SCM-NV · dormrod · Feb 26, 2026 · Feb 26, 2026 · Feb 26, 2026
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -30,7 +30,26 @@ jobs:
       - run: conda --version
       - run: python --version
       - run: conda install python=${{ matrix.python-version }}
+      - name: Configure SCM package index
+        shell: bash
+        env:
+          SCM_DOWNLOADS_USERNAME: ${{ secrets.SCM_DOWNLOADS_USERNAME }}
+          SCM_DOWNLOADS_PASSWORD: ${{ secrets.SCM_DOWNLOADS_PASSWORD }}
+        run: |
+          if [[ -z "${SCM_DOWNLOADS_USERNAME}" || -z "${SCM_DOWNLOADS_PASSWORD}" ]]; then
+            echo "Missing SCM_DOWNLOADS_USERNAME or SCM_DOWNLOADS_PASSWORD secret."
+            exit 1
+          fi
+
+          cat << EOF > "${HOME}/.netrc"
+          machine downloads.scm.com
+            login ${SCM_DOWNLOADS_USERNAME}
+            password ${SCM_DOWNLOADS_PASSWORD}
+          EOF
+          chmod 600 "${HOME}/.netrc"
       - name: Build
+        env:
+          PIP_EXTRA_INDEX_URL: https://downloads.scm.com/Downloads/packages/uv/channels/2026.1/simple/
         run: |
           pip3 install .[test,doc]
           pip3 install build

diff --git a/...test_ZacrosParametersScanJob.data/logfile → tests/test_ParamScan.data/logfile b/...test_ZacrosParametersScanJob.data/logfile → tests/test_ParamScan.data/logfile
diff --git a/...metersScanJob.data/plamsjob/plamsjob.dill → ...est_ParamScan.data/plamsjob/plamsjob.dill b/...metersScanJob.data/plamsjob/plamsjob.dill → ...est_ParamScan.data/plamsjob/plamsjob.dill
diff --git a/.../plamsjob_ps_cond000/energetics_input.dat → .../plamsjob_ps_cond000/energetics_input.dat b/.../plamsjob_ps_cond000/energetics_input.dat → .../plamsjob_ps_cond000/energetics_input.dat
diff --git a/...ob/plamsjob_ps_cond000/general_output.txt → ...ob/plamsjob_ps_cond000/general_output.txt b/...ob/plamsjob_ps_cond000/general_output.txt → ...ob/plamsjob_ps_cond000/general_output.txt
diff --git a/...ob/plamsjob_ps_cond000/history_output.txt → ...ob/plamsjob_ps_cond000/history_output.txt b/...ob/plamsjob_ps_cond000/history_output.txt → ...ob/plamsjob_ps_cond000/history_output.txt
diff --git a/...job/plamsjob_ps_cond000/lattice_input.dat → ...job/plamsjob_ps_cond000/lattice_input.dat b/...job/plamsjob_ps_cond000/lattice_input.dat → ...job/plamsjob_ps_cond000/lattice_input.dat
diff --git a/...ob/plamsjob_ps_cond000/lattice_output.txt → ...ob/plamsjob_ps_cond000/lattice_output.txt b/...ob/plamsjob_ps_cond000/lattice_output.txt → ...ob/plamsjob_ps_cond000/lattice_output.txt
diff --git a/...b/plamsjob_ps_cond000/mechanism_input.dat → ...b/plamsjob_ps_cond000/mechanism_input.dat b/...b/plamsjob_ps_cond000/mechanism_input.dat → ...b/plamsjob_ps_cond000/mechanism_input.dat
diff --git a/...msjob_ps_cond000/plamsjob_ps_cond000.dill → ...msjob_ps_cond000/plamsjob_ps_cond000.dill b/...msjob_ps_cond000/plamsjob_ps_cond000.dill → ...msjob_ps_cond000/plamsjob_ps_cond000.dill
diff --git a/.../plamsjob/plamsjob_ps_cond000/restart.inf → .../plamsjob/plamsjob_ps_cond000/restart.inf b/.../plamsjob/plamsjob_ps_cond000/restart.inf → .../plamsjob/plamsjob_ps_cond000/restart.inf
