### Output log for SCF driver setup Source: https://veloxchem.org/docs/uv-vis Example output log showing the initialization and configuration of the Self Consistent Field driver. ```text Reading ethylene from PubChem... Reference: S. Kim, J. Chen, T. Cheng, A. Gindulyte, J. He, S. He, Q. Li, B. A. Shoemaker, P. A. Thiessen, B. Yu, L. Zaslavsky, J. Zhang, E. E. Bolton, Nucleic Acids Res., 2025, 53, D1516-D1525. Please double-check the compound since names may refer to more than one record. Self Consistent Field Driver Setup ==================================== Wave Function Model : Spin-Restricted Kohn-Sham Initial Guess Model : Superposition of Atomic Densities Convergence Accelerator : Two Level Direct Inversion of Iterative Subspace Max. Number of Iterations : 50 Max. Number of Error Vectors : 10 Convergence Threshold : 1.0e-06 ERI Screening Threshold : 1.0e-12 Linear Dependence Threshold : 1.0e-06 Exchange-Correlation Functional : CAM-B3LYP Molecular Grid Level : 4 * Info * Using the CAM-B3LYP functional. T. Yanai, D. P. Tew, and N. C. Handy., Chem. Phys. Lett. 393, 51 (2004) * Info * Using the Libxc library (v7.0.0). ``` -------------------------------- ### Install on Ubuntu Source: https://veloxchem.org/docs/installation Commands to install system dependencies, set up a virtual environment, and install VeloxChem on Ubuntu. ```bash $ sudo apt update $ sudo apt install build-essential wget cmake git python3 python3-pip python3-venv $ sudo apt install libopenblas-openmp-dev liblapacke-dev libeigen3-dev libboost-math-dev mpich ``` ```bash $ python3 -m venv vlxenv $ source vlxenv/bin/activate $ python3 -m pip install --upgrade pip setuptools wheel $ python3 -m pip install numpy mpi4py h5py cmake pybind11-global scikit-build ``` ```bash $ cd VeloxChem $ export SKBUILD_CONFIGURE_OPTIONS="-DCMAKE_CXX_COMPILER=mpicxx" $ export CMAKE_PREFIX_PATH=/path/to/your/libxc:$CMAKE_PREFIX_PATH $ export LD_LIBRARY_PATH=/path/to/your/libxc/lib:$LD_LIBRARY_PATH $ python3 -m pip install --no-build-isolation -v . ``` -------------------------------- ### SCF Driver setup output Source: https://veloxchem.org/docs/run-cluster Example output showing the configuration of the Self Consistent Field Driver, including the wave function model, convergence settings, and functional information. ```text Self Consistent Field Driver Setup ==================================== Wave Function Model : Spin-Restricted Kohn-Sham Initial Guess Model : Superposition of Atomic Densities Convergence Accelerator : Two Level Direct Inversion of Iterative Subspace Max. Number of Iterations : 50 Max. Number of Error Vectors : 10 Convergence Threshold : 1.0e-06 ERI Screening Threshold : 1.0e-12 Linear Dependence Threshold : 1.0e-06 Exchange-Correlation Functional : B3LYP Molecular Grid Level : 4 * Info * Using the B3LYP functional. P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch., J. Phys. Chem. 98, 11623 (1994) * Info * Using the Libxc library (v7.0.0). S. Lehtola, C. Steigemann, M. J.T. Oliveira, and M. A.L. Marques., SoftwareX 7, 1–5 (2018) * Info * Using the following algorithm for XC numerical integration. ``` -------------------------------- ### Install on Unix-like systems with conda-forge Source: https://veloxchem.org/docs/installation Commands to navigate to the source folder, create the conda environment, configure build options, and install the package. ```bash $ cd VeloxChem ``` ```bash $ conda env create -f vlx_env.yml $ conda activate vlxenv ``` ```bash $ export SKBUILD_CONFIGURE_OPTIONS="-DCMAKE_CXX_COMPILER=mpicxx" ``` ```bash $ python3 -m pip install --no-build-isolation -v . ``` -------------------------------- ### Example SCF output for LoProp calculation Source: https://veloxchem.org/docs/loc-prop Shows the SCF driver setup and convergence information for the LoProp calculation, including the nuclear repulsion energy and SCF energy in the reduced basis set. ```text Self Consistent Field Driver Setup ==================================== Wave