | # Input: `i`, `j`, `k`, `l` index of molecule's atom; where `k` is the central atom, and angle is i - j-k-l 91 | # Output: Test if `i`-`j`-`k` is a valid out-of-plane bond angle 92 | # if i != j != k != l 93 | # and if angle j-k-l is valid bond angle 94 | # and if i-k bond length smaller than 3 Angstrom 95 | # and bond angle of j-k-l is not linear 96 | return len({i, j, k, l}) == 4 and self.is_valid_bond_angle(j, k, l) and self.bond_length(k, i) < 3 and self.bond_angle(j, k, l) < 179 97 | 98 | def print_out_of_plane_angle(self): 99 | # Usage: Print all out-of-plane bond angle i-j-k-l which is considered as valid 100 | print("=== Out-of-Plane Angle ===") 101 | for j in range(self.natm): 102 | for k in range(j + 1, self.natm): 103 | for l in range(k + 1, self.natm): 104 | for tup in [(j, k, l), (k, j, l), (j, l, k)]: 105 | if self.is_valid_bond_angle(*tup): 106 | for i in range(self.natm): 107 | if i not in [j, k, l] and self.is_valid_out_of_plane_angle(i, *tup): 108 | print("{:3d} - {:3d} - {:3d} - {:3d}: {:10.5f} Degree".format(i, *tup, self.out_of_plane_angle(i, *tup))) 109 | 110 | def dihedral_angle(self, i: int, j: int, k: int, l: int) -> float: 111 | # Input: `i`, `j`, `k`, `l` index of molecule's atom; where `k` is the central atom, and angle is i - j-k-l 112 | # Output: Dihedral angle for atoms `i`-`j`-`k`-`l` 113 | res = np.cross(self.bond_unit_vector(j, i), self.bond_unit_vector(j, k)).dot(np.cross(self.bond_unit_vector(k, j), self.bond_unit_vector(k, l))) 114 | res /= np.sin(self.bond_angle(i, j, k) / 180 * np.pi) * np.sin(self.bond_angle(j, k, l) / 180 * np.pi) 115 | assert(np.abs(res) < 1 + 1e-7) 116 | res = np.sign(res) if np.abs(res) > 1 else res 117 | return np.arccos(res) * 180 / np.pi 118 | 119 | def is_valid_dihedral_angle(self, i: int, j: int, k: int, l: int) -> bool: 120 | # Input: `i`, `j`, `k`, `l` index of molecule's atom; where `k` is the central atom, and angle is i - j-k-l 121 | # Output: Test if `i`-`j`-`k` is a valid dihedral bond angle 122 | # if i != j != k != l 123 | # and if i, j, k construct a valid bond angle (with j-k bonded) 124 | # and if j, k, l construct a valid bond angle (with j-k bonded) 125 | return len({i, j, k, l}) == 4 \ 126 | and (self.is_valid_bond_angle(i, j, k) or self.is_valid_bond_angle(i, k, j)) \ 127 | and (self.is_valid_bond_angle(j, k, l) or self.is_valid_bond_angle(k, j, l)) 128 | 129 | def print_dihedral_angle(self): 130 | # Usage: Print all dihedral bond angle i-j-k-l which is considered as valid 131 | print("=== Dihedral Angle ===") 132 | for j in range(self.natm): 133 | for k in range(j + 1, self.natm): 134 | for i in range(self.natm): 135 | for l in range(i + 1, self.natm): 136 | if self.is_valid_dihedral_angle(i, j, k, l): 137 | print("{:3d} - {:3d} - {:3d} - {:3d}: {:10.5f} Degree".format(i, j, k, l, self.dihedral_angle(i, j, k, l))) 138 | 139 | def center_of_mass(self) -> np.ndarray or list: 140 | # Output: Center of mass for this molecule 141 | sum_of_vec, sum_of_mass = np.zeros(3), 0 142 | for i in range(self.natm): 143 | sum_of_vec += ELEMENTS[self.atom_charges[i]].mass * self.atom_coords[i] 144 | sum_of_mass += ELEMENTS[self.atom_charges[i]].mass 145 | return sum_of_vec / sum_of_mass 146 | 147 | def moment_of_inertia(self): 148 | # Output: Principle of moments of intertia 149 | atom_weights = np.array([ELEMENTS[c].mass for c in self.atom_charges]) 150 | trans_coords = self.atom_coords - self.center_of_mass() 151 | res = - np.einsum("i, ix, iy -> xy", atom_weights, trans_coords, trans_coords) 152 | np.fill_diagonal(res, res.diagonal() - res.diagonal().sum()) 153 | return np.linalg.eigvalsh(res) 154 | 155 | def print_moment_of_interia(self): 156 | # Output: Print moments of inertia in amu bohr2, amu Å2, and g cm2 157 | moment_in_amu_bohr = self.moment_of_inertia() 158 | print("In {:>15}: {:16.8e} {:16.8e} {:16.8e}".format( 159 | "amu bohr^2", *(moment_in_amu_bohr))) 160 | print("In {:>15}: {:16.8e} {:16.8e} {:16.8e}".format( 161 | "amu angstrom^2", *(moment_in_amu_bohr * a_0**2 / angstrom**2))) 162 | print("In {:>15}: {:16.8e} {:16.8e} {:16.8e}".format( 163 | "g cm^2", *(moment_in_amu_bohr * amu * kilo * a_0**2 / centi**2))) 164 | 165 | def type_of_moment_of_interia(self) -> str: 166 | # Output: Judge which type of moment of interia is 167 | m = self.moment_of_inertia() 168 | if np.abs(m[0] - m[1]) < 1e-4: 169 | return "Spherical" if np.abs(m[1] - m[2]) < 1e-4 else "Oblate" 170 | elif np.abs(m[0]) < 1e-4 or np.abs((m[1] - m[0]) / m[0]) > 1e4: 171 | return "Linear" 172 | else: 173 | return "Prolate" if np.abs(m[1] - m[2]) < 1e-4 else "Asymmetric" 174 | 175 | def rotational_constants(self) -> np.ndarray or list: 176 | # Output: Rotational constant in cm^-1 177 | return h / (8 * np.pi**2 * c_0 * self.moment_of_inertia()) / amu / a_0**2 * centi 178 | 179 | def print_solution_01(self): 180 | print("=== Atom Charges ===") 181 | print(self.atom_charges) 182 | print("=== Coordinates ===") 183 | print(self.atom_coords) 184 | self.print_bond_length() 185 | self.print_bond_angle() 186 | self.print_out_of_plane_angle() 187 | self.print_dihedral_angle() 188 | print("=== Center of Mass ===") 189 | print("{:10.5f} {:10.5f} {:10.5f}".format(*self.center_of_mass())) 190 | print("=== Moments of Inertia ===") 191 | self.print_moment_of_interia() 192 | print("Type: ", self.type_of_moment_of_interia()) 193 | print("=== Rotational Constants ===") 194 | print("In cm^-1: {:12.5f} {:12.5f} {:12.5f}".format(*self.rotational_constants())) 195 | print("In MHz: {:12.5f} {:12.5f} {:12.5f}".format(*(self.rotational_constants() * c_0 / centi / mega))) 196 | 197 | 198 | if __name__ == '__main__': 199 | mole = Molecule() 200 | mole.construct_from_dat_file("input/acetaldehyde.dat") 201 | mole.print_solution_01() 202 | -------------------------------------------------------------------------------- /source/Project_02/input/3c1b_geom.txt: -------------------------------------------------------------------------------- 1 | 12 2 | 6.0000000000 0.1690059610 3.1233433100 -0.3345553720 3 | 6.0000000000 -0.0386421959 0.4206229820 0.7520430680 4 | 6.0000000000 2.0569045600 -1.3758742600 -0.1486055380 5 | 6.0000000000 4.4719971000 -0.8585641720 -0.0315570842 6 | 1.0000000000 5.1968623000 0.9074367080 0.6974099730 7 | 1.0000000000 -1.3822808500 4.2799539600 0.3473315670 8 | 1.0000000000 5.8762121500 -2.2019961400 -0.6625964520 9 | 1.0000000000 1.4102155500 -3.1763622600 -0.8785797820 10 | 1.0000000000 -0.0505049904 0.5084677190 2.8179601800 11 | 1.0000000000 0.1191743850 3.0814658800 -2.3848397600 12 | 1.0000000000 1.9378539900 3.9710910300 0.2692445360 13 | 17.0000000000 -3.1213603000 -0.8957190610 -0.0958753352 14 | -------------------------------------------------------------------------------- /source/Project_02/input/benzene_geom.txt: -------------------------------------------------------------------------------- 1 | 12 2 | 6.00000000 0.00000000 2.62065942 0.00000000 3 | 6.00000000 -2.26955763 1.31032971 0.00000000 4 | 6.00000000 -2.26955763 -1.31032971 0.00000000 5 | 6.00000000 0.00000000 -2.62065942 0.00000000 6 | 6.00000000 2.26955763 -1.31032971 0.00000000 7 | 6.00000000 2.26955763 1.31032971 0.00000000 8 | 1.00000000 -4.04130651 2.33324940 0.00000000 9 | 1.00000000 -4.04130651 -2.33324940 0.00000000 10 | 1.00000000 0.00000000 -4.66649880 0.00000000 11 | 1.00000000 4.04130651 -2.33324940 0.00000000 12 | 1.00000000 4.04130651 2.33324940 0.00000000 13 | 1.00000000 0.00000000 4.66649880 0.00000000 14 | -------------------------------------------------------------------------------- /source/Project_02/input/h2o_geom.txt: -------------------------------------------------------------------------------- 1 | 3 2 | 8.00000000000 0.000000000000 0.000000000000 -0.134503695264 3 | 1.00000000000 0.000000000000 -1.684916670000 1.067335684736 4 | 1.00000000000 0.000000000000 1.684916670000 1.067335684736 5 | -------------------------------------------------------------------------------- /source/Project_02/input/h2o_hessian.txt: -------------------------------------------------------------------------------- 1 | 3 2 | 0.0927643390 0.0000000000 0.0000000000 3 | -0.0463821695 0.0000000000 0.0000000000 4 | -0.0463821695 0.0000000000 0.0000000000 5 | 0.0000000000 0.3171327134 0.0000000000 6 | 0.0000000000 -0.1585663567 0.0800202030 7 | 0.0000000000 -0.1585663567 -0.0800202030 8 | 0.0000000000 0.0000000000 0.2800907293 9 | 0.0000000000 0.0347765865 -0.1400453646 10 | 0.0000000000 -0.0347765865 -0.1400453646 11 | -0.0463821695 0.0000000000 0.0000000000 12 | 0.0514668232 0.0000000000 0.0000000000 13 | -0.0050846537 0.0000000000 0.0000000000 14 | 0.0000000000 -0.1585663567 0.0347765865 15 | 0.0000000000 0.1730075524 -0.0573983947 16 | 0.0000000000 -0.0144411957 0.0226218083 17 | 0.0000000000 0.0800202030 -0.1400453646 18 | 0.0000000000 -0.0573983947 0.1268373488 19 | 0.0000000000 -0.0226218083 0.0132080159 20 | -0.0463821695 0.0000000000 0.0000000000 21 | -0.0050846537 0.0000000000 0.0000000000 22 | 0.0514668232 0.0000000000 0.0000000000 23 | 0.0000000000 -0.1585663567 -0.0347765865 24 | 0.0000000000 -0.0144411957 -0.0226218083 25 | 0.0000000000 0.1730075524 0.0573983947 26 | 0.0000000000 -0.0800202030 -0.1400453646 27 | 0.0000000000 0.0226218083 0.0132080159 28 | 0.0000000000 0.0573983947 0.1268373488 29 | -------------------------------------------------------------------------------- /source/Project_02/solution_02.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | from molmass import ELEMENTS 3 | from scipy import constants 4 | from scipy.constants import physical_constants 5 | np.set_printoptions(precision=7, linewidth=120, suppress=True) 6 | 7 | E_h = physical_constants["Hartree energy"][0] 8 | a_0 = physical_constants["Bohr radius"][0] 9 | amu = physical_constants["atomic mass constant"][0] 10 | c_0 = physical_constants["speed of light in vacuum"][0] 11 | centi = constants.centi 12 | 13 | 14 | class Molecule: 15 | 16 | def __init__(self): 17 | self.atom_charges = NotImplemented # type: np.ndarray 18 | self.atom_coords = NotImplemented # type: np.ndarray 19 | self.natm = NotImplemented # type: int 20 | self.hess = NotImplemented # type: np.ndarray 21 | 22 | def construct_from_dat_file(self, file_path: str): 23 | # Same to Project 01 24 | with open(file_path, "r") as f: 25 | dat = np.array([line.split() for line in f.readlines()][1:]) 26 | self.atom_charges = np.array(dat[:, 0], dtype=float).astype(int) 27 | self.atom_coords = np.array(dat[:, 1:4], dtype=float) 28 | self.natm = self.atom_charges.shape[0] 29 | 30 | def obtain_hessian(self, file_path: str): 31 | # Input: Read Hessian file from `file_path` 32 | # Attribute modification: Obtain raw Hessian to `self.hess` 33 | with open(file_path, "r") as f: 34 | self.hess = np.array([line.split() for line in f.readlines()][1:], dtype=float).reshape((self.natm * 3, self.natm * 3)) 35 | 36 | def mass_weighted_hess(self) -> np.ndarray or list: 37 | # Output: Mass-weighted Hessian matrix (in unit Eh/(amu*a0^2)) 38 | atom_weights = np.array([ELEMENTS[c].mass for c in self.atom_charges]) 39 | freq_weights = np.sqrt(np.repeat(atom_weights, 3)) 40 | return self.hess / freq_weights[:, None] / freq_weights[None, :] 41 | 42 | def eig_mass_weight_hess(self) -> np.ndarray or list: 43 | # Output: Eigenvalue of mass-weighted Hessian matrix (in unit Eh/(amu*a0^2)) 44 | return np.linalg.eigvalsh(self.mass_weighted_hess()) 45 | 46 | def harmonic_vib_freq(self) -> np.ndarray or list: 47 | # Output: Harmonic vibrational frequencies (in unit cm^-1) 48 | coef = np.sqrt(E_h / amu / a_0**2) / (2 * np.pi * c_0) * centi 49 | eigs = self.eig_mass_weight_hess() 50 | return np.sign(eigs) * np.sqrt(np.abs(eigs)) * coef 51 | 52 | def print_solution_02(self): 53 | print("=== Mass-Weighted Hessian Matrix (in unit Eh/(amu*a0^2)) ===") 54 | print(self.mass_weighted_hess()) 55 | print("=== Eigenvalue of Mass-Weighted Hessian Matrix (in unit Eh/(amu*a0^2)) ===") 56 | print(self.eig_mass_weight_hess()) 57 | print("=== Harmonic Vibrational Frequencies (in unit cm^-1) ===") 58 | print(self.harmonic_vib_freq()) 59 | 60 | 61 | if __name__ == '__main__': 62 | mole = Molecule() 63 | mole.construct_from_dat_file("input/h2o_geom.txt") 64 | mole.obtain_hessian("input/h2o_hessian.txt") 65 | mole.print_solution_02() 66 | -------------------------------------------------------------------------------- /source/Project_03/assets/Duv.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajz34/PyCrawfordProgProj/a3c5670d1d3b9f5271208884594435b58398bf63/source/Project_03/assets/Duv.png -------------------------------------------------------------------------------- /source/Project_03/input/ch4/STO-3G/enuc.dat: -------------------------------------------------------------------------------- 1 | 13.497304462036480 2 | -------------------------------------------------------------------------------- /source/Project_03/input/ch4/STO-3G/geom.dat: -------------------------------------------------------------------------------- 1 | 5 2 | 6.000000000000 -0.000000000000 0.000000000000 0.000000000000 3 | 1.000000000000 1.183771681898 -1.183771681898 -1.183771681898 4 | 1.000000000000 1.183771681898 1.183771681898 1.183771681898 5 | 1.000000000000 -1.183771681898 1.183771681898 -1.183771681898 6 | 1.000000000000 -1.183771681898 -1.183771681898 1.183771681898 7 | -------------------------------------------------------------------------------- /source/Project_03/input/ch4/STO-3G/input.dat: -------------------------------------------------------------------------------- 1 | psi: ( 2 | label = "CH4 SCF Test Case" 3 | wfn = scf 4 | jobtype = oeprop 5 | reference = rhf 6 | basis = "STO-3G" 7 | units = angstrom 8 | subgroup = c1 9 | delete_tei = false 10 | delete_oei = false 11 | zmat = ( 12 | C 13 | H 1 r 14 | H 1 r 2 td 15 | H 1 r 2 td 3 d 16 | H 1 r 2 td 4 d 17 | ) 18 | zvars = ( 19 | r 1.085 20 | td 109.47122063449069136958 21 | d 120.0 22 | ) 23 | ) 24 | 25 | basis: ( 26 | carbon: "STO-3G" = 27 | ( (S ( 71.61683730 0.15432900) 28 | ( 13.04509630 0.53532810) 29 | ( 3.53051220 0.44463450) ) 30 | (S ( 2.94124940 -0.09996720) 31 | ( 0.68348310 0.39951280) 32 | ( 0.22228990 0.70011550) ) 33 | (P ( 2.94124940 0.15591630) 34 | ( 0.68348310 0.60768370) 35 | ( 0.22228990 0.39195740) ) 36 | ) 37 | 38 | hydrogen: "STO-3G"= 39 | ( (S ( 3.42525090 0.15432890) 40 | ( 0.62391370 0.53532810) 41 | ( 0.16885540 0.44463450) ) 42 | ) 43 | ) 44 | -------------------------------------------------------------------------------- /source/Project_03/input/ch4/STO-3G/mux.dat: -------------------------------------------------------------------------------- 1 | 1 1 0.000000000000000 2 | 2 1 0.000000000000000 3 | 2 2 0.000000000000000 4 | 3 1 -0.071855488532817 5 | 3 2 -0.838743574800986 6 | 3 3 0.000000000000000 7 | 4 1 -0.000000000000000 8 | 4 2 0.000000000000000 9 | 4 3 -0.000000000000000 10 | 4 4 0.000000000000000 11 | 5 1 0.000000000000000 12 | 5 2 0.000000000000000 13 | 5 3 -0.000000000000000 14 | 5 4 