diff --git a/.../plamsjob_ps_cond000/simulation_input.dat → .../plamsjob_ps_cond000/simulation_input.dat b/.../plamsjob_ps_cond000/simulation_input.dat → .../plamsjob_ps_cond000/simulation_input.dat
diff --git a/...ta/plamsjob/plamsjob_ps_cond000/slurm.run → ...ta/plamsjob/plamsjob_ps_cond000/slurm.run b/...ta/plamsjob/plamsjob_ps_cond000/slurm.run → ...ta/plamsjob/plamsjob_ps_cond000/slurm.run
diff --git a/...ob/plamsjob_ps_cond000/specnum_output.txt → ...ob/plamsjob_ps_cond000/specnum_output.txt b/...ob/plamsjob_ps_cond000/specnum_output.txt → ...ob/plamsjob_ps_cond000/specnum_output.txt
diff --git a/...data/plamsjob/plamsjob_ps_cond000/std.err → ...data/plamsjob/plamsjob_ps_cond000/std.err b/...data/plamsjob/plamsjob_ps_cond000/std.err → ...data/plamsjob/plamsjob_ps_cond000/std.err
diff --git a/...data/plamsjob/plamsjob_ps_cond000/std.out → ...data/plamsjob/plamsjob_ps_cond000/std.out b/...data/plamsjob/plamsjob_ps_cond000/std.out → ...data/plamsjob/plamsjob_ps_cond000/std.out
diff --git a/.../plamsjob_ps_cond001/energetics_input.dat → .../plamsjob_ps_cond001/energetics_input.dat b/.../plamsjob_ps_cond001/energetics_input.dat → .../plamsjob_ps_cond001/energetics_input.dat
diff --git a/...ob/plamsjob_ps_cond001/general_output.txt → ...ob/plamsjob_ps_cond001/general_output.txt b/...ob/plamsjob_ps_cond001/general_output.txt → ...ob/plamsjob_ps_cond001/general_output.txt
diff --git a/...ob/plamsjob_ps_cond001/history_output.txt → ...ob/plamsjob_ps_cond001/history_output.txt b/...ob/plamsjob_ps_cond001/history_output.txt → ...ob/plamsjob_ps_cond001/history_output.txt
diff --git a/...job/plamsjob_ps_cond001/lattice_input.dat → ...job/plamsjob_ps_cond001/lattice_input.dat b/...job/plamsjob_ps_cond001/lattice_input.dat → ...job/plamsjob_ps_cond001/lattice_input.dat
diff --git a/...ob/plamsjob_ps_cond001/lattice_output.txt → ...ob/plamsjob_ps_cond001/lattice_output.txt b/...ob/plamsjob_ps_cond001/lattice_output.txt → ...ob/plamsjob_ps_cond001/lattice_output.txt
diff --git a/...b/plamsjob_ps_cond001/mechanism_input.dat → ...b/plamsjob_ps_cond001/mechanism_input.dat b/...b/plamsjob_ps_cond001/mechanism_input.dat → ...b/plamsjob_ps_cond001/mechanism_input.dat
diff --git a/...msjob_ps_cond001/plamsjob_ps_cond001.dill → ...msjob_ps_cond001/plamsjob_ps_cond001.dill b/...msjob_ps_cond001/plamsjob_ps_cond001.dill → ...msjob_ps_cond001/plamsjob_ps_cond001.dill
diff --git a/.../plamsjob/plamsjob_ps_cond001/restart.inf → .../plamsjob/plamsjob_ps_cond001/restart.inf b/.../plamsjob/plamsjob_ps_cond001/restart.inf → .../plamsjob/plamsjob_ps_cond001/restart.inf
diff --git a/.../plamsjob_ps_cond001/simulation_input.dat → .../plamsjob_ps_cond001/simulation_input.dat b/.../plamsjob_ps_cond001/simulation_input.dat → .../plamsjob_ps_cond001/simulation_input.dat
diff --git a/...ta/plamsjob/plamsjob_ps_cond001/slurm.run → ...ta/plamsjob/plamsjob_ps_cond001/slurm.run b/...ta/plamsjob/plamsjob_ps_cond001/slurm.run → ...ta/plamsjob/plamsjob_ps_cond001/slurm.run