Function Model : Spin-Restricted Hartree-Fock Initial Guess Model : Superposition of Atomic Densities Convergence Accelerator : Two Level Direct Inversion of Iterative Subspace Max. Number of Iterations : 50 Max. Number of Error Vectors : 10 Convergence Threshold : 1.0e-06 ERI Screening Threshold : 1.0e-12 Linear Dependence Threshold : 1.0e-06 * Info * Nuclear repulsion energy: 9.1282837280 a.u. * Info * Overlap matrix computed in 0.00 sec. * Info * Kinetic energy matrix computed in 0.00 sec. * Info * Nuclear potential matrix computed in 0.00 sec. * Info * Orthogonalization matrix computed in 0.00 sec. * Info * Starting Reduced Basis SCF calculation... * Info * ...done. SCF energy in reduced basis set: -75.995389009040 a.u. Time: 0.41 sec. ``` -------------------------------- ### Start JupyterLab Source: https://veloxchem.org/docs/installation Starts JupyterLab in the active environment, which should open in the default web browser. ```bash $ jupyter-lab ``` -------------------------------- ### Restarting a calculation with VeloxChem Source: https://veloxchem.org/docs/restart This example demonstrates how to initialize a calculation by reading from a previously generated SCF checkpoint file. ```python import veloxchem as vlx fname = "../output_files/c2h4" molecule, basis = vlx.read_molecule_and_basis(f"{fname}_scf.h5") scf_drv = vlx.ScfRestrictedDriver() scf_drv.filename = fname scf_results = scf_drv.compute(molecule, basis) rsp_drv = vlx.LinearResponseEigenSolver() rsp_drv.nstates = 5 rsp_drv.filename = fname rsp_results = rsp_drv.compute(molecule, basis, scf_results) ``` -------------------------------- ### SCF Driver Setup Output Source: https://veloxchem.org/docs/xray Example of the output generated by the SCF driver setup in VeloxChem. ```text Self Consistent Field Driver Setup ==================================== Wave Function Model : Spin-Restricted Kohn-Sham Initial Guess Model : Superposition of Atomic Densities Convergence Accelerator : Two Level Direct Inversion of Iterative Subspace Max. Number of Iterations : 50 Max. Number of Error Vectors : 10 Convergence Threshold : 1.0e-06 ERI Screening Threshold : 1.0e-12 Linear Dependence Threshold : 1.0e-06 Exchange-Correlation Functional : CAM-B3LYP-100 Molecular Grid Level : 4 * Info * Using the CAM-B3LYP-100 functional. ``` -------------------------------- ### OpenMMDynamics system initialization log Source: https://veloxchem.org/docs/conf-search Example log output showing charge compensation and bond length updates during system creation. ```text * Info * Sum of partial charges is not a whole number. * Info * Compensating by removing 4.000e-06 from the largest charge. * Info * Using GAFF (v2.11) parameters. Reference: J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, D. A. Case, J. Comput. Chem. 2004, 25, 1157-1174. * Info * Updated bond length 10-14 (cc-ss) to 0.169 nm * Info * Updated bond length 13-14 (cc-ss) to 0.168 nm * Info * Updated bond length 36-37 (os-c3) to 0.138 nm * Info * Updated bond length 43-44 (os-c3) to 0.138 nm * Info * Updated bond length 51-57 (ca-cc) to 0.151 nm * Info * Updated bond length 57-61 (cc-ss) to 0.169 nm * Info * Updated bond length 60-61 (cd-ss) to 0.168 nm * Info * Updated bond length 60-106 (cd-ca) to 0.151 nm * Info * Updated bond length 84-85 (os-c3) to 0.138 nm * Info * Updated bond length 91-92 (os-c3) to 0.138 nm * Info * Updated bond length 103-110 (ca-cc) to 0.151 nm * Info * Updated bond length 110-114 (cc-ss) to 0.169 nm * Info * Updated bond length 113-114 (cc-ss) to 0.169 nm * Info * Updated bond length 113-154 (cc-ca) to 0.151 nm * Info * Updated bond length 136-137 (os-c3) to 0.138 nm * Info * Updated bond length 143-144 (os-c3) to 0.138 nm * Info * Updated bond length 151-157 (ca-cc) to 0.151 nm * Info * Updated bond length 157-161 (cc-ss) to 0.169 nm * Info * Updated bond length 160-161 (cc-ss) to 0.169 nm * Info * Updated bond length 160-204 (cc-ca) to 0.151 nm * Info * Updated bond length 184-185 (os-c3) to 0.138 nm * Info * Updated bond length 191-192 (os-c3) to 0.138 nm * Info * Updated bond length 201-208 (ca-cc) to 0.151 nm * Info * Updated bond length 208-212 (cc-ss) to 0.169 nm * Info * Updated bond length 211-212 (cc-ss) to 0.169 nm * Info * Updated bond length 211-252 (cc-ca) to 0.151 nm * Info * Updated bond length 234-235 (os-c3) to 0.138 nm * Info * Updated bond length 241-242 (os-c3) to 0.138 nm * Info * Updated bond length 249-255 (ca-cc) to 0.151 nm * Info * Updated bond length 255-259 (cc-ss) to 0.169 nm * Info * Updated bond length 258-259 (cc-ss) to 0.169 nm * Info * Updated bond length 258-304 (cc-ca) to 0.151 nm ``` -------------------------------- ### Install on Cray systems Source: https://veloxchem.org/docs/installation Steps to load modules, set up a virtual environment, and compile VeloxChem on a Cray system. ```bash $ module load PrgEnv-gnu $ module load cpe $ module load cray-python ``` ```bash $ python3 -m venv --system-site-packages vlxenv $ source vlxenv/bin/activate $ python3 -m pip install --upgrade pip setuptools wheel $ python3 -m pip install h5py pytest psutil geometric cmake pybind11-global scikit-build ninja rdkit ``` ```bash $ cd VeloxChem $ export EIGEN_INCLUDE_DIR=/path/to/your/eigen $ export BOOST_INCLUDE_DIR=/path/to/your/boost-math $ export SKBUILD_CONFIGURE_OPTIONS="-DCMAKE_CXX_COMPILER=CC" $ export CMAKE_PREFIX_PATH=/path/to/your/libxc:$CMAKE_PREFIX_PATH $ export LD_LIBRARY_PATH=/path/to/your/libxc/lib:$LD_LIBRARY_PATH $ python3 -m pip install --no-build-isolation -v . ``` -------------------------------- ### Conformation 1 energy and weight output Source: https://veloxchem.org/docs/conf-search Example output showing energy and weight for the first conformation. ```text * Info * Conformation 1: Energy: 1617.202 kJ/mol, Weight: 0.3124 ``` -------------------------------- ### C6 coefficient output example Source: https://veloxchem.org/docs/weak-interactions Example of the formatted output string for a C6 coefficient. ```text C6 coefficient: 127.7308 (a.u.) ``` -------------------------------- ### Configure vibrational Raman job Source: https://veloxchem.org/docs/vib-spect Example configuration for a vibrational analysis job with Raman enabled. ```text @jobs task: vibrational @end @method settings xcfun: b3lyp basis: def2-svp @end @vibrational do_raman: yes @end @molecule charge: 0 multiplicity: 1 xyz: ... @end ``` -------------------------------- ### Conformation 2 energy and weight output Source: https://veloxchem.org/docs/conf-search Example output showing energy and weight for the second conformation. ```text * Info * Conformation 2: Energy: 1617.256 kJ/mol, Weight: 0.3057 ``` -------------------------------- ### Conformation 3 energy and weight output Source: https://veloxchem.org/docs/conf-search Example output showing energy and weight for the third conformation. ```text * Info * Conformation 3: Energy: 1617.828 kJ/mol, Weight: 0.2431 ``` -------------------------------- ### SCF restart output log Source: https://veloxchem.org/docs/restart Example output showing the SCF driver successfully restarting from a checkpoint file. ```text Self Consistent Field Driver Setup ==================================== Wave Function Model : Spin-Restricted Hartree-Fock Initial Guess Model : Restart from Checkpoint Convergence Accelerator : Direct Inversion of Iterative Subspace Max. Number of Iterations : 50 Max. Number of Error Vectors : 10 Convergence Threshold : 1.0e-06 ERI Screening Threshold : 1.0e-12 Linear Dependence Threshold : 1.0e-06 * Info * Restarting from checkpoint file: ../output_files/c2h4_scf.h5 Iter. | Hartree-Fock Energy | Energy Change | Gradient Norm | Max. Gradient | Density Change -------------------------------------------------------------------------------------------- 1 -77.977992711737 0.0000000000 0.00000030 0.00000005 0.00000000 * Info * Checkpoint written to file: ../output_files/c2h4_scf.h5 * Info * SCF results written to file: ../output_files/c2h4.h5 *** SCF converged in 1 iterations. Time: 0.02 sec. Spin-Restricted Hartree-Fock: ----------------------------- Total Energy : -77.9779927117 a.u. Electronic Energy : -111.5154198613 a.u. Nuclear Repulsion Energy : 33.5374271495 a.u. ------------------------------------ Gradient Norm : 0.0000002992 a.u. Ground State Information ``` -------------------------------- ### Solvation free energy output Source: https://veloxchem.org/docs/solvation Example output showing the calculated solvation free energy value. ```text Solvation free energy: -375.315 kJ/mol ``` -------------------------------- ### Install with custom build jobs Source: https://veloxchem.org/docs/installation Control the number of parallel build jobs using the VLX_NUM_BUILD_JOBS environment variable. ```bash $ VLX_NUM_BUILD_JOBS=N python3 -m pip install --no-build-isolation -v . ``` -------------------------------- ### Restart optimization from checkpoint file Source: https://veloxchem.org/docs/restart Restarts a geometry optimization from a checkpoint file. Reads the molecule and basis from the SCF checkpoint file, sets the SCF and optimization driver filenames to the same base name, and computes the optimization. The output shows the optimization driver setup and the start of the optimization. ```python import veloxchem as vlx fname = "../output_files/c2h4" molecule, basis = vlx.read_molecule_and_basis(f"{fname}_scf.h5") scf_drv = vlx.ScfRestrictedDriver() scf_drv.filename = fname opt_drv = vlx.OptimizationDriver(scf_drv) opt_drv.filename = fname opt_results = opt_drv.compute(molecule, basis) ``` ```text Optimization Driver Setup =========================== Coordinate System : TRIC Constraints : No Max. Number of Steps : 300 Transition State : No IRC : No Hessian : never * Info * Using geomeTRIC for geometry optimization. L.-P. Wang and C.C. Song, J. Chem. Phys. 2016, 144, 214108 * Info * Reading molecular geometry from checkpoint file... Optimization Step 0 ===================== ``` -------------------------------- ### Initialize Absorption driver and print keywords Source: https://veloxchem.org/docs/keywords Creates an Absorption object, initializes the driver, and prints the available keywords. Use this to start a UV/vis absorption spectrum calculation. ```python prop = vlx.Absorption() prop.init_driver() prop.print_keywords() ``` -------------------------------- ### SCF driver output log for restart Source: https://veloxchem.org/docs/restart Example log output showing the initialization of the SCF driver and the confirmation that it is restarting from the specified checkpoint file. ```text Reading water from PubChem... Reference: S. Kim, J. Chen, T. Cheng, A. Gindulyte, J. He, S. He, Q. Li, B. A. Shoemaker, P. A. Thiessen, B. Yu, L. Zaslavsky, J. Zhang, E. E. Bolton, Nucleic Acids Res., 2025, 53, D1516-D1525. Please double-check the compound since names may refer to more than one record. Self Consistent Field Driver Setup ==================================== Wave Function Model : Spin-Restricted Kohn-Sham Initial Guess Model : Restart from Checkpoint Convergence Accelerator : Direct Inversion of Iterative Subspace Max. Number of Iterations : 50 Max. Number of Error Vectors : 10 Convergence Threshold : 1.0e-06 ERI Screening Threshold : 1.0e-12 Linear Dependence Threshold : 1.0e-06 Exchange-Correlation Functional : B3LYP Molecular Grid Level : 4 * Info * Using the B3LYP functional. P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch., J. Phys. Chem. 98, 11623 (1994) * Info * Using the Libxc library (v7.0.0). S. Lehtola, C. Steigemann, M. J.T. Oliveira, and M. A.L. Marques., SoftwareX 7, 1–5 (2018) * Info * Using the following algorithm for XC numerical integration. J. Kussmann, H. Laqua and C. Ochsenfeld, J. Chem. Theory Comput. 