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| on: [push] | ||
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| jobs: | ||
| paper: | ||
| runs-on: ubuntu-latest | ||
| name: Paper Draft | ||
| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@v3 | ||
| - name: Build draft PDF | ||
| uses: openjournals/openjournals-draft-action@master | ||
| with: | ||
| journal: joss | ||
| # This should be the path to the paper within your repo. | ||
| paper-path: paper/paper.md | ||
| - name: Upload | ||
| uses: actions/upload-artifact@v1 | ||
| with: | ||
| name: paper | ||
| # This is the output path where Pandoc will write the compiled | ||
| # PDF. Note, this should be the same directory as the input | ||
| # paper.md | ||
| path: paper/paper.pdf |
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| # Read the Docs configuration file for Sphinx projects | ||
| # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details | ||
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| # Required | ||
| version: 2 | ||
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| # Set the OS, Python version and other tools you might need | ||
| build: | ||
| os: ubuntu-22.04 | ||
| tools: | ||
| python: "3.12" | ||
| # You can also specify other tool versions: | ||
| # nodejs: "20" | ||
| # rust: "1.70" | ||
| # golang: "1.20" | ||
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| # Build documentation in the "docs/" directory with Sphinx | ||
| sphinx: | ||
| configuration: docs/conf.py | ||
| # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs | ||
| # builder: "dirhtml" | ||
| # Fail on all warnings to avoid broken references | ||
| # fail_on_warning: true | ||
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| # Optionally build your docs in additional formats such as PDF and ePub | ||
| # formats: | ||
| # - epub | ||
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| # Optional but recommended, declare the Python requirements required | ||
| # to build your documentation | ||
| # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html | ||
| python: | ||
| install: | ||
| - requirements: docs/requirements.txt |
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| {"cells":[{"attachments":{},"cell_type":"markdown","metadata":{"colab_type":"text","id":"PA9WOB4zJfCu"},"source":["# Installation on Google Collab\n","To install `QMCTorch` copy the code from one of the 3 text cells below in a code cell and run that cell. "]},{"cell_type":"markdown","metadata":{"colab_type":"text","id":"6KLOhN_dGQ11"},"source":["## Install QMCTorch from Pypi Package manager\n","\n","```\n","! pip install qmctorch\n","```\n","\n"]},{"cell_type":"markdown","metadata":{"colab_type":"text","id":"Eb9wI3eOGfz1"},"source":["## Install QMCTorch from GitHub\n","```\n","from google.colab import drive\n","drive.mount('/content/gdrive')\n","% cd gdrive/My Drive/\n","! git clone https://github.com/NLESC-JCER/QMCTorch\n","% cd QMCTorch\n","! pip install -e .\n","% cd ../\n","```"]},{"cell_type":"markdown","metadata":{"colab_type":"text","id":"_VNw5sAeHC7M"},"source":["## Pull latest code from Github\n","```\n","from google.colab import drive\n","drive.mount('/content/gdrive')\n","% cd gdrive/My Drive/QMCTorch\n","! git pull origin master\n","! pip install -e .\n","% cd ../\n","```"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{"base_uri":"https://localhost:8080/","height":671},"colab_type":"code","executionInfo":{"elapsed":9770,"status":"ok","timestamp":1588617088336,"user":{"displayName":"Nicolas Renaud","photoUrl":"","userId":"07120063468244602126"},"user_tz":-120},"id":"khGd1-ewHZWF","outputId":"674fbe9e-7817-4e11-cc91-cd508bda8107","vscode":{"languageId":"python"}},"outputs":[],"source":["# from google.colab import drive\n","# drive.mount('/content/gdrive')\n","# % cd gdrive/My Drive/QMCTorch\n","# ! git pull origin master\n","# ! pip install -e .\n","# % cd .."]},{"cell_type":"markdown","metadata":{"colab_type":"text","id":"MGNu_L-OJ-7u"},"source":["# Using QMCTorch"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{"base_uri":"https://localhost:8080/","height":52},"colab_type":"code","executionInfo":{"elapsed":11632,"status":"ok","timestamp":1588617090211,"user":{"displayName":"Nicolas Renaud","photoUrl":"","userId":"07120063468244602126"},"user_tz":-120},"id":"p7qEQTV2HB4h","outputId":"52c2bbce-3775-442c-95de-d18bd432c2e3","vscode":{"languageId":"python"}},"outputs":[],"source":["import torch\n","from torch import optim\n","from qmctorch.scf import Molecule\n","from qmctorch.wavefunction import SlaterJastrow\n","from qmctorch.solver import