diff --git a/...ob/plamsjob_ps_cond001/specnum_output.txt → ...ob/plamsjob_ps_cond001/specnum_output.txt b/...ob/plamsjob_ps_cond001/specnum_output.txt → ...ob/plamsjob_ps_cond001/specnum_output.txt
diff --git a/...data/plamsjob/plamsjob_ps_cond001/std.err → ...data/plamsjob/plamsjob_ps_cond001/std.err b/...data/plamsjob/plamsjob_ps_cond001/std.err → ...data/plamsjob/plamsjob_ps_cond001/std.err
diff --git a/...data/plamsjob/plamsjob_ps_cond001/std.out → ...data/plamsjob/plamsjob_ps_cond001/std.out b/...data/plamsjob/plamsjob_ps_cond001/std.out → ...data/plamsjob/plamsjob_ps_cond001/std.out
diff --git a/.../plamsjob_ps_cond002/energetics_input.dat → .../plamsjob_ps_cond002/energetics_input.dat b/.../plamsjob_ps_cond002/energetics_input.dat → .../plamsjob_ps_cond002/energetics_input.dat
diff --git a/...ob/plamsjob_ps_cond002/general_output.txt → ...ob/plamsjob_ps_cond002/general_output.txt b/...ob/plamsjob_ps_cond002/general_output.txt → ...ob/plamsjob_ps_cond002/general_output.txt
diff --git a/...ob/plamsjob_ps_cond002/history_output.txt → ...ob/plamsjob_ps_cond002/history_output.txt b/...ob/plamsjob_ps_cond002/history_output.txt → ...ob/plamsjob_ps_cond002/history_output.txt
diff --git a/...job/plamsjob_ps_cond002/lattice_input.dat → ...job/plamsjob_ps_cond002/lattice_input.dat b/...job/plamsjob_ps_cond002/lattice_input.dat → ...job/plamsjob_ps_cond002/lattice_input.dat
diff --git a/...ob/plamsjob_ps_cond002/lattice_output.txt → ...ob/plamsjob_ps_cond002/lattice_output.txt b/...ob/plamsjob_ps_cond002/lattice_output.txt → ...ob/plamsjob_ps_cond002/lattice_output.txt
diff --git a/...b/plamsjob_ps_cond002/mechanism_input.dat → ...b/plamsjob_ps_cond002/mechanism_input.dat b/...b/plamsjob_ps_cond002/mechanism_input.dat → ...b/plamsjob_ps_cond002/mechanism_input.dat
diff --git a/...msjob_ps_cond002/plamsjob_ps_cond002.dill → ...msjob_ps_cond002/plamsjob_ps_cond002.dill b/...msjob_ps_cond002/plamsjob_ps_cond002.dill → ...msjob_ps_cond002/plamsjob_ps_cond002.dill
diff --git a/.../plamsjob/plamsjob_ps_cond002/restart.inf → .../plamsjob/plamsjob_ps_cond002/restart.inf b/.../plamsjob/plamsjob_ps_cond002/restart.inf → .../plamsjob/plamsjob_ps_cond002/restart.inf
diff --git a/.../plamsjob_ps_cond002/simulation_input.dat → .../plamsjob_ps_cond002/simulation_input.dat b/.../plamsjob_ps_cond002/simulation_input.dat → .../plamsjob_ps_cond002/simulation_input.dat
diff --git a/...ta/plamsjob/plamsjob_ps_cond002/slurm.run → ...ta/plamsjob/plamsjob_ps_cond002/slurm.run b/...ta/plamsjob/plamsjob_ps_cond002/slurm.run → ...ta/plamsjob/plamsjob_ps_cond002/slurm.run
diff --git a/...ob/plamsjob_ps_cond002/specnum_output.txt → ...ob/plamsjob_ps_cond002/specnum_output.txt b/...ob/plamsjob_ps_cond002/specnum_output.txt → ...ob/plamsjob_ps_cond002/specnum_output.txt
diff --git a/...data/plamsjob/plamsjob_ps_cond002/std.err → ...data/plamsjob/plamsjob_ps_cond002/std.err b/...data/plamsjob/plamsjob_ps_cond002/std.err → ...data/plamsjob/plamsjob_ps_cond002/std.err
diff --git a/...data/plamsjob/plamsjob_ps_cond002/std.out → ...data/plamsjob/plamsjob_ps_cond002/std.out b/...data/plamsjob/plamsjob_ps_cond002/std.out → ...data/plamsjob/plamsjob_ps_cond002/std.out