0.000000000000000 15 | 5 5 0.000000000000000 16 | 6 1 -0.004780775261548 17 | 6 2 -0.306592476518555 18 | 6 3 -0.519567036508228 19 | 6 4 0.163831354490276 20 | 6 5 0.163831354490276 21 | 6 6 -1.183771681897730 22 | 7 1 -0.004780775261548 23 | 7 2 -0.306592476518555 24 | 7 3 -0.519567036508228 25 | 7 4 -0.163831354490276 26 | 7 5 -0.163831354490276 27 | 7 6 -0.202918556316052 28 | 7 7 -1.183771681897730 29 | 8 1 0.004780775261548 30 | 8 2 0.306592476518555 31 | 8 3 -0.519567036508228 32 | 8 4 0.163831354490276 33 | 8 5 -0.163831354490276 34 | 8 6 -0.000000000000000 35 | 8 7 -0.000000000000000 36 | 8 8 1.183771681897730 37 | 9 1 0.004780775261548 38 | 9 2 0.306592476518555 39 | 9 3 -0.519567036508228 40 | 9 4 -0.163831354490276 41 | 9 5 0.163831354490276 42 | 9 6 0.000000000000000 43 | 9 7 0.000000000000000 44 | 9 8 0.202918556316052 45 | 9 9 1.183771681897731 46 | -------------------------------------------------------------------------------- /source/Project_03/input/ch4/STO-3G/muy.dat: -------------------------------------------------------------------------------- 1 | 1 1 -0.000000000000000 2 | 2 1 -0.000000000000000 3 | 2 2 -0.000000000000000 4 | 3 1 -0.000000000000000 5 | 3 2 0.000000000000000 6 | 3 3 -0.000000000000000 7 | 4 1 -0.071855488532817 8 | 4 2 -0.838743574800986 9 | 4 3 0.000000000000000 10 | 4 4 -0.000000000000000 11 | 5 1 -0.000000000000000 12 | 5 2 -0.000000000000000 13 | 5 3 0.000000000000000 14 | 5 4 -0.000000000000000 15 | 5 5 -0.000000000000000 16 | 6 1 0.004780775261548 17 | 6 2 0.306592476518555 18 | 6 3 0.163831354490276 19 | 6 4 -0.519567036508228 20 | 6 5 -0.163831354490276 21 | 6 6 1.183771681897730 22 | 7 1 -0.004780775261548 23 | 7 2 -0.306592476518555 24 | 7 3 -0.163831354490276 25 | 7 4 -0.519567036508228 26 | 7 5 -0.163831354490276 27 | 7 6 -0.000000000000000 28 | 7 7 -1.183771681897730 29 | 8 1 -0.004780775261548 30 | 8 2 -0.306592476518555 31 | 8 3 0.163831354490276 32 | 8 4 -0.519567036508228 33 | 8 5 0.163831354490276 34 | 8 6 -0.000000000000000 35 | 8 7 -0.202918556316052 36 | 8 8 -1.183771681897730 37 | 9 1 0.004780775261548 38 | 9 2 0.306592476518555 39 | 9 3 -0.163831354490276 40 | 9 4 -0.519567036508228 41 | 9 5 0.163831354490276 42 | 9 6 0.202918556316052 43 | 9 7 0.000000000000000 44 | 9 8 0.000000000000000 45 | 9 9 1.183771681897731 46 | -------------------------------------------------------------------------------- /source/Project_03/input/ch4/STO-3G/muz.dat: -------------------------------------------------------------------------------- 1 | 1 1 -0.000000000000000 2 | 2 1 -0.000000000000000 3 | 2 2 -0.000000000000000 4 | 3 1 -0.000000000000000 5 | 3 2 0.000000000000000 6 | 3 3 -0.000000000000000 7 | 4 1 0.000000000000000 8 | 4 2 -0.000000000000000 9 | 4 3 0.000000000000000 10 | 4 4 -0.000000000000000 11 | 5 1 -0.071855488532817 12 | 5 2 -0.838743574800986 13 | 5 3 0.000000000000000 14 | 5 4 -0.000000000000000 15 | 5 5 -0.000000000000000 16 | 6 1 0.004780775261548 17 | 6 2 0.306592476518555 18 | 6 3 0.163831354490276 19 | 6 4 -0.163831354490276 20 | 6 5 -0.519567036508228 21 | 6 6 1.183771681897730 22 | 7 1 -0.004780775261548 23 | 7 2 -0.306592476518555 24 | 7 3 -0.163831354490276 25 | 7 4 -0.163831354490276 26 | 7 5 -0.519567036508228 27 | 7 6 0.000000000000000 28 | 7 7 -1.183771681897730 29 | 8 1 0.004780775261548 30 | 8 2 0.306592476518555 31 | 8 3 -0.163831354490276 32 | 8 4 0.163831354490276 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-------------------------------------------------------------------------------- /source/Project_03/input/h2o/DZP/enuc.dat: -------------------------------------------------------------------------------- 1 | 8.002367061810450 2 | -------------------------------------------------------------------------------- /source/Project_03/input/h2o/DZP/geom.dat: -------------------------------------------------------------------------------- 1 | 3 2 | 8.000000000000 0.000000000000 -0.143225816552 0.000000000000 3 | 1.000000000000 1.638036840407 1.136548822547 -0.000000000000 4 | 1.000000000000 -1.638036840407 1.136548822547 -0.000000000000 5 | -------------------------------------------------------------------------------- /source/Project_03/input/h2o/DZP/input.dat: -------------------------------------------------------------------------------- 1 | psi: ( 2 | label = "H2O SCF Test Case" 3 | memory = (10.0 MB) 4 | wfn = scf 5 | jobtype = oeprop 6 | delete_tei = false 7 | delete_oei = false 8 | reference = rhf 9 | puream = false 10 | basis = "DZP" 11 | subgroup = c1 12 | zmat = ((o) (h 1 1.1) (h 1 1.1 2 104.0)) 13 | ) 14 | -------------------------------------------------------------------------------- /source/Project_03/input/h2o/STO-3G/enuc.dat: -------------------------------------------------------------------------------- 1 | 8.002367061810450 2 | -------------------------------------------------------------------------------- /source/Project_03/input/h2o/STO-3G/eri.dat: -------------------------------------------------------------------------------- 1 | 1 1 1 1 4.785065404705506 2 | 2 1 1 1 0.741380351973408 3 | 2 2 1 1 1.118946866342470 4 | 2 1 2 1 0.136873385354388 5 | 2 2 2 1 0.256633394730974 6 | 2 2 2 2 0.817206321526058 7 | 3 3 1 1 1.115813812152428 8 | 4 4 1 1 1.115813812152428 9 | 5 5 1 1 1.115813812152428 10 | 3 1 3 1 0.024477412258099 11 | 4 1 4 1 0.024477412258099 12 | 5 1 5 1 0.024477412258099 13 | 3 3 2 1 0.256683985810103 14 | 4 4 2 1 0.256683985810103 15 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-------------------------------------------------------------------------------- 1 | 3 2 | 8.000000000000 0.000000000000 -0.143225816552 0.000000000000 3 | 1.000000000000 1.638036840407 1.136548822547 -0.000000000000 4 | 1.000000000000 -1.638036840407 1.136548822547 -0.000000000000 5 | -------------------------------------------------------------------------------- /source/Project_03/input/h2o/STO-3G/input.dat: -------------------------------------------------------------------------------- 1 | psi: ( 2 | label = "H2O SCF Test Case" 3 | memory = (10.0 MB) 4 | wfn = scf 5 | jobtype = oeprop 6 | delete_tei = false 7 | delete_oei = false 8 | reference = rhf 9 | basis = "STO-3G" 10 | subgroup = c1 11 | zmat = ((o) (h 1 1.1) (h 1 1.1 2 104.0)) 12 | ) 13 | -------------------------------------------------------------------------------- /source/Project_03/input/h2o/STO-3G/mux.dat: -------------------------------------------------------------------------------- 1 | 1 1 -0.000000000000000 2 | 2 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-------------------------------------------------------------------------------- 1 | 5 2 | 6.000000000000 -0.000000000000 0.000000000000 0.000000000000 3 | 1.000000000000 1.183771681898 -1.183771681898 -1.183771681898 4 | 1.000000000000 1.183771681898 1.183771681898 1.183771681898 5 | 1.000000000000 -1.183771681898 1.183771681898 -1.183771681898 6 | 1.000000000000 -1.183771681898 -1.183771681898 1.183771681898 7 | -------------------------------------------------------------------------------- /source/Project_04/input/ch4/STO-3G/input.dat: -------------------------------------------------------------------------------- 1 | psi: ( 2 | label = "CH4 SCF Test Case" 3 | wfn = scf 4 | jobtype = oeprop 5 | reference = rhf 6 | basis = "STO-3G" 7 | units = angstrom 8 | subgroup = c1 9 | delete_tei = false 10 | delete_oei = false 11 | zmat = ( 12 | C 13 | H 1 r 14 | H 1 r 2 td 15 | H 1 r 2 td 3 d 16 | H 1 r 2 td 