2021, 17, 1512-1521 * Info * Restarting from checkpoint file: my_vlx_calc_scf.h5 ``` -------------------------------- ### Install required Python packages Source: https://veloxchem.org/docs/installation Install the necessary Python dependencies for VeloxChem. ```bash $ python3 -m pip install h5py pybind11 pytest psutil ``` -------------------------------- ### Configure and compile for NVIDIA GPUs Source: https://veloxchem.org/docs/installation Copy the CUDA setup file, edit the Makefile, and compile the project. Set OMP_NUM_THREADS to the number of GPU devices per node. ```bash $ cd $VLXHOME $ cp src/Makefile.setup_cuda src/Makefile.setup ``` ```bash cd $VLXHOME make -C src -j ... export PYTHONPATH=$VLXHOME/build/python:$PYTHONPATH export PATH=$VLXHOME/build/bin:$PATH export OMP_NUM_THREADS=... export OMP_PLACES=cores ``` -------------------------------- ### Run MD simulation with solvation Source: https://veloxchem.org/docs/md Demonstrates creating a system with the 'tip3p' solvent and running an NVT ensemble simulation. ```python opm_dyn = vlx.OpenMMDynamics() opm_dyn.create_system_from_molecule( molecule, ff_gen, filename="ethanol", # system parameters and coordinates written to .xml and .pdb solvent="tip3p", residue_name="ETH", ) opm_dyn.run_md( ensemble="NVT", temperature=300, # in Kelvin timestep=2.0, # in fs nsteps=10000, snapshots=200, traj_file="ethanol_md.pdb", ) ``` -------------------------------- ### Install dftd4-python via conda Source: https://veloxchem.org/docs/installation Recommended way to install the dftd4-python package in a conda environment. ```bash $ conda install dftd4-python -c conda-forge ``` -------------------------------- ### Install MPI4Py for GPU builds Source: https://veloxchem.org/docs/installation Install MPI4Py using the same compiler intended for the VeloxChem build process. ```bash $ export CC=... $ export MPICC=... $ python3 -m pip install --no-deps --no-binary=mpi4py --no-cache-dir -v mpi4py ``` -------------------------------- ### Example output of keys in SCF restart file Source: https://veloxchem.org/docs/restart Shows the typical keys found in an SCF restart file, including orbital energies, occupations, coordinates, and settings. ```text alpha_energies alpha_occupations alpha_orbitals atom_basis_labels_flattened atom_coordinates basis_set dft_func_label method_settings molecular_charge nuclear_charges nuclear_repulsion number_of_alpha_electrons number_of_atoms number_of_beta_electrons potfile_text scf_settings scf_type spin_multiplicity ``` -------------------------------- ### Workaround for macOS pip install error: set CMAKE_OSX_DEPLOYMENT_TARGET Source: https://veloxchem.org/docs/installation Workaround for the macOS pip install error. Manually add the CMAKE_OSX_DEPLOYMENT_TARGET option to CMAKE_ARGS and redo the pip install step. First check the platform with python3 -c 'import sysconfig; print(sysconfig.get_platform())'. ```bash $ python3 -c 'import sysconfig; print(sysconfig.get_platform())' macosx-10.9-x86_64 $ export CMAKE_ARGS="-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.9" $ python3 -m pip install --no-build-isolation . ``` -------------------------------- ### SCF Driver output example Source: https://veloxchem.org/docs/loc-prop Example output from the Self Consistent Field (SCF) driver showing the convergence of the Hartree-Fock energy. ```text Self Consistent Field Driver Setup ==================================== Wave Function Model : Spin-Restricted Hartree-Fock Initial Guess Model : Superposition of Atomic Densities Convergence Accelerator : Two Level Direct Inversion of Iterative Subspace Max. Number of Iterations : 50 Max. Number of Error Vectors : 10 Convergence Threshold : 1.0e-06 ERI Screening Threshold : 1.0e-12 Linear Dependence Threshold : 1.0e-06 * Info * Starting Reduced Basis SCF calculation... * Info * ...done. SCF energy in reduced basis set: -114.985032880309 a.u. Time: 0.05 sec. Iter. | Hartree-Fock Energy | Energy Change | Gradient Norm | Max. Gradient | Density Change -------------------------------------------------------------------------------------------- 1 -115.032021654336 0.0000000000 0.10560685 0.01073554 0.00000000 2 -115.033365303353 -0.0013436490 