diff --git a/.../plamsjob_ps_cond003/energetics_input.dat → .../plamsjob_ps_cond003/energetics_input.dat b/.../plamsjob_ps_cond003/energetics_input.dat → .../plamsjob_ps_cond003/energetics_input.dat
diff --git a/...ob/plamsjob_ps_cond003/general_output.txt → ...ob/plamsjob_ps_cond003/general_output.txt b/...ob/plamsjob_ps_cond003/general_output.txt → ...ob/plamsjob_ps_cond003/general_output.txt
diff --git a/...ob/plamsjob_ps_cond003/history_output.txt → ...ob/plamsjob_ps_cond003/history_output.txt b/...ob/plamsjob_ps_cond003/history_output.txt → ...ob/plamsjob_ps_cond003/history_output.txt
diff --git a/...job/plamsjob_ps_cond003/lattice_input.dat → ...job/plamsjob_ps_cond003/lattice_input.dat b/...job/plamsjob_ps_cond003/lattice_input.dat → ...job/plamsjob_ps_cond003/lattice_input.dat
diff --git a/...ob/plamsjob_ps_cond003/lattice_output.txt → ...ob/plamsjob_ps_cond003/lattice_output.txt b/...ob/plamsjob_ps_cond003/lattice_output.txt → ...ob/plamsjob_ps_cond003/lattice_output.txt
diff --git a/...b/plamsjob_ps_cond003/mechanism_input.dat → ...b/plamsjob_ps_cond003/mechanism_input.dat b/...b/plamsjob_ps_cond003/mechanism_input.dat → ...b/plamsjob_ps_cond003/mechanism_input.dat
diff --git a/...msjob_ps_cond003/plamsjob_ps_cond003.dill → ...msjob_ps_cond003/plamsjob_ps_cond003.dill b/...msjob_ps_cond003/plamsjob_ps_cond003.dill → ...msjob_ps_cond003/plamsjob_ps_cond003.dill
diff --git a/.../plamsjob/plamsjob_ps_cond003/restart.inf → .../plamsjob/plamsjob_ps_cond003/restart.inf b/.../plamsjob/plamsjob_ps_cond003/restart.inf → .../plamsjob/plamsjob_ps_cond003/restart.inf
diff --git a/.../plamsjob_ps_cond003/simulation_input.dat → .../plamsjob_ps_cond003/simulation_input.dat b/.../plamsjob_ps_cond003/simulation_input.dat → .../plamsjob_ps_cond003/simulation_input.dat
diff --git a/...ta/plamsjob/plamsjob_ps_cond003/slurm.run → ...ta/plamsjob/plamsjob_ps_cond003/slurm.run b/...ta/plamsjob/plamsjob_ps_cond003/slurm.run → ...ta/plamsjob/plamsjob_ps_cond003/slurm.run
diff --git a/...ob/plamsjob_ps_cond003/specnum_output.txt → ...ob/plamsjob_ps_cond003/specnum_output.txt b/...ob/plamsjob_ps_cond003/specnum_output.txt → ...ob/plamsjob_ps_cond003/specnum_output.txt
diff --git a/...data/plamsjob/plamsjob_ps_cond003/std.err → ...data/plamsjob/plamsjob_ps_cond003/std.err b/...data/plamsjob/plamsjob_ps_cond003/std.err → ...data/plamsjob/plamsjob_ps_cond003/std.err
diff --git a/...data/plamsjob/plamsjob_ps_cond003/std.out → ...data/plamsjob/plamsjob_ps_cond003/std.out b/...data/plamsjob/plamsjob_ps_cond003/std.out → ...data/plamsjob/plamsjob_ps_cond003/std.out
diff --git a/.../plamsjob_ps_cond004/energetics_input.dat → .../plamsjob_ps_cond004/energetics_input.dat b/.../plamsjob_ps_cond004/energetics_input.dat → .../plamsjob_ps_cond004/energetics_input.dat
diff --git a/...ob/plamsjob_ps_cond004/general_output.txt → ...ob/plamsjob_ps_cond004/general_output.txt b/...ob/plamsjob_ps_cond004/general_output.txt → ...ob/plamsjob_ps_cond004/general_output.txt