Solver\n","from qmctorch.sampler import Metropolis\n","from qmctorch.utils import set_torch_double_precision\n","from qmctorch.utils import plot_energy, plot_data"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{},"colab_type":"code","id":"x-s06JyaHUdN","vscode":{"languageId":"python"}},"outputs":[],"source":["use_gpu = torch.cuda.is_available()\n","set_torch_double_precision()"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{"base_uri":"https://localhost:8080/","height":52},"colab_type":"code","executionInfo":{"elapsed":11608,"status":"ok","timestamp":1588617090213,"user":{"displayName":"Nicolas Renaud","photoUrl":"","userId":"07120063468244602126"},"user_tz":-120},"id":"7HO4cNaAID-F","outputId":"a1f652aa-9bcb-4e9b-c038-833b29da2eae","vscode":{"languageId":"python"}},"outputs":[],"source":["mol = Molecule(atom='H 0 0 0.69; H 0 0 -0.69', unit='bohr', \\\n"," calculator='pyscf', basis='sto-3g')"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{},"colab_type":"code","id":"hFZg-XanIOeY","vscode":{"languageId":"python"}},"outputs":[],"source":["wf = SlaterJastrow(mol, configs='cas(2,2)', cuda=use_gpu)"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{},"colab_type":"code","id":"Mqlk1N3tIVXN","vscode":{"languageId":"python"}},"outputs":[],"source":["sampler = Metropolis(nwalkers=2000, nstep=2000, step_size=0.2, \\\n"," ntherm=-1, ndecor=100, nelec=wf.nelec, \\\n"," init=mol.domain('atomic'), \\\n"," move={'type':'all-elec', 'proba':'normal'},\n"," cuda=use_gpu)"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{},"colab_type":"code","id":"5-I7abLxI5qG","vscode":{"languageId":"python"}},"outputs":[],"source":["lr_dict = [{'params': wf.jastrow.parameters(), 'lr': 3E-3},\n"," {'params': wf.ao.parameters(), 'lr': 1E-6},\n"," {'params': wf.mo.parameters(), 'lr': 1E-3},\n"," {'params': wf.fc.parameters(), 'lr': 2E-3}]\n","opt = optim.Adam(lr_dict, lr=1E-3)"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{},"colab_type":"code","id":"xgXSp8JwJIr9","vscode":{"languageId":"python"}},"outputs":[],"source":["scheduler = optim.lr_scheduler.StepLR(opt, step_size=100, gamma=0.90)"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{},"colab_type":"code","id":"g6TE--nNJL1H","vscode":{"languageId":"python"}},"outputs":[],"source":["solver = Solver(wf=wf, sampler=sampler,\n"," optimizer=opt, scheduler=scheduler)"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{"base_uri":"https://localhost:8080/","height":87},"colab_type":"code","executionInfo":{"elapsed":26805,"status":"ok","timestamp":1588617105475,"user":{"displayName":"Nicolas Renaud","photoUrl":"","userId":"07120063468244602126"},"user_tz":-120},"id":"Y5MPLiv2JTCy","outputId":"ef067f86-11b3-48e0-9dac-dc8ff5784905","vscode":{"languageId":"python"}},"outputs":[],"source":["# obs = solver.single_point()"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{},"colab_type":"code","id":"yfx4g1Luz9Z-","vscode":{"languageId":"python"}},"outputs":[],"source":["# solver.configure(freeze=['ao', 'mo'], loss='energy', grad='manual')\n","# solver.track_observable(['local_energy'])\n","\n","# solver.configure_resampling(mode='update',\n","# resample_every=1,\n","# nstep_update=50)\n","# solver.ortho_mo = False"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{"base_uri":"https://localhost:8080/","height":1000},"colab_type":"code","executionInfo":{"elapsed":52595,"status":"ok","timestamp":1588617131289,"user":{"displayName":"Nicolas Renaud","photoUrl":"","userId":"07120063468244602126"},"user_tz":-120},"id":"VtrVSk620A1A","outputId":"32ad9904-40e5-4efa-bcee-27145e04cfd4","vscode":{"languageId":"python"}},"outputs":[],"source":["# obs = solver.run(50)"]}],"metadata":{"accelerator":"GPU","colab":{"authorship_tag":"ABX9TyMr6DKmNBGlyg+0pzpuupgz","name":"qmctorch.ipynb","provenance":[]},"kernelspec":{"display_name":"Python 3","name":"python3"}},"nbformat":4,"nbformat_minor":0} |
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| from qmctorch.scf import Molecule | ||
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| # Select the SCF calculator | ||
| calc = ['pyscf', # pyscf | ||
| 'adf', # adf 2019 | ||
| 'adf2019' # adf 2020+ | ||
| ][1] | ||
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| # select an appropriate basis | ||
| basis = { | ||
| 'pyscf' : 'sto-6g', | ||
| 'adf' : 'VB1', | ||
| 'adf2019': 'dz' | ||
| }[calc] | ||
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| # do the scf calculation | ||
| mol = Molecule(atom='H 0 0 -0.69; H 0 0 0.69', | ||
| calculator=calc, | ||
| basis=basis, | ||
| unit='bohr') | ||
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