0.02909872 0.00322626 0.03152624 3 -115.033457176279 -0.0000918729 0.00644690 0.00095115 0.00787787 4 -115.033464315327 -0.0000071390 0.00211836 0.00024088 0.00282760 5 -115.033465123956 -0.0000008086 0.00065282 0.00008165 0.00126450 6 -115.033465189352 -0.0000000654 0.00017067 0.00002207 0.00027179 7 -115.033465196950 -0.0000000076 0.00003215 0.00000409 0.00012239 8 -115.033465197230 -0.0000000003 0.00000526 0.00000072 0.00002194 ``` -------------------------------- ### Create OptimizationDriver and print keywords Source: https://veloxchem.org/docs/keywords Creates an OptimizationDriver instance and prints its available keywords. The output shows the driver's configuration options, including coordinate system, constraints, trust radius, maximum iterations, and convergence criteria. ```python opt_drv = vlx.OptimizationDriver(scf_drv) opt_drv.print_keywords() ``` -------------------------------- ### SCF driver setup output for methane Source: https://veloxchem.org/docs/polarizability Console output from a VeloxChem SCF calculation for methane, showing the B3LYP functional and the SCF driver setup parameters. Includes a PubChem reference and a warning to double-check the compound name. ```text Reading methane from PubChem... Reference: S. Kim, J. Chen, T. Cheng, A. Gindulyte, J. He, S. He, Q. Li, B. A. Shoemaker, P. A. Thiessen, B. Yu, L. Zaslavsky, J. Zhang, E. E. Bolton, Nucleic Acids Res., 2025, 53, D1516-D1525. Please double-check the compound since names may refer to more than one record. Self Consistent Field Driver Setup ==================================== Wave Function Model : Spin-Restricted Kohn-Sham Initial Guess Model : Superposition of Atomic Densities Convergence Accelerator : Two Level Direct Inversion of Iterative Subspace Max. Number of Iterations : 50 Max. Number of Error Vectors : 10 Convergence Threshold : 1.0e-06 ERI Screening Threshold : 1.0e-12 Linear Dependence Threshold : 1.0e-06 Exchange-Correlation Functional : B3LYP Molecular Grid Level : 4 * Info * Using the B3LYP functional. P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch., J. Phys. Chem. 98, 11623 (1994) ``` -------------------------------- ### Initialize OpenMMDynamics system Source: https://veloxchem.org/docs/conf-search Configures an OpenMMDynamics instance using a molecule and force field generator. ```python opm_dyn = vlx.OpenMMDynamics() opm_dyn.create_system_from_molecule(molecule, ff_gen, filename='tq-polymer', residue_name='MOL') ``` -------------------------------- ### macOS pip install error: ValueError invalid literal for int() Source: https://veloxchem.org/docs/installation Error output encountered at the end of the pip install step on macOS. The error shows a ValueError with 'invalid literal for int() with base 10: '''. This is a known issue. ```text ... base_version = tuple(int(x) for x in base_version.split(".")) ValueError: invalid literal for int() with base 10: '' error: subprocess-exited-with-error ... ``` -------------------------------- ### Configure and compile for AMD GPUs Source: https://veloxchem.org/docs/installation Copy the HIP setup file, edit the Makefile, and compile the project. Ensure OMP_NUM_THREADS matches the number of GPU devices per node. ```bash $ cd $VLXHOME $ cp src/Makefile.setup_hip src/Makefile.setup ``` ```bash $ cd $VLXHOME $ make -C src -j ... $ export PYTHONPATH=$VLXHOME/build/python:$PYTHONPATH $ export PATH=$VLXHOME/build/bin:$PATH $ export OMP_NUM_THREADS=... $ export OMP_PLACES=cores ``` -------------------------------- ### Resonance Raman setup with VeloxChem (formaldehyde) Source: https://veloxchem.org/docs/vib-spect Sets up a resonance Raman calculation for formaldehyde using the CAM-B3LYP functional and the def2-svp basis set. It performs an SCF calculation and then a linear response calculation with 5 states. The output shows the SCF driver setup and the reduced basis SCF energy. ```python import veloxchem as vlx molecule = vlx.Molecule.read_name("formaldehyde") basis = vlx.MolecularBasis.read(molecule, "def2-svp") scf_drv = vlx.ScfRestrictedDriver() scf_drv.xcfun = "cam-b3lyp" scf_results = scf_drv.compute(molecule, basis) rsp_drv = vlx.LinearResponseEigenSolver() rsp_drv.nstates = 5 rsp_results = rsp_drv.compute(molecule, basis, scf_results) ``` ```text Reading formaldehyde from PubChem... Reference: S. Kim, J. Chen, T. Cheng, A. Gindulyte, J. He, S. He, Q. Li, B. A. Shoemaker, P. A. Thiessen, B. Yu, L. Zaslavsky, J. Zhang, E. E. Bolton, Nucleic Acids Res., 2025, 53, D1516-D1525. Please double-check the compound since names may refer to more than one record. Self Consistent Field Driver Setup ==================================== Wave Function Model : Spin-Restricted Kohn-Sham Initial Guess Model : Superposition of Atomic Densities Convergence Accelerator : Two Level Direct Inversion of Iterative Subspace Max. Number of Iterations : 50 Max. Number of Error Vectors : 10 Convergence Threshold : 1.0e-06 ERI Screening Threshold : 1.0e-12 Linear Dependence Threshold : 1.0e-06 Exchange-Correlation Functional : CAM-B3LYP Molecular Grid Level : 4 * Info * Using the CAM-B3LYP functional. T. Yanai, D. P. Tew, and N. C. Handy., Chem. Phys. Lett. 393, 51 (2004) * Info * Using the Libxc library (v7.0.0). S. Lehtola, C. Steigemann, M. J.T. Oliveira, and M. A.L. Marques., SoftwareX 7, 1–5 (2018) * Info * Using the following algorithm for XC numerical integration. J. Kussmann, H. Laqua and C. Ochsenfeld, J. Chem. Theory Comput. 2021, 17, 1512-1521 * Info * Starting Reduced Basis SCF calculation... * Info * ...done. SCF energy in reduced basis set: -113.714598826273 a.u. Time: 0.25 sec. ``` -------------------------------- ### Configuration for response property jobs Source: https://veloxchem.org/docs/opt-act Example configuration file for setting up a response property job, specifically for electronic circular dichroism (ECD) calculations. ```text @jobs task: response @end @method settings basis: def2-svpd xcfun: b3lyp @end @response property: ecd (cpp) # frequency region (and resolution) frequencies: 0.207-0.325 (0.0025) @end @molecule charge: 0 multiplicity: 1 xyz: ... @end ``` -------------------------------- ### VeloxChem input file example: myjob.inp Source: https://veloxchem.org/docs/run-desktop Example input file for a VeloxChem SCF calculation. It defines the job type, method settings (B3LYP functional and def2-svp basis set), and the molecular geometry in Cartesian coordinates (Angstrom units). The file uses @group and @end markers to delimit sections. ```text @jobs task: scf @end @method settings xcfun: b3lyp basis: def2-svp @end @molecule charge: 0 multiplicity: 1 xyz: O 0.00000 0.00000 0.00000 H 0.00000 0.00000 1.79524 H 1.69319 0.00000 -0.59904 @end ``` -------------------------------- ### Input file configuration for absorption spectra Source: https://veloxchem.org/docs/uv-vis Example configuration for calculating UV/vis and ECD spectra. The absorption property is specified in the response block, and natural transition orbitals can be saved using the nto keyword. ```text @jobs task: response @end @method settings xcfun: cam-b3lyp basis: def2-svp @end @response property: absorption nstates: 10 nto: yes @end @molecule charge: 0 multiplicity: 1 xyz: ... @end ``` -------------------------------- ### Conformational search execution output Source: https://veloxchem.org/docs/conf-search Example log output showing the system generation, water model detection, and energy minimization steps during the MD simulation. ```text * Info * Generating system... * Info * Water molecule detected. Using tip3p water model. *********** * Warning * CONECT records not found in the PDB file.The connectivity matrix will be used to determine the bonds. *********** * Info * Unique Residues: [('M01', 1), ('M02', 2), ('M03', 3)], saved as molecules. * Info * PBC detected from the PDB file. * Info * Added XML Files: ['molecule_1.xml', 'molecule_2.xml'] * Info * Applying centroid bond force to the system... * Info * Running