diff --git a/...ob/plamsjob_ps_cond004/history_output.txt → ...ob/plamsjob_ps_cond004/history_output.txt b/...ob/plamsjob_ps_cond004/history_output.txt → ...ob/plamsjob_ps_cond004/history_output.txt
diff --git a/...job/plamsjob_ps_cond004/lattice_input.dat → ...job/plamsjob_ps_cond004/lattice_input.dat b/...job/plamsjob_ps_cond004/lattice_input.dat → ...job/plamsjob_ps_cond004/lattice_input.dat
diff --git a/...ob/plamsjob_ps_cond004/lattice_output.txt → ...ob/plamsjob_ps_cond004/lattice_output.txt b/...ob/plamsjob_ps_cond004/lattice_output.txt → ...ob/plamsjob_ps_cond004/lattice_output.txt
diff --git a/...b/plamsjob_ps_cond004/mechanism_input.dat → ...b/plamsjob_ps_cond004/mechanism_input.dat b/...b/plamsjob_ps_cond004/mechanism_input.dat → ...b/plamsjob_ps_cond004/mechanism_input.dat
diff --git a/...msjob_ps_cond004/plamsjob_ps_cond004.dill → ...msjob_ps_cond004/plamsjob_ps_cond004.dill b/...msjob_ps_cond004/plamsjob_ps_cond004.dill → ...msjob_ps_cond004/plamsjob_ps_cond004.dill
diff --git a/.../plamsjob/plamsjob_ps_cond004/restart.inf → .../plamsjob/plamsjob_ps_cond004/restart.inf b/.../plamsjob/plamsjob_ps_cond004/restart.inf → .../plamsjob/plamsjob_ps_cond004/restart.inf
diff --git a/.../plamsjob_ps_cond004/simulation_input.dat → .../plamsjob_ps_cond004/simulation_input.dat b/.../plamsjob_ps_cond004/simulation_input.dat → .../plamsjob_ps_cond004/simulation_input.dat
diff --git a/...ta/plamsjob/plamsjob_ps_cond004/slurm.run → ...ta/plamsjob/plamsjob_ps_cond004/slurm.run b/...ta/plamsjob/plamsjob_ps_cond004/slurm.run → ...ta/plamsjob/plamsjob_ps_cond004/slurm.run
diff --git a/...ob/plamsjob_ps_cond004/specnum_output.txt → ...ob/plamsjob_ps_cond004/specnum_output.txt b/...ob/plamsjob_ps_cond004/specnum_output.txt → ...ob/plamsjob_ps_cond004/specnum_output.txt
diff --git a/...data/plamsjob/plamsjob_ps_cond004/std.err → ...data/plamsjob/plamsjob_ps_cond004/std.err b/...data/plamsjob/plamsjob_ps_cond004/std.err → ...data/plamsjob/plamsjob_ps_cond004/std.err
diff --git a/...data/plamsjob/plamsjob_ps_cond004/std.out → ...data/plamsjob/plamsjob_ps_cond004/std.out b/...data/plamsjob/plamsjob_ps_cond004/std.out → ...data/plamsjob/plamsjob_ps_cond004/std.out
diff --git a/.../plamsjob_ps_cond005/energetics_input.dat → .../plamsjob_ps_cond005/energetics_input.dat b/.../plamsjob_ps_cond005/energetics_input.dat → .../plamsjob_ps_cond005/energetics_input.dat
diff --git a/...ob/plamsjob_ps_cond005/general_output.txt → ...ob/plamsjob_ps_cond005/general_output.txt b/...ob/plamsjob_ps_cond005/general_output.txt → ...ob/plamsjob_ps_cond005/general_output.txt
diff --git a/...ob/plamsjob_ps_cond005/history_output.txt → ...ob/plamsjob_ps_cond005/history_output.txt b/...ob/plamsjob_ps_cond005/history_output.txt → ...ob/plamsjob_ps_cond005/history_output.txt
diff --git a/...job/plamsjob_ps_cond005/lattice_input.dat → ...job/plamsjob_ps_cond005/lattice_input.dat b/...job/plamsjob_ps_cond005/lattice_input.dat → ...job/plamsjob_ps_cond005/lattice_input.dat
diff --git a/...ob/plamsjob_ps_cond005/lattice_output.txt → ...ob/plamsjob_ps_cond005/lattice_output.txt b/...ob/plamsjob_ps_cond005/lattice_output.txt → ...ob/plamsjob_ps_cond005/lattice_output.txt
