copy 2020 materials from Google Drive

Author: loriab

DavidSherrill_Some-SAPT-Papers/bakr_2018_18241.pdf

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+## Common git commands:
+  0. `git clone <https://github.com/some_repo/some_repo.git>` Obtain exact copy of repo from github
+  1. `git add <file>` Adds local file to git tracking
+  2. `git log` Shows local history of commits
+  3. `git status` Shows any changes to local files, in addition to any untracked files
+  4. `git commit -m "text message"` Commits any files that have been added to stage with message
+  5. `git commit -a` Adds then commits all changes in tracked files
+  6. `git pull <remote> <branch>` Merges github history to local, taken from remote (usually origin) and branch (often master).
+  7. `git push <remote> <branch>` Moves local commits to github repository at remote/branch
+  8. `git checkout -b <branch_name>` Makes a new branch and switch to it
+  9. `git checkout <branch_name>` Move to branch_name
+  10. `git branch` Lists branches, shows which branch you are on
+  11. `git branch -d` Delete branch locally
+  12. `git push <remote> :<branch_name>` Deletes branch on remote.
+  13. `git checkout <file>` Reverts any changes in `file` to state determined by current git hash
+  14. `git init` Create a new git repository
+  15. `git remote add origin <server>` Connects repository to a remote server
+  16. `git diff` View all local changes relative to remote
+  17. `git rm` Removes a tracked file
+  18. `git remote -v` Shows identity of origin and other remotes
+  19. `git remote add upstream <parent repo>` Adds upstream remote for a parent repo
+
+
+## Making a new repo
+1. First make repo on github
+2. `git clone` your new repo locally.
+3. Make some new file, `file.dat`
+4. See your new untracked file: `git status`
+5. Stage file for commit: `git add file.dat`
+6. Commit change, enter message, close file: `git commit -a`
+7. See your new history!: `git log`
+8. Push your changes to your repo on github.com: `git push origin master`
+
+## Making a fork
+### Good practice for making changes to shared code
+1. On a parent repo page in github.com, click Fork on the top right.
+2. Clone to local machine: `git clone <your fork>`
+3. Setup upstream: `git remote add upstream <parent repository>`
+4. Make a branch of your fork: `git checkout -b new_branch` (branch name should be descriptive of changes)
+5. Make some local change: `vi new_file.dat`
+6. Add and commit change: `git add new_file.dat`, `git commit -m "Add new file"`
+7. Rebase to resolve any merge conflicts: `git pull --rebase upstream master`
+8. If your local branch differs from origin, you will need to make your changes and then push with force:
+`git push --force origin new_branch`
+9. Push changes: `git push origin new_branch` (this will create a new branch on github.com)
+10. On your fork on github.com, create a pull request pushing the "Compare & pull request" button.
+11. Open the pull request by by writing a description and clicking "Create pull request"
+12. Delete branch once PR is merged

DavidSherrill_Some-SAPT-Papers/carson_2015_19168.pdf

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+import psi4
+import optking
+
+# Test optimization with explicit loop using externally provided gradients
+# In this case, using Leonard-Jones potential
+h2o = psi4.geometry("""
+     O
+     H 1 1.0
+     H 1 1.0 2 104.5
+""")
+
+psi4_options = {
+  'basis': 'sto-3g',
+  'g_convergence': 'gau_verytight',
+  'intrafrag_step_limit_max': 0.2
+}
+psi4.set_options(psi4_options)
+
+# Create an OptHelper object.  The comp_type == 'user' implies that the
+# user will provide the gradients directly.
+opt = optking.OptHelper('hf', comp_type='user')
+opt.build_coordinates()
+
+for step in range(30):
+    # Compute one's own energy and gradient
+    E, gX = optking.lj_functions.calc_energy_and_gradient(opt.geom, 2.5, 0.01, True)
+
+    # Insert these values into the 'user' computer.
+    opt.E = E
+    opt.gX = gX
+    opt.energy_gradient_hessian()
+
+    # Take step
+    opt.step()
+    conv = opt.test_convergence()
+    if conv is True:
+        print("Optimization SUCCESS:")
+        break
+else:
+    print("Optimization FAILURE:\n")
+
+json_output = opt.close()
+
+assert conv is True
+E = json_output['energies'][-1]  # TEST
+RefEnergy = -0.03  # - epsilon * 3, where -epsilon is depth of each Vij well
+assert psi4.compare_values(RefEnergy, E, 6, "L-J Energy upon optimization")
+

DavidSherrill_Some-SAPT-Papers/parker_2014_094106.pdf

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+# Demonstration of python optking using psi api.
+# See optking/tests for lots of psi api examples.
+import psi4
+import optking
+
+psi4.core.set_output_file('psi-out.dat')
+h2o = psi4.geometry("""
+     O
+     H 1 1.0
+     H 1 1.0 2 104.5
+""")
+psi4_options = { 'basis': 'cc-pvdz' }
+psi4.set_options(psi4_options)
+
+json_output = optking.optimize_psi4('hf')
+
+print('Contents of QCSchema output:')
+for k in json_output.keys():
+    print('\t' + k)
+
+print('Properties of (next to) last geom:')
+for k in json_output['trajectory'][-1]['properties']:
+    print('\t' + k)
+
+print('Extras of (next to) last geom:')
+for k in json_output['trajectory'][-1]['extras']['qcvars']:
+    print('\t' + k)
+
+print('Energy {:15.10f}'.format(json_output['energies'][-1]))
+print('NRE    {:15.10f}'.format(json_output['trajectory'][-1]['properties']['nuclear_repulsion_energy']))

DavidSherrill_Some-SAPT-Papers/parrish_2017_7887.pdf

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+# From psi4/tests/opt1
+REF_NRE = 8.9064890670
+REF_HF_ENERGY = -74.965901192
+
+molecule h2o {
+     O
+     H 1 1.0
+     H 1 1.0 2 104.5
+}
+
+set {
+  diis false
+  basis sto-3g
+  e_convergence 10
+  d_convergence 10
+  scf_type pk
+}
+# Runs C++ optimizer
+#thisenergy = optimize('scf')
+#compare_values(REF_NRE, h2o.nuclear_repulsion_energy(), 3, "Nuclear repulsion energy")
+#compare_values(REF_HF_ENERGY, thisenergy, 6, "Reference energy")
+
+# Runs python optimizer
+import optking
+rval = optking.optimize_psi4('scf')
+
+nre = rval['trajectory'][-1]['properties']['nuclear_repulsion_energy']
+hf_energy = rval['energies'][-1]
+compare_values(REF_NRE, nre, 3, "Nuclear repulsion energy")
+compare_values(REF_HF_ENERGY, hf_energy, 6, "Reference energy")
+