4 d 17 | ) 18 | zvars = ( 19 | r 1.085 20 | td 109.47122063449069136958 21 | d 120.0 22 | ) 23 | ) 24 | 25 | basis: ( 26 | carbon: "STO-3G" = 27 | ( (S ( 71.61683730 0.15432900) 28 | ( 13.04509630 0.53532810) 29 | ( 3.53051220 0.44463450) ) 30 | (S ( 2.94124940 -0.09996720) 31 | ( 0.68348310 0.39951280) 32 | ( 0.22228990 0.70011550) ) 33 | (P ( 2.94124940 0.15591630) 34 | ( 0.68348310 0.60768370) 35 | ( 0.22228990 0.39195740) ) 36 | ) 37 | 38 | hydrogen: "STO-3G"= 39 | ( (S ( 3.42525090 0.15432890) 40 | ( 0.62391370 0.53532810) 41 | ( 0.16885540 0.44463450) ) 42 | ) 43 | ) 44 | -------------------------------------------------------------------------------- /source/Project_04/input/ch4/STO-3G/mux.dat: -------------------------------------------------------------------------------- 1 | 1 1 0.000000000000000 2 | 2 1 0.000000000000000 3 | 2 2 0.000000000000000 4 | 3 1 -0.071855488532817 5 | 3 2 -0.838743574800986 6 | 3 3 0.000000000000000 7 | 4 1 -0.000000000000000 8 | 4 2 0.000000000000000 9 | 4 3 -0.000000000000000 10 | 4 4 0.000000000000000 11 | 5 1 0.000000000000000 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/source/Project_04/input/h2o/DZ/input.dat: -------------------------------------------------------------------------------- 1 | psi: ( 2 | label = "H2O SCF Test Case" 3 | memory = (10.0 MB) 4 | wfn = scf 5 | jobtype = oeprop 6 | delete_tei = false 7 | delete_oei = false 8 | reference = rhf 9 | basis = "DZ" 10 | subgroup = c1 11 | zmat = ((o) (h 1 1.1) (h 1 1.1 2 104.0)) 12 | ) 13 | -------------------------------------------------------------------------------- /source/Project_04/input/h2o/DZ/mux.dat: -------------------------------------------------------------------------------- 1 | 1 1 -0.000000000000000 2 | 2 1 -0.000000000000000 3 | 2 2 -0.000000000000000 4 | 3 1 -0.000000000000000 5 | 3 2 -0.000000000000000 6 | 3 3 -0.000000000000000 7 | 4 1 -0.000000000000000 8 | 4 2 -0.000000000000000 9 | 4 3 -0.000000000000000 10 | 4 4 -0.000000000000000 11 | 5 1 -0.065756994029223 12 | 5 2 -0.076390812514647 13 | 5 3 -0.495548317796719 14 | 5 4 -0.578524588047388 15 | 5 5 -0.000000000000000 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0.000000000000 3 | 1.000000000000 1.638036840407 1.136548822547 -0.000000000000 4 | 1.000000000000 -1.638036840407 1.136548822547 -0.000000000000 5 | -------------------------------------------------------------------------------- /source/Project_04/input/h2o/DZP/input.dat: -------------------------------------------------------------------------------- 1 | psi: ( 2 | label = "H2O SCF Test Case" 3 | memory = (10.0 MB) 4 | wfn = scf 5 | jobtype = oeprop 6 | delete_tei = false 7 | delete_oei = false 8 | reference = rhf 9 | puream = false 10 | basis = "DZP" 11 | subgroup = c1 12 | zmat = ((o) (h 1 1.1) (h 1 1.1 2 104.0)) 13 | ) 14 | -------------------------------------------------------------------------------- /source/Project_04/input/h2o/STO-3G/enuc.dat: -------------------------------------------------------------------------------- 1 | 8.002367061810450 2 | -------------------------------------------------------------------------------- /source/Project_04/input/h2o/STO-3G/eri.dat: 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0.025974451190177 188 | 7 3 6 6 -0.073615422819083 189 | 7 4 6 6 0.096752175289782 190 | 7 6 6 6 0.091353706761488 191 | 7 7 1 1 0.470723326368778 192 | 7 1 7 1 0.003683107960076 193 | 7 7 2 1 0.111191806911617 194 | 7 2 7 1 0.012121617421746 195 | 7 7 2 2 0.454660662254829 196 | 7 2 7 2 0.103816561020432 197 | 7 7 3 1 -0.008115429695629 198 | 7 7 4 1 0.006340468574121 199 | 7 3 7 1 -0.007487641649768 200 | 7 4 7 1 0.005849986797397 201 | 7 7 3 2 -0.088850240147481 202 | 7 7 4 2 0.069417415538897 203 | 7 3 7 2 -0.079876222072782 204 | 7 4 7 2 0.062406144205123 205 | 7 7 3 3 0.469762103528713 206 | 7 7 4 3 -0.025791716791396 207 | 7 7 4 4 0.456900909053721 208 | 7 7 5 5 0.436750211441671 209 | 7 3 7 3 0.075103217640351 210 | 7 4 7 3 -0.047460399285077 211 | 7 4 7 4 0.051436804504574 212 | 7 5 7 5 0.014356676714874 213 | 7 7 6 1 0.017890930404213 214 | 7 6 7 1 0.004091767456984 215 | 7 7 6 2 0.151924586584762 216 | 7 6 7 2 0.038415486590652 217 | 7 7 6 3 0.073615422819083 218 | 7 7 6 4 0.096752175289782 219 | 7 6 7 3 -0.025685197500691 220 | 7 6 7 4 0.025974451190177 221 | 7 7 6 6 0.302537910673863 222 | 7 6 7 6 0.017861326916860 223 | 7 7 7 1 0.018641085379951 224 | 7 7 7 2 0.235420950941441 225 | 7 7 7 3 -0.206690042488560 226 | 7 7 7 4 0.161483959338374 227 | 7 7 7 6 0.091353706761488 228 | 7 7 7 7 0.774605943919898 229 | -------------------------------------------------------------------------------- /source/Project_04/input/h2o/STO-3G/geom.dat: -------------------------------------------------------------------------------- 1 | 3 2 | 8.000000000000 0.000000000000 -0.143225816552 0.000000000000 3 | 1.000000000000 1.638036840407 1.136548822547 -0.000000000000 4 | 1.000000000000 -1.638036840407 1.136548822547 -0.000000000000 5 | -------------------------------------------------------------------------------- /source/Project_04/input/h2o/STO-3G/input.dat: -------------------------------------------------------------------------------- 1 | psi: ( 2 | label = "H2O SCF Test Case" 3 | memory = (10.0 MB) 4 | wfn = scf 5 | jobtype = oeprop 6 | delete_tei = false 7 | delete_oei = false 8 | reference = rhf 9 | basis = "STO-3G" 10 | subgroup = c1 11 | zmat = ((o) (h 1 1.1) (h 1 1.1 2 104.0)) 12 | ) 13 | -------------------------------------------------------------------------------- /source/Project_04/input/h2o/STO-3G/mux.dat: -------------------------------------------------------------------------------- 1 | 1 1 -0.000000000000000 2 | 2 1 -0.000000000000000 3 | 2 2 -0.000000000000000 4 | 3 1 -0.050791929587912 5 | 3 2 -0.641172844324925 6 | 3 3 -0.000000000000000 7 | 4 1 0.000000000000000 8 | 4 2 0.000000000000000 9 | 4 3 0.000000000000000 10 | 4 4 -0.000000000000000 11 | 5 1 0.000000000000000 12 | 5 2 -0.000000000000000 13 | 5 3 -0.000000000000000 14 | 5 4 0.000000000000000 15 | 5 5 -0.000000000000000 16 | 6 1 -0.002229654052248 17 | 6 2 -0.262742503532769 18 | 6 3 -0.437630646182039 19 | 6 4 -0.147399448800486 20 | 6 5 0.000000000000000 21 | 6 6 -1.638036840407314 22 | 7 1 0.002229654052248 23 | 7 2 0.262742503532769 24 | 7 3 -0.437630646182039 25 | 7 4 0.147399448800486 26 | 7 5 -0.000000000000000 27 | 7 6 0.000000000000000 28 | 7 7 1.638036840407314 29 | -------------------------------------------------------------------------------- /source/Project_04/input/h2o/STO-3G/muy.dat: -------------------------------------------------------------------------------- 1 | 1 1 0.143225816551918 2 | 2 1 0.033902114587819 3 | 2 2 0.143225816551918 4 | 3 1 -0.000000000000000 5 | 3 2 0.000000000000000 6 | 3 3 0.143225816551918 7 | 4 1 -0.050791929587912 8 | 4 2 -0.641172844324925 9 | 4 3 -0.000000000000000 10 | 4 4 0.143225816551918 11 | 5 1 -0.000000000000000 12 | 5 2 0.000000000000000 13 | 5 3 0.000000000000000 14 | 5 4 -0.000000000000000 15 | 5 5 0.143225816551918 16 | 6 1 0.003758676726377 17 | 6 2 -0.149971890752635 18 | 6 3 -0.108952162150434 19 | 6 4 -0.334090713364948 20 | 6 5 0.000000000000000 21 | 6 6 -1.136548822546795 22 | 7 1 0.003758676726377 23 | 7 2 -0.149971890752635 24 | 7 3 0.108952162150434 25 | 7 4 -0.334090713364948 26 | 7 5 0.000000000000000 27 | 7 6 -0.206578984758302 28 | 7 7 -1.136548822546794 29 | -------------------------------------------------------------------------------- /source/Project_04/input/h2o/STO-3G/muz.dat: -------------------------------------------------------------------------------- 1 | 1 1 -0.000000000000000 2 | 2 1 -0.000000000000000 3 | 2 2 -0.000000000000000 4 | 3 1 0.000000000000000 5 | 3 2 -0.000000000000000 6 | 3 3 -0.000000000000000 7 | 4 1 0.000000000000000 8 | 4 2 0.000000000000000 9 | 4 3 0.000000000000000 10 | 4 4 -0.000000000000000 11 | 5 1 -0.050791929587912 12 | 5 2 -0.641172844324925 13 | 5 3 -0.000000000000000 14 | 5 4 0.000000000000000 15 | 5 5 -0.000000000000000 16 | 6 1 -0.000000000000000 17 | 6 2 0.000000000000000 18 | 6 3 0.000000000000000 19 | 6 4 0.000000000000000 20 | 6 5 -0.248967955099984 21 | 6 6 0.000000000000000 22 | 7 1 -0.000000000000000 23 | 7 2 0.000000000000000 24 | 7 3 -0.000000000000000 25 | 7 4 0.000000000000000 26 | 7 5 -0.248967955099984 27 | 7 6 0.000000000000000 28 | 7 7 0.000000000000000 29 | -------------------------------------------------------------------------------- /source/Project_04/input/h2o/STO-3G/s.dat: -------------------------------------------------------------------------------- 1 | 1 1 1.000000000000000 2 | 2 1 0.236703936510848 3 | 2 2 1.000000000000000 4 | 3 1 -0.000000000000000 5 | 3 2 0.000000000000000 6 | 3 3 1.000000000000000 7 | 4 1 -0.000000000000000 8 | 4 2 -0.000000000000000 9 | 4 3 -0.000000000000000 10 | 4 4 1.000000000000000 11 | 5 1 -0.000000000000000 12 | 5 2 0.000000000000000 13 | 5 3 0.000000000000000 14 | 5 4 -0.000000000000000 15 | 5 5 1.000000000000000 16 | 6 1 0.038405599785757 17 | 6 2 0.386138840478249 18 | 6 3 0.268438243716457 19 | 6 4 0.209726941420375 20 | 6 5 -0.000000000000000 21 | 6 6 1.000000000000000 22 | 7 1 0.038405599785757 23 | 7 2 0.386138840478250 24 | 7 3 -0.268438243716457 25 | 7 4 0.209726941420375 26 | 7 5 -0.000000000000000 27 | 7 6 0.181759886298063 28 | 7 7 1.000000000000000 29 | -------------------------------------------------------------------------------- /source/Project_04/input/h2o/STO-3G/t.dat: -------------------------------------------------------------------------------- 1 | 1 1 29.003199945539588 2 | 2 1 -0.168010939316492 3 | 2 2 0.808127954930347 4 | 3 1 0.000000000000000 5 | 3 2 0.000000000000000 6 | 3 3 2.528731198194763 7 | 4 1 0.000000000000000 8 | 4 2 -0.000000000000000 9 | 4 3 -0.000000000000000 10 | 4 4 2.528731198194763 11 | 5 1 -0.000000000000000 12 | 5 2 0.000000000000000 13 | 5 3 0.000000000000000 14 | 5 4 -0.000000000000000 15 | 5 5 2.528731198194763 16 | 6 1 -0.008416383544591 17 | 6 2 0.070517372751001 18 | 6 3 0.147090913304052 19 | 6 4 0.114920016354202 20 | 6 5 -0.000000000000000 21 | 6 6 0.760031883566609 22 | 7 1 -0.008416383544591 23 | 7 2 0.070517372751002 24 | 7 3 -0.147090913304052 25 | 7 4 0.114920016354202 26 | 7 5 -0.000000000000000 27 | 7 6 -0.003979868621841 28 | 7 7 0.760031883566609 29 | -------------------------------------------------------------------------------- /source/Project_04/input/h2o/STO-3G/v.dat: -------------------------------------------------------------------------------- 1 | 1 1 -61.580595358149914 2 | 2 1 -7.410821877330996 3 | 2 2 -10.009071226859687 4 | 3 1 0.000000000000000 5 | 3 2 0.000000000000000 6 | 3 3 -9.987550507419133 7 | 4 1 -0.014473835903318 8 | 4 2 -0.176890246723779 9 | 4 3 0.000000000000000 10 | 4 4 -9.944042952440439 11 | 5 1 0.000000000000000 12 | 5 2 0.000000000000000 13 | 5 3 -0.000000000000000 14 | 5 4 0.000000000000000 15 | 5 5 -9.875876065926128 16 | 6 1 -1.231685872788711 17 | 6 2 -2.977227202971528 18 | 6 3 -1.822241058022723 19 | 6 4 -1.471788274313766 20 | 6 5 0.000000000000000 21 | 6 6 -5.300202953839792 22 | 7 1 -1.231685872788712 23 | 7 2 -2.977227202971529 24 | 7 3 1.822241058022724 25 | 7 4 -1.471788274313766 26 | 7 5 0.000000000000001 27 | 7 6 -1.067166014696110 28 | 7 7 -5.300202953839793 29 | -------------------------------------------------------------------------------- /source/Project_04/solution_04.py: -------------------------------------------------------------------------------- 1 | from pyscf import gto 2 | import numpy as np 3 | import scipy.linalg 4 | from scipy.linalg import fractional_matrix_power 5 | from typing import Tuple 6 | np.set_printoptions(precision=7, linewidth=120, suppress=True) 7 | 8 | 9 | class Molecule: 10 | def __init__(self): 11 | # Project 03 existed 12 | self.atom_charges = NotImplemented # type: np.ndarray 13 | self.atom_coords = NotImplemented # type: np.ndarray 14 | self.natm = NotImplemented # type: int 15 | self.mol = NotImplemented # type: gto.Mole 16 | self.nao = NotImplemented # type: int 17 | self.charge = 0 # type: int 18 | self.nocc = NotImplemented # type: int 19 | # Project 04 added 20 | self.mo_coeff = NotImplemented # type: np.ndarray 21 | self.mo_energy = NotImplemented # type: np.ndarray 22 | self.eri_ao = NotImplemented # type: np.ndarray 23 | self.eri_mo = NotImplemented # type: np.ndarray 24 | self.energy_rhf = NotImplemented # type: np.ndarray 25 | self.energy_corr = NotImplemented # type: np.ndarray 26 | 27 | def construct_from_dat_file(self, file_path: str): 28 | # Same to Project 01 29 | with open(file_path, "r") as f: 30 | dat = np.array([line.split() for line in f.readlines()][1:]) 31 | self.atom_charges = np.array(dat[:, 0], dtype=float).astype(int) 32 | self.atom_coords = np.array(dat[:, 1:4], dtype=float) 33 | self.natm = self.atom_charges.shape[0] 34 | 35 | def obtain_mol_instance(self, basis: str, verbose=0): 36 | # Same to Project 03 37 | mol = gto.Mole() 38 | mol.unit = "Bohr" 39 | mol.atom = "\n".join([("{:3d} " + " ".join(["{:25.18f}"] * 3)).format(chg, *coord) for chg, coord in zip(self.atom_charges, self.atom_coords)]) 40 | mol.basis = basis 41 | mol.charge = self.charge 42 | mol.spin = 0 43 | mol.verbose = verbose 44 | self.mol = mol.build() 45 | 46 | def eng_nuclear_repulsion(self) -> float: 47 | # Same to Project 03, PySCF approach 48 | return self.mol.energy_nuc() 49 | 50 | def obtain_nao(self): 51 | # Same to Project 03, PySCF approach 52 | self.nao = self.mol.nao_nr() 53 | 54 | def obtain_nocc(self): 55 | # Same to Project 03 56 | assert (self.atom_charges.sum() - self.charge) % 2 == 0 57 | self.nocc = (self.atom_charges.sum() - self.charge) // 2 58 | 59 | def integral_ovlp(self) -> np.ndarray: 60 | # Same to Project 03, PySCF approach 61 | return self.mol.intor("int1e_ovlp") 62 | 63 | def integral_kin(self) -> np.ndarray: 64 | # Same to Project 03, PySCF approach 65 | return self.mol.intor("int1e_kin") 66 | 67 | def integral_nuc(self) -> np.ndarray: 68 | # Same to Project 03, PySCF approach 69 | return self.mol.intor("int1e_nuc") 70 | 71 | def get_hcore(self) -> np.ndarray: 72 | # Same to Project 03 73 | return self.integral_kin() + self.integral_nuc() 74 | 75 | def integral_eri(self) -> np.ndarray: 76 | # Same to Project 03, PySCF approach 77 | return self.mol.intor("int2e") 78 | 79 | def integral_ovlp_m1d2(self) -> np.ndarray: 80 | # Same to Project 03, SciPy approach 81 | return fractional_matrix_power(self.integral_ovlp(), -1/2) 82 | 83 | def obtain_eri_ao(self): 84 | # Attribute Modification: `eri_ao` atomic orbital electron repulsion integral 85 | self.eri_ao = self.integral_eri() 86 | 87 | def get_fock(self, dm: np.ndarray) -> np.ndarray: 88 | # Same to Project 03, but use self.eri_ao 89 | return self.get_hcore() + (self.eri_ao * dm).sum(axis=(-1, -2)) - 0.5 * (self.eri_ao * dm[:, None, :]).sum(axis=(-1, -3)) 90 | 91 | def get_coeff_from_fock_diag(self, fock: np.ndarray) -> np.ndarray: 92 | # Same to Project 03, Scipy Approach 93 | return scipy.linalg.eigh(fock, self.integral_ovlp())[1] 94 | 95 | def make_rdm1(self, coeff: np.ndarray) -> np.ndarray: 96 | # Same to Project 03 97 | return 2 * coeff[:, :self.nocc] @ coeff[:, :self.nocc].T 98 | 99 | def get_updated_dm(self, dm: np.ndarray) -> np.ndarray: 100 | # Same to Project 03 101 | return self.make_rdm1(self.get_coeff_from_fock_diag(self.get_fock(dm))) 102 | 103 | def eng_total(self, dm: np.ndarray) -> float: 104 | # Same to Project 03 105 | return (0.5 * (self.get_hcore() + self.get_fock(dm)) * dm).sum() + self.eng_nuclear_repulsion() 106 | 107 | def scf_process(self, dm_guess: np.ndarray=None) -> Tuple[float, np.ndarray]: 108 | # Same to Project 03, but do not make debug output 109 | eng, dm = 0., np.zeros((self.nao, self.nao)) if dm_guess is None else np.copy(dm_guess) 110 | max_iter, thresh_eng, thresh_dm = 64, 1e-10, 1e-8 111 | for epoch in range(max_iter): 112 | eng_next, dm_next = self.eng_total(dm), self.get_updated_dm(dm) 113 | if np.abs(eng_next - eng) < thresh_eng and np.linalg.norm(dm_next - dm) < thresh_dm: 114 | eng, dm = eng_next, dm_next 115 | break 116 | eng, dm = eng_next, dm_next 117 | return eng, dm 118 | 119 | def obtain_scf_intermediates(self, dm_guess: np.ndarray=None): 120 | # Attribute Modification: `energy_rhf` Total energy of RHF 121 | # Attribute Modification: `mo_energy` Molecular orbital energies 122 | # Attribute Modification: `mo_coeff` Molecular orbital coefficients 123 | eng, dm = self.scf_process(dm_guess) 124 | self.energy_rhf = eng 125 | self.mo_energy, self.mo_coeff = scipy.linalg.eigh(self.get_fock(dm), self.integral_ovlp()) 126 | 127 | @staticmethod 128 | def repeat_loop(dim: int, nested: int) -> np.ndarray: 129 | return np.array([np.tile(np.repeat(np.arange(dim), dim**(nested - 1 - i)), dim**i) for i in range(nested)]).T 130 | 131 | def get_eri_mo_naive(self) -> np.ndarray: 132 | # Naive algorithm 133 | # Output: MO electron repulsion integral 134 | eri_ao, coeff = self.eri_ao, self.mo_coeff 135 | loop_indices = self.repeat_loop(self.nao, 4) 136 | eri_mo = np.zeros((self.nao, self.nao, self.nao, self.nao)) 137 | for p, q, r, s in loop_indices: 138 | for u, v, k, l in loop_indices: 139 | eri_mo[p, q, r, s] += eri_ao[u, v, k, l] * coeff[u, p] * coeff[v, q] * coeff[k, r] * coeff[l, s] 140 | return eri_mo 141 | 142 | def get_eri_mo_smarter(self): 143 | # Smarter algorithm 144 | # Output: MO electron repulsion integral 145 | eri_ao, coeff = self.eri_ao, self.mo_coeff 146 | loop_indices = self.repeat_loop(self.nao, 4) 147 | tmp_1 = np.zeros((self.nao, self.nao, self.nao, self.nao)) 148 | for u, v, k, l in loop_indices: 149 | for p in range(self.nao): 150 | tmp_1[p, v, k, l] += eri_ao[u, v, k, l] * coeff[u, p] 151 | tmp_2 = np.zeros((self.nao, self.nao, self.nao, self.nao)) 152 | for p, v, k, l in loop_indices: 153 | for q in range(self.nao): 154 | tmp_2[p, q, k, l] += tmp_1[p, v, k, l] * coeff[v, q] 155 | tmp_1.fill(0) 156 | for p, q, k, l in loop_indices: 157 | for r in range(self.nao): 158 | tmp_1[p, q, r, l] += tmp_2[p, q, k, l] * coeff[k, r] 159 | tmp_2.fill(0) 160 | for p, q, r, l in loop_indices: 161 | for s in range(self.nao): 162 | tmp_2[p, q, r, s] += tmp_1[p, q, r, l] * coeff[l, s] 163 | return tmp_2 164 | 165 | def get_eri_mo_einsum(self): 166 | # Use numpy.einsum to automatically find optimal contraction path 167 | # Output: MO electron repulsion integral 168 | return np.einsum("uvkl, up, vq, kr, ls -> pqrs", self.eri_ao, self.mo_coeff, self.mo_coeff, self.mo_coeff, self.mo_coeff, optimize=True) 169 | 170 | def obtain_eri_mo(self): 171 | # Attribute Modification: `eri_mo` Molecular orbital electron repulsion integral 172 | self.eri_mo = self.get_eri_mo_einsum() 173 | 174 | def eng_mp2_corr(self): 175 | # Output: (Restricted) MP2 correlation energy 176 | nocc, e = self.nocc, self.mo_energy 177 | eri_iajb = self.eri_mo[:nocc, nocc:, :nocc, nocc:] 178 | D_iajb = e[:nocc, None, None, None] - e[None, nocc:, None, None] + e[None, None, :nocc, None] - e[None, None, None, nocc:] 179 | return (eri_iajb * (2 * eri_iajb - eri_iajb.swapaxes(-1, -3)) / D_iajb).sum() 180 | 181 | def obtain_mp2_corr(self): 182 | # Attribute Modification: `energy_corr` Post-HF (in this project is RMP2) correlation energy 183 | self.energy_corr = self.eng_mp2_corr() 184 | 185 | def print_solution_04(self): 186 | self.obtain_nao() 187 | self.obtain_nocc() 188 | self.obtain_eri_ao() 189 | self.obtain_scf_intermediates() 190 | self.obtain_eri_mo() 191 | self.obtain_mp2_corr() 192 | print("SCF total energy: {:16.8f}".format(self.energy_rhf)) 193 | print("MP2 correlation energy: {:16.8f}".format(self.energy_corr)) 194 | print("MP2 total energy: {:16.8f}".format(self.energy_rhf + self.energy_corr)) 195 | 196 | 197 | if __name__ == '__main__': 198 | sol_mole = Molecule() 199 | sol_mole.construct_from_dat_file("input/h2o/STO-3G/geom.dat") 200 | sol_mole.obtain_mol_instance(basis="STO-3G") 201 | sol_mole.print_solution_04() 202 | 203 | -------------------------------------------------------------------------------- /source/Project_05/demo_data_h2o_sto3g.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajz34/PyCrawfordProgProj/a3c5670d1d3b9f5271208884594435b58398bf63/source/Project_05/demo_data_h2o_sto3g.dat -------------------------------------------------------------------------------- /source/Project_05/input/ch4/STO-3G/enuc.dat: -------------------------------------------------------------------------------- 1 | 13.497304462036480 2 | -------------------------------------------------------------------------------- /source/Project_05/input/ch4/STO-3G/geom.dat: -------------------------------------------------------------------------------- 1 | 5 2 | 6.000000000000 -0.000000000000 0.000000000000 0.000000000000 3 | 1.000000000000 1.183771681898 -1.183771681898 -1.183771681898 4 | 1.000000000000 1.183771681898 1.183771681898 1.183771681898 5 | 1.000000000000 -1.183771681898 1.183771681898 -1.183771681898 6 | 1.000000000000 -1.183771681898 -1.183771681898 1.183771681898 7 | -------------------------------------------------------------------------------- /source/Project_05/input/ch4/STO-3G/input.dat: -------------------------------------------------------------------------------- 1 | psi: ( 2 | label = "CH4 SCF Test Case" 3 | wfn = scf 4 | jobtype = oeprop 5 | reference = rhf 6 | basis = "STO-3G" 7 | units = angstrom 8 | subgroup = c1 9 | delete_tei = false 10 | delete_oei = false 11 | zmat = ( 12 | C 13 | H 1 r 14 | H 1 r 2 td 15 | H 1 r 2 td 3 d 16 | H 1 r 2 td 4 d 17 | ) 18 | zvars = ( 19 | r 1.085 20 | td 109.47122063449069136958 21 | d 120.0 22 | ) 23 | ) 24 | 25 | basis: ( 26 | carbon: "STO-3G" = 27 | ( (S ( 71.61683730 0.15432900) 28 | ( 13.04509630 0.53532810) 29 | ( 3.53051220 0.44463450) ) 30 | (S ( 2.94124940 -0.09996720) 31 | ( 0.68348310 0.39951280) 32 | ( 0.22228990 0.70011550) ) 33 | (P ( 2.94124940 0.15591630) 34 | ( 0.68348310 0.60768370) 35 | ( 0.22228990 0.39195740) ) 36 | ) 37 | 38 | hydrogen: "STO-3G"= 39 | ( (S ( 3.42525090 0.15432890) 40 | ( 0.62391370 0.53532810) 41 | ( 0.16885540 0.44463450) ) 42 | ) 43 | ) 44 | -------------------------------------------------------------------------------- /source/Project_05/input/ch4/STO-3G/mux.dat: -------------------------------------------------------------------------------- 1 | 1 1 0.000000000000000 2 | 2 1 0.000000000000000 3 | 2 2 0.000000000000000 4 | 3 1 -0.071855488532817 5 | 3 2 -0.838743574800986 