diff --git a/...b/plamsjob_ps_cond005/mechanism_input.dat → ...b/plamsjob_ps_cond005/mechanism_input.dat b/...b/plamsjob_ps_cond005/mechanism_input.dat → ...b/plamsjob_ps_cond005/mechanism_input.dat
diff --git a/...msjob_ps_cond005/plamsjob_ps_cond005.dill → ...msjob_ps_cond005/plamsjob_ps_cond005.dill b/...msjob_ps_cond005/plamsjob_ps_cond005.dill → ...msjob_ps_cond005/plamsjob_ps_cond005.dill
diff --git a/.../plamsjob/plamsjob_ps_cond005/restart.inf → .../plamsjob/plamsjob_ps_cond005/restart.inf b/.../plamsjob/plamsjob_ps_cond005/restart.inf → .../plamsjob/plamsjob_ps_cond005/restart.inf
diff --git a/.../plamsjob_ps_cond005/simulation_input.dat → .../plamsjob_ps_cond005/simulation_input.dat b/.../plamsjob_ps_cond005/simulation_input.dat → .../plamsjob_ps_cond005/simulation_input.dat
diff --git a/...ta/plamsjob/plamsjob_ps_cond005/slurm.run → ...ta/plamsjob/plamsjob_ps_cond005/slurm.run b/...ta/plamsjob/plamsjob_ps_cond005/slurm.run → ...ta/plamsjob/plamsjob_ps_cond005/slurm.run
diff --git a/...ob/plamsjob_ps_cond005/specnum_output.txt → ...ob/plamsjob_ps_cond005/specnum_output.txt b/...ob/plamsjob_ps_cond005/specnum_output.txt → ...ob/plamsjob_ps_cond005/specnum_output.txt
diff --git a/...data/plamsjob/plamsjob_ps_cond005/std.err → ...data/plamsjob/plamsjob_ps_cond005/std.err b/...data/plamsjob/plamsjob_ps_cond005/std.err → ...data/plamsjob/plamsjob_ps_cond005/std.err
diff --git a/...data/plamsjob/plamsjob_ps_cond005/std.out → ...data/plamsjob/plamsjob_ps_cond005/std.out b/...data/plamsjob/plamsjob_ps_cond005/std.out → ...data/plamsjob/plamsjob_ps_cond005/std.out
diff --git a/.../plamsjob_ps_cond006/energetics_input.dat → .../plamsjob_ps_cond006/energetics_input.dat b/.../plamsjob_ps_cond006/energetics_input.dat → .../plamsjob_ps_cond006/energetics_input.dat
diff --git a/...ob/plamsjob_ps_cond006/general_output.txt → ...ob/plamsjob_ps_cond006/general_output.txt b/...ob/plamsjob_ps_cond006/general_output.txt → ...ob/plamsjob_ps_cond006/general_output.txt
diff --git a/...ob/plamsjob_ps_cond006/history_output.txt → ...ob/plamsjob_ps_cond006/history_output.txt b/...ob/plamsjob_ps_cond006/history_output.txt → ...ob/plamsjob_ps_cond006/history_output.txt
diff --git a/...job/plamsjob_ps_cond006/lattice_input.dat → ...job/plamsjob_ps_cond006/lattice_input.dat b/...job/plamsjob_ps_cond006/lattice_input.dat → ...job/plamsjob_ps_cond006/lattice_input.dat
diff --git a/...ob/plamsjob_ps_cond006/lattice_output.txt → ...ob/plamsjob_ps_cond006/lattice_output.txt b/...ob/plamsjob_ps_cond006/lattice_output.txt → ...ob/plamsjob_ps_cond006/lattice_output.txt
diff --git a/...b/plamsjob_ps_cond006/mechanism_input.dat → ...b/plamsjob_ps_cond006/mechanism_input.dat b/...b/plamsjob_ps_cond006/mechanism_input.dat → ...b/plamsjob_ps_cond006/mechanism_input.dat
diff --git a/...msjob_ps_cond006/plamsjob_ps_cond006.dill → ...msjob_ps_cond006/plamsjob_ps_cond006.dill b/...msjob_ps_cond006/plamsjob_ps_cond006.dill → ...msjob_ps_cond006/plamsjob_ps_cond006.dill