high-temperature MD for 0.20 ns... * Info * Saved coordinates for step 2500 * Info * Energy for conformer 1/40: 395.1134 kJ/mol * Info * Saved coordinates for step 5000 * Info * Energy for conformer 2/40: 352.5593 kJ/mol * Info * Saved coordinates for step 7500 * Info * Energy for conformer 3/40: 437.1005 kJ/mol * Info * Saved coordinates for step 10000 * Info * Energy for conformer 4/40: 375.8574 kJ/mol * Info * Saved coordinates for step 12500 * Info * Energy for conformer 5/40: 427.6551 kJ/mol * Info * Saved coordinates for step 15000 * Info * Energy for conformer 6/40: 424.2773 kJ/mol * Info * Saved coordinates for step 17500 * Info * Energy for conformer 7/40: 377.2951 kJ/mol * Info * Saved coordinates for step 20000 * Info * Energy for conformer 8/40: 423.5491 kJ/mol * Info * Saved coordinates for step 22500 * Info * Energy for conformer 9/40: 420.5697 kJ/mol * Info * Saved coordinates for step 25000 * Info * Energy for conformer 10/40: 388.6808 kJ/mol ``` -------------------------------- ### Create a simulation box with SolvationBuilder Source: https://veloxchem.org/docs/solvation Use the SolvationBuilder to create a simulation box with default padding and solvent. The output provides details on the box dimensions and solvent packing. ```python solvator = vlx.SolvationBuilder() solvator.solvate(solute, equilibrate=False, neutralize=False) ``` ```text VeloxChem Solvation Builder ============================= * Info * Solvating the solute with cspce molecules * Info * Padding: 1.0 nm * Info * The box size is: 2.79 x 2.79 x 2.79 nm^3 * Info * The volume of the solute is: 0.23 nm^3 * Info * The volume available for the solvent is: 21.43 nm^3 * Info * The experimental density of cspce is: 1000 kg/m^3 * Info * Warning: 90 attempts have been made to insert the solvent molecule * Info * Consider reducing the target density * Info * Solvated system with 713 solvent molecules out of 713 requested * Info * Time to solvate the system: 0.36 s * Info * The density of the solvent after packing is: 994 kg/m^3 ``` -------------------------------- ### Vibrational analysis input file Source: https://veloxchem.org/docs/vib-spect Example configuration file for a vibrational analysis job in VeloxChem. ```text @jobs task: vibrational @end @method settings xcfun: b3lyp basis: def2-svp @end @vibrational do_ir: yes @end @molecule charge: 0 multiplicity: 1 xyz: ... @end ``` -------------------------------- ### SCF calculation output log Source: https://veloxchem.org/docs/elec-vis Example output log from a Self Consistent Field calculation. ```text Reading ethylene from PubChem... Reference: S. Kim, J. Chen, T. Cheng, A. Gindulyte, J. He, S. He, Q. Li, B. A. Shoemaker, P. A. Thiessen, B. Yu, L. Zaslavsky, J. Zhang, E. E. Bolton, Nucleic Acids Res., 2025, 53, D1516-D1525. Please double-check the compound since names may refer to more than one record. Self Consistent Field Driver Setup ==================================== Wave Function Model : Spin-Restricted Hartree-Fock Initial Guess Model : Superposition of Atomic Densities Convergence Accelerator : Two Level Direct Inversion of Iterative Subspace Max. Number of Iterations : 50 Max. Number of Error Vectors : 10 Convergence Threshold : 1.0e-06 ERI Screening Threshold : 1.0e-12 Linear Dependence Threshold : 1.0e-06 * Info * Starting Reduced Basis SCF calculation... * Info * ...done. SCF energy in reduced basis set: -78.004791675958 a.u. Time: 0.26 sec. ``` -------------------------------- ### CPP input file configuration Source: https://veloxchem.org/docs/uv-vis Example configuration for a CPP absorption property calculation, specifying the functional, basis set, frequency range, and damping parameter. ```text @jobs task: response @end @method settings xcfun: b3lyp basis: def2-svp @end @response property: absorption (cpp) # frequency region (and resolution) frequencies: 0.10-0.25 (0.0025) damping: 0.0045563 # this is the default value @end @molecule charge: 0 multiplicity: 1 xyz: ... @end ```