6 | 3 3 0.000000000000000 7 | 4 1 -0.000000000000000 8 | 4 2 0.000000000000000 9 | 4 3 -0.000000000000000 10 | 4 4 0.000000000000000 11 | 5 1 0.000000000000000 12 | 5 2 0.000000000000000 13 | 5 3 -0.000000000000000 14 | 5 4 0.000000000000000 15 | 5 5 0.000000000000000 16 | 6 1 -0.004780775261548 17 | 6 2 -0.306592476518555 18 | 6 3 -0.519567036508228 19 | 6 4 0.163831354490276 20 | 6 5 0.163831354490276 21 | 6 6 -1.183771681897730 22 | 7 1 -0.004780775261548 23 | 7 2 -0.306592476518555 24 | 7 3 -0.519567036508228 25 | 7 4 -0.163831354490276 26 | 7 5 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8.002367061810450 2 | -------------------------------------------------------------------------------- /source/Project_05/input/h2o/DZ/geom.dat: -------------------------------------------------------------------------------- 1 | 3 2 | 8.000000000000 0.000000000000 -0.143225816552 0.000000000000 3 | 1.000000000000 1.638036840407 1.136548822547 -0.000000000000 4 | 1.000000000000 -1.638036840407 1.136548822547 -0.000000000000 5 | -------------------------------------------------------------------------------- /source/Project_05/input/h2o/DZ/input.dat: -------------------------------------------------------------------------------- 1 | psi: ( 2 | label = "H2O SCF Test Case" 3 | memory = (10.0 MB) 4 | wfn = scf 5 | jobtype = oeprop 6 | delete_tei = false 7 | delete_oei = false 8 | reference = rhf 9 | basis = "DZ" 10 | subgroup = c1 11 | zmat = ((o) (h 1 1.1) (h 1 1.1 2 104.0)) 12 | ) 13 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /source/Project_05/input/h2o/DZP/enuc.dat: -------------------------------------------------------------------------------- 1 | 8.002367061810450 2 | -------------------------------------------------------------------------------- /source/Project_05/input/h2o/DZP/geom.dat: -------------------------------------------------------------------------------- 1 | 3 2 | 8.000000000000 0.000000000000 -0.143225816552 0.000000000000 3 | 1.000000000000 1.638036840407 1.136548822547 -0.000000000000 4 | 1.000000000000 -1.638036840407 1.136548822547 -0.000000000000 5 | -------------------------------------------------------------------------------- /source/Project_05/input/h2o/DZP/input.dat: -------------------------------------------------------------------------------- 1 | psi: ( 2 | label = "H2O SCF Test Case" 3 | memory = (10.0 MB) 4 | wfn = scf 5 | jobtype = oeprop 6 | delete_tei = false 7 | delete_oei = false 8 | reference = rhf 9 | puream = false 10 | basis = "DZP" 11 | subgroup = c1 12 | zmat = ((o) (h 1 1.1) (h 1 1.1 2 104.0)) 13 | ) 14 | -------------------------------------------------------------------------------- /source/Project_05/input/h2o/STO-3G/enuc.dat: -------------------------------------------------------------------------------- 1 | 8.002367061810450 2 | -------------------------------------------------------------------------------- /source/Project_05/input/h2o/STO-3G/eri.dat: -------------------------------------------------------------------------------- 1 | 1 1 1 1 4.785065404705506 2 | 2 1 1 1 0.741380351973408 3 | 2 2 1 1 1.118946866342470 4 | 2 1 2 1 0.136873385354388 5 | 2 2 2 1 0.256633394730974 6 | 2 2 2 2 0.817206321526058 7 | 3 3 1 1 1.115813812152428 8 | 4 4 1 1 1.115813812152428 9 | 5 5 1 1 1.115813812152428 10 | 3 1 3 1 0.024477412258099 11 | 4 1 4 1 0.024477412258099 12 | 5 1 5 1 0.024477412258099 13 | 3 3 2 1 0.256683985810103 14 | 4 4 2 1 0.256683985810103 15 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-------------------------------------------------------------------------------- 1 | 3 2 | 8.000000000000 0.000000000000 -0.143225816552 0.000000000000 3 | 1.000000000000 1.638036840407 1.136548822547 -0.000000000000 4 | 1.000000000000 -1.638036840407 1.136548822547 -0.000000000000 5 | -------------------------------------------------------------------------------- /source/Project_05/input/h2o/STO-3G/input.dat: -------------------------------------------------------------------------------- 1 | psi: ( 2 | label = "H2O SCF Test Case" 3 | memory = (10.0 MB) 4 | wfn = scf 5 | jobtype = oeprop 6 | delete_tei = false 7 | delete_oei = false 8 | reference = rhf 9 | basis = "STO-3G" 10 | subgroup = c1 11 | zmat = ((o) (h 1 1.1) (h 1 1.1 2 104.0)) 12 | ) 13 | -------------------------------------------------------------------------------- /source/Project_05/input/h2o/STO-3G/mux.dat: -------------------------------------------------------------------------------- 1 | 1 1 -0.000000000000000 2 | 2 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2 0.143225816551918 4 | 3 1 -0.000000000000000 5 | 3 2 0.000000000000000 6 | 3 3 0.143225816551918 7 | 4 1 -0.050791929587912 8 | 4 2 -0.641172844324925 9 | 4 3 -0.000000000000000 10 | 4 4 0.143225816551918 11 | 5 1 -0.000000000000000 12 | 5 2 0.000000000000000 13 | 5 3 0.000000000000000 14 | 5 4 -0.000000000000000 15 | 5 5 0.143225816551918 16 | 6 1 0.003758676726377 17 | 6 2 -0.149971890752635 18 | 6 3 -0.108952162150434 19 | 6 4 -0.334090713364948 20 | 6 5 0.000000000000000 21 | 6 6 -1.136548822546795 22 | 7 1 0.003758676726377 23 | 7 2 -0.149971890752635 24 | 7 3 0.108952162150434 25 | 7 4 -0.334090713364948 26 | 7 5 0.000000000000000 27 | 7 6 -0.206578984758302 28 | 7 7 -1.136548822546794 29 | -------------------------------------------------------------------------------- /source/Project_05/input/h2o/STO-3G/muz.dat: -------------------------------------------------------------------------------- 1 | 1 1 -0.000000000000000 2 | 2 1 -0.000000000000000 3 | 2 2 -0.000000000000000 4 | 3 1 0.000000000000000 5 | 3 2 -0.000000000000000 6 | 3 3 -0.000000000000000 7 | 4 1 0.000000000000000 8 | 4 2 0.000000000000000 9 | 4 3 0.000000000000000 10 | 4 4 -0.000000000000000 11 | 5 1 -0.050791929587912 12 | 5 2 -0.641172844324925 13 | 5 3 -0.000000000000000 14 | 5 4 0.000000000000000 15 | 5 5 -0.000000000000000 16 | 6 1 -0.000000000000000 17 | 6 2 0.000000000000000 18 | 6 3 0.000000000000000 19 | 6 4 0.000000000000000 20 | 6 5 -0.248967955099984 21 | 6 6 0.000000000000000 22 | 7 1 -0.000000000000000 23 | 7 2 0.000000000000000 24 | 7 3 -0.000000000000000 25 | 7 4 0.000000000000000 26 | 7 5 -0.248967955099984 27 | 7 6 0.000000000000000 28 | 7 7 0.000000000000000 29 | -------------------------------------------------------------------------------- /source/Project_05/input/h2o/STO-3G/s.dat: -------------------------------------------------------------------------------- 1 | 1 1 1.000000000000000 2 | 2 1 0.236703936510848 3 | 2 2 1.000000000000000 4 | 3 1 -0.000000000000000 5 | 3 2 0.000000000000000 6 | 3 3 1.000000000000000 7 | 4 1 -0.000000000000000 8 | 4 2 -0.000000000000000 9 | 4 3 -0.000000000000000 10 | 4 4 1.000000000000000 11 | 5 1 -0.000000000000000 12 | 5 2 0.000000000000000 13 | 5 3 0.000000000000000 14 | 5 4 -0.000000000000000 15 | 5 5 1.000000000000000 16 | 6 1 0.038405599785757 17 | 6 2 0.386138840478249 18 | 6 3 0.268438243716457 19 | 6 4 0.209726941420375 20 | 6 5 -0.000000000000000 21 | 6 6 1.000000000000000 22 | 7 1 0.038405599785757 23 | 7 2 0.386138840478250 24 | 7 3 -0.268438243716457 25 | 7 4 0.209726941420375 26 | 7 5 -0.000000000000000 27 | 7 6 0.181759886298063 28 | 7 7 1.000000000000000 29 | -------------------------------------------------------------------------------- /source/Project_05/input/h2o/STO-3G/t.dat: -------------------------------------------------------------------------------- 1 | 1 1 29.003199945539588 2 | 2 1 -0.168010939316492 