diff --git a/.../plamsjob/plamsjob_ps_cond006/restart.inf → .../plamsjob/plamsjob_ps_cond006/restart.inf b/.../plamsjob/plamsjob_ps_cond006/restart.inf → .../plamsjob/plamsjob_ps_cond006/restart.inf
diff --git a/.../plamsjob_ps_cond006/simulation_input.dat → .../plamsjob_ps_cond006/simulation_input.dat b/.../plamsjob_ps_cond006/simulation_input.dat → .../plamsjob_ps_cond006/simulation_input.dat
diff --git a/...ta/plamsjob/plamsjob_ps_cond006/slurm.run → ...ta/plamsjob/plamsjob_ps_cond006/slurm.run b/...ta/plamsjob/plamsjob_ps_cond006/slurm.run → ...ta/plamsjob/plamsjob_ps_cond006/slurm.run
diff --git a/...ob/plamsjob_ps_cond006/specnum_output.txt → ...ob/plamsjob_ps_cond006/specnum_output.txt b/...ob/plamsjob_ps_cond006/specnum_output.txt → ...ob/plamsjob_ps_cond006/specnum_output.txt
diff --git a/...data/plamsjob/plamsjob_ps_cond006/std.err → ...data/plamsjob/plamsjob_ps_cond006/std.err b/...data/plamsjob/plamsjob_ps_cond006/std.err → ...data/plamsjob/plamsjob_ps_cond006/std.err
diff --git a/...data/plamsjob/plamsjob_ps_cond006/std.out → ...data/plamsjob/plamsjob_ps_cond006/std.out b/...data/plamsjob/plamsjob_ps_cond006/std.out → ...data/plamsjob/plamsjob_ps_cond006/std.out
diff --git a/...ParametersScanSteadyStateJob.data/logfile → tests/test_ParamScanSteadyState.data/logfile b/...ParametersScanSteadyStateJob.data/logfile → tests/test_ParamScanSteadyState.data/logfile
diff --git a/...teadyStateJob.data/plamsjob/plamsjob.dill → ...anSteadyState.data/plamsjob/plamsjob.dill b/...teadyStateJob.data/plamsjob/plamsjob.dill → ...anSteadyState.data/plamsjob/plamsjob.dill
diff --git a/...msjob_ps_cond000/plamsjob_ps_cond000.dill → ...msjob_ps_cond000/plamsjob_ps_cond000.dill b/...msjob_ps_cond000/plamsjob_ps_cond000.dill → ...msjob_ps_cond000/plamsjob_ps_cond000.dill
diff --git a/...00_ss_iter000_rep000/energetics_input.dat → ...00_ss_iter000_rep000/energetics_input.dat b/...00_ss_iter000_rep000/energetics_input.dat → ...00_ss_iter000_rep000/energetics_input.dat
diff --git a/...d000_ss_iter000_rep000/general_output.txt → ...d000_ss_iter000_rep000/general_output.txt b/...d000_ss_iter000_rep000/general_output.txt → ...d000_ss_iter000_rep000/general_output.txt
diff --git a/...nd000_ss_iter000_rep000/lattice_input.dat → ...nd000_ss_iter000_rep000/lattice_input.dat b/...nd000_ss_iter000_rep000/lattice_input.dat → ...nd000_ss_iter000_rep000/lattice_input.dat
diff --git a/...d000_ss_iter000_rep000/lattice_output.txt → ...d000_ss_iter000_rep000/lattice_output.txt b/...d000_ss_iter000_rep000/lattice_output.txt → ...d000_ss_iter000_rep000/lattice_output.txt
diff --git a/...000_ss_iter000_rep000/mechanism_input.dat → ...000_ss_iter000_rep000/mechanism_input.dat b/...000_ss_iter000_rep000/mechanism_input.dat → ...000_ss_iter000_rep000/mechanism_input.dat
diff --git a/...lamsjob_ps_cond000_ss_iter000_rep000.dill → ...lamsjob_ps_cond000_ss_iter000_rep000.dill b/...lamsjob_ps_cond000_ss_iter000_rep000.dill → ...lamsjob_ps_cond000_ss_iter000_rep000.dill
diff --git a/..._ps_cond000_ss_iter000_rep000/restart.inf → ..._ps_cond000_ss_iter000_rep000/restart.inf b/..._ps_cond000_ss_iter000_rep000/restart.inf → ..._ps_cond000_ss_iter000_rep000/restart.inf
