├── .bashrc ├── .gitattributes ├── .gitignore ├── CONTRIBUTING.md ├── COPYING ├── C_API ├── MolEmb.cpp ├── SH.hpp ├── test.py └── test │ ├── Make_CM.cpp │ ├── setup.py │ └── test.py ├── JAMS ├── README.md ├── TensorMol ├── Containers │ ├── Digest.py │ ├── DigestMol.py │ ├── Mol.py │ ├── MolFrag.py │ ├── MolGraph.py │ ├── PickleTM.py │ ├── Sets.py │ ├── TensorData.py │ ├── TensorMolData.py │ ├── TensorMolDataEE.py │ └── __init__.py ├── ForceModels │ ├── Electrostatics.py │ ├── ElectrostaticsTF.py │ ├── TFForces.py │ ├── TFModels.py │ ├── TFPeriodicForces.py │ └── __init__.py ├── ForceModifiers │ ├── Accommodator.py │ ├── Neighbors.py │ ├── NeighborsMB.py │ ├── Periodic.py │ ├── Transformer.py │ └── __init__.py ├── Interfaces │ ├── AbInitio.py │ ├── TMIPIinterface.py │ └── __init__.py ├── MBE │ ├── MBE.py │ ├── MBEData.py │ ├── MBE_Opt.py │ └── NN_MBE.py ├── Math │ ├── BFGS.py │ ├── Basis.py │ ├── DIIS.py │ ├── EmbOpt.py │ ├── Grids.py │ ├── Ipecac.py │ ├── LinearOperations.py │ ├── QuasiNewtonTools.py │ ├── Statistics.py │ ├── TFMath.py │ └── __init__.py ├── PhysicalData.py ├── Simulations │ ├── InfraredMD.py │ ├── MetaDynamics.py │ ├── Neb.py │ ├── Opt.py │ ├── OptPeriodic.py │ ├── PeriodicMC.py │ ├── PeriodicMD.py │ ├── SimpleMD.py │ ├── Web.py │ └── __init__.py ├── SystemBuilders │ └── MolBuilders.py ├── TFDescriptors │ ├── PairProviderTF.py │ ├── RawSH.py │ ├── RawSymFunc.py │ └── __init__.py ├── TFNetworks │ ├── TFBehlerParinello.py │ ├── TFBehlerParinelloSymEE.py │ ├── TFInstance.py │ ├── TFManage.py │ ├── TFMolInstance.py │ ├── TFMolInstanceDirect.py │ ├── TFMolInstanceEE.py │ ├── TFMolManage.py │ ├── TFMolManageQ.py │ └── __init__.py ├── TMParams.py ├── Util.py └── __init__.py ├── TensorMolServer.py ├── _config.yml ├── clean.sh ├── datasets ├── 1_1_Ostrech.xyz ├── 2evq.xyz ├── 2mzx_tm_opt.xyz ├── CxHy_test.xyz ├── Endiandric.xyz ├── H2O_cluster.xyz ├── H2O_cluster_meta.xyz ├── H2O_force_test.xyz ├── H2O_trimer_move.xyz ├── NEB.xyz ├── NEB_Berg.xyz ├── NaClH2O.xyz ├── NeigborMB_test.xyz ├── OptMols.xyz ├── gdb9.pdb ├── h2o.xyz ├── johnsonmols.xyz ├── md_test.xyz ├── mol.xyz ├── morphine.xyz ├── nicotine_stretch_tmp.xyz ├── reactor.xyz ├── rna_solvate.py ├── rot_const_test_mol.xyz ├── solvate.py ├── water10.xyz ├── water_mini.pdb └── water_tiny.xyz ├── densities ├── IRSpectrum.nb ├── PlotDens.nb └── morph.xyz ├── doc ├── About.rst ├── Makefile ├── TensorMol.rst ├── Tutorials.rst ├── _build │ └── html │ │ ├── .buildinfo │ │ ├── TensorMol.html │ │ ├── _sources │ │ ├── TensorMol.rst.txt │ │ └── index.rst.txt │ │ ├── _static │ │ ├── ajax-loader.gif │ │ ├── alabaster.css │ │ ├── basic.css │ │ ├── comment-bright.png │ │ ├── comment-close.png │ │ ├── comment.png │ │ ├── custom.css │ │ ├── doctools.js │ │ ├── down-pressed.png │ │ ├── down.png │ │ ├── file.png │ │ ├── jquery-3.1.0.js │ │ ├── jquery.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ ├── underscore.js │ │ ├── up-pressed.png │ │ ├── up.png │ │ └── websupport.js │ │ ├── genindex.html │ │ ├── index.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── search.html │ │ └── searchindex.js ├── conf.py ├── images │ ├── 2evq.gif │ ├── PeriodicTimings.png │ ├── TensorMol.png │ ├── Timings.png │ ├── cascade.gif │ ├── monster.png │ ├── neb.png │ ├── newtitle.png │ ├── pes.pdf │ ├── pes.png │ ├── tyrosine.png │ └── water.png └── index.rst ├── git_find_big.sh ├── logs └── README ├── memory_util.py ├── notebooks ├── DFT Optimization and Harmonic Analysis.ipynb ├── ForceMatching.ipynb ├── H2 analysis.nb ├── Harmonic Analysis Routine with Annealing.ipynb ├── How to doctor a PDB. .ipynb ├── InnerProduct.py ├── MatchFrequency.py ├── MatchNormalModes.py ├── PairPotential.ipynb ├── Simple Geometry Optimization And Harmonic Analysis.ipynb ├── TFsym.ipynb ├── Untitled.ipynb └── Untitled1.ipynb ├── qchem └── README ├── results └── README ├── samples ├── README ├── SampleMethodsTest.py ├── i-pi_interface │ ├── 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