3 | 2 2 0.808127954930347 4 | 3 1 0.000000000000000 5 | 3 2 0.000000000000000 6 | 3 3 2.528731198194763 7 | 4 1 0.000000000000000 8 | 4 2 -0.000000000000000 9 | 4 3 -0.000000000000000 10 | 4 4 2.528731198194763 11 | 5 1 -0.000000000000000 12 | 5 2 0.000000000000000 13 | 5 3 0.000000000000000 14 | 5 4 -0.000000000000000 15 | 5 5 2.528731198194763 16 | 6 1 -0.008416383544591 17 | 6 2 0.070517372751001 18 | 6 3 0.147090913304052 19 | 6 4 0.114920016354202 20 | 6 5 -0.000000000000000 21 | 6 6 0.760031883566609 22 | 7 1 -0.008416383544591 23 | 7 2 0.070517372751002 24 | 7 3 -0.147090913304052 25 | 7 4 0.114920016354202 26 | 7 5 -0.000000000000000 27 | 7 6 -0.003979868621841 28 | 7 7 0.760031883566609 29 | -------------------------------------------------------------------------------- /source/Project_05/input/h2o/STO-3G/v.dat: -------------------------------------------------------------------------------- 1 | 1 1 -61.580595358149914 2 | 2 1 -7.410821877330996 3 | 2 2 -10.009071226859687 4 | 3 1 0.000000000000000 5 | 3 2 0.000000000000000 6 | 3 3 -9.987550507419133 7 | 4 1 -0.014473835903318 8 | 4 2 -0.176890246723779 9 | 4 3 0.000000000000000 10 | 4 4 -9.944042952440439 11 | 5 1 0.000000000000000 12 | 5 2 0.000000000000000 13 | 5 3 -0.000000000000000 14 | 5 4 0.000000000000000 15 | 5 5 -9.875876065926128 16 | 6 1 -1.231685872788711 17 | 6 2 -2.977227202971528 18 | 6 3 -1.822241058022723 19 | 6 4 -1.471788274313766 20 | 6 5 0.000000000000000 21 | 6 6 -5.300202953839792 22 | 7 1 -1.231685872788712 23 | 7 2 -2.977227202971529 24 | 7 3 1.822241058022724 25 | 7 4 -1.471788274313766 26 | 7 5 0.000000000000001 27 | 7 6 -1.067166014696110 28 | 7 7 -5.300202953839793 29 | -------------------------------------------------------------------------------- /source/conf.py: -------------------------------------------------------------------------------- 1 | # Configuration file for the Sphinx documentation builder. 2 | # 3 | # This file only contains a selection of the most common options. For a full 4 | # list see the documentation: 5 | # https://www.sphinx-doc.org/en/master/usage/configuration.html 6 | 7 | # -- Path setup -------------------------------------------------------------- 8 | 9 | # If extensions (or modules to document with autodoc) are in another directory, 10 | # add these directories to sys.path here. If the directory is relative to the 11 | # documentation root, use os.path.abspath to make it absolute, like shown here. 12 | # 13 | # import os 14 | # import sys 15 | # sys.path.insert(0, os.path.abspath('.')) 16 | 17 | 18 | # -- Project information ----------------------------------------------------- 19 | 20 | project = 'Programming Tutorial in Chemistry by Python' 21 | copyright = '2020, ajz34' 22 | author = 'ajz34' 23 | 24 | 25 | # -- General configuration --------------------------------------------------- 26 | 27 | # Add any Sphinx extension module names here, as strings. They can be 28 | # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom 29 | # ones. 30 | extensions = [ 31 | "myst_nb", 32 | "sphinx_copybutton", 33 | "sphinx_togglebutton", 34 | "sphinx_thebe", 35 | ] 36 | 37 | # Add any paths that contain templates here, relative to this directory. 38 | templates_path = ['_templates'] 39 | 40 | # List of patterns, relative to source directory, that match files and 41 | # directories to ignore when looking for source files. 42 | # This pattern also affects html_static_path and html_extra_path. 43 | exclude_patterns = [] 44 | 45 | 46 | # -- Options for HTML output ------------------------------------------------- 47 | 48 | # The theme to use for HTML and HTML Help pages. See the documentation for 49 | # a list of builtin themes. 50 | # 51 | html_theme = 'sphinx_book_theme' 52 | thml_title = "Programming Tutorial in Chemistry by Python" 53 | 54 | # Add any paths that contain custom static files (such as style sheets) here, 55 | # relative to this directory. They are copied after the builtin static files, 56 | # so a file named "default.css" will overwrite the builtin "default.css". 57 | html_static_path = ['_static'] 58 | 59 | # -- Options for HTML output ------------------------------------------------- 60 | 61 | # https://myst-nb.readthedocs.io/en/latest/use/execute.html 62 | jupyter_execute_notebooks = "off" 63 | 64 | thebe_config = { 65 | "repository_url": "https://github.com/ajz34/PyCrawfordProgProj", 66 | "repository_branch": "master", 67 | } 68 | 69 | html_theme_options = { 70 | "repository_url": "https://github.com/ajz34/PyCrawfordProgProj", 71 | "launch_buttons": { 72 | "binderhub_url": "https://mybinder.org", 73 | "notebook_interface": "jupyterlab", 74 | "thebe": True, 75 | }, 76 | "path_to_docs": "source", 77 | "use_edit_page_button": True, 78 | "use_issues_button": True, 79 | "use_repository_button": True, 80 | "expand_sections": ["reference/index"] 81 | } 82 | -------------------------------------------------------------------------------- /source/index.rst: -------------------------------------------------------------------------------- 1 | .. PyCrowfordProgProj documentation master file, created by 2 | sphinx-quickstart on Thu Aug 13 14:49:10 2020. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Programming Tutorial in Chemistry by Python 7 | =========================================== 8 | 9 | .. admonition:: This project is under-construction and not original! 10 | :class: warning 11 | 12 | This is an on-going project which uses awesome `Crawford's Programming Projects `_ as original materials, so in many cases, several sentences may be shamelessly ctrl-c/ctrl-v'ed with little or a little modification. The author of this repository really thanks authors of the origin of this tutorial. 13 | 14 | The author also regards `PySCF `_ as one of the magnificent quantum packages. In this tutorial, PySCF may become the default SCF and orbital integral engine/interface. 15 | 16 | The author also thanks developers of `Executable Book Project `_, which provides pretty, toggleable and executable notebooks. Devs there are really enthusiasts. 17 | 18 | This tutorial is intended to touch on many, but certainly not all, of the fundamentals of Python/PySCF programming with an emphasis on quantum chemistry. 19 | 20 | Currently, the author is not going to write fundamentals of python. So before heading to the first project, the reader is suggested to review his/hers comperhension of python. Knowledge of other languages with OOP (object-oriented programming), and scientific calculation/simulation software (Matlab, Mathematica, etc.) is also appreciated. 21 | 22 | To begin work on the projects you can create a clone of this repository. First navigate to the directory where you would like to keep your programming projects. Then create the clone by this command 23 | 24 | .. code-block:: bash 25 | 26 | git clone https://github.com/ajz34/PyCrawfordProgProj.git 27 | 28 | Now you should see a directory called :code:`PyCrawfordProgProj/source` inside. You will find all of the files that you can see on github. 29 | 30 | 31 | Contents 32 | ======== 33 | 34 | .. toctree:: 35 | :maxdepth: 1 36 | 37 | Project_01/Project_01 38 | Project_02/Project_02 39 | Project_03/Project_03 40 | Project_04/Project_04 41 | Project_05/Project_05 42 | 43 | 44 | Indices and tables 45 | ================== 46 | 47 | * :ref:`genindex` 48 | * :ref:`modindex` 49 | * :ref:`search` 50 | --------------------------------------------------------------------------------