diff --git a/...00_ss_iter000_rep000/simulation_input.dat → ...00_ss_iter000_rep000/simulation_input.dat b/...00_ss_iter000_rep000/simulation_input.dat → ...00_ss_iter000_rep000/simulation_input.dat
diff --git a/...ob_ps_cond000_ss_iter000_rep000/slurm.run → ...ob_ps_cond000_ss_iter000_rep000/slurm.run b/...ob_ps_cond000_ss_iter000_rep000/slurm.run → ...ob_ps_cond000_ss_iter000_rep000/slurm.run
diff --git a/...d000_ss_iter000_rep000/specnum_output.txt → ...d000_ss_iter000_rep000/specnum_output.txt b/...d000_ss_iter000_rep000/specnum_output.txt → ...d000_ss_iter000_rep000/specnum_output.txt
diff --git a/...sjob_ps_cond000_ss_iter000_rep000/std.err → ...sjob_ps_cond000_ss_iter000_rep000/std.err b/...sjob_ps_cond000_ss_iter000_rep000/std.err → ...sjob_ps_cond000_ss_iter000_rep000/std.err
diff --git a/...sjob_ps_cond000_ss_iter000_rep000/std.out → ...sjob_ps_cond000_ss_iter000_rep000/std.out b/...sjob_ps_cond000_ss_iter000_rep000/std.out → ...sjob_ps_cond000_ss_iter000_rep000/std.out
diff --git a/...00_ss_iter000_rep001/energetics_input.dat → ...00_ss_iter000_rep001/energetics_input.dat b/...00_ss_iter000_rep001/energetics_input.dat → ...00_ss_iter000_rep001/energetics_input.dat
diff --git a/...d000_ss_iter000_rep001/general_output.txt → ...d000_ss_iter000_rep001/general_output.txt b/...d000_ss_iter000_rep001/general_output.txt → ...d000_ss_iter000_rep001/general_output.txt
diff --git a/...nd000_ss_iter000_rep001/lattice_input.dat → ...nd000_ss_iter000_rep001/lattice_input.dat b/...nd000_ss_iter000_rep001/lattice_input.dat → ...nd000_ss_iter000_rep001/lattice_input.dat
diff --git a/...d000_ss_iter000_rep001/lattice_output.txt → ...d000_ss_iter000_rep001/lattice_output.txt b/...d000_ss_iter000_rep001/lattice_output.txt → ...d000_ss_iter000_rep001/lattice_output.txt
diff --git a/...000_ss_iter000_rep001/mechanism_input.dat → ...000_ss_iter000_rep001/mechanism_input.dat b/...000_ss_iter000_rep001/mechanism_input.dat → ...000_ss_iter000_rep001/mechanism_input.dat
diff --git a/...lamsjob_ps_cond000_ss_iter000_rep001.dill → ...lamsjob_ps_cond000_ss_iter000_rep001.dill b/...lamsjob_ps_cond000_ss_iter000_rep001.dill → ...lamsjob_ps_cond000_ss_iter000_rep001.dill
diff --git a/..._ps_cond000_ss_iter000_rep001/restart.inf → ..._ps_cond000_ss_iter000_rep001/restart.inf b/..._ps_cond000_ss_iter000_rep001/restart.inf → ..._ps_cond000_ss_iter000_rep001/restart.inf
diff --git a/...00_ss_iter000_rep001/simulation_input.dat → ...00_ss_iter000_rep001/simulation_input.dat b/...00_ss_iter000_rep001/simulation_input.dat → ...00_ss_iter000_rep001/simulation_input.dat
diff --git a/...ob_ps_cond000_ss_iter000_rep001/slurm.run → ...ob_ps_cond000_ss_iter000_rep001/slurm.run b/...ob_ps_cond000_ss_iter000_rep001/slurm.run → ...ob_ps_cond000_ss_iter000_rep001/slurm.run
diff --git a/...d000_ss_iter000_rep001/specnum_output.txt → ...d000_ss_iter000_rep001/specnum_output.txt b/...d000_ss_iter000_rep001/specnum_output.txt → ...d000_ss_iter000_rep001/specnum_output.txt
diff --git a/...sjob_ps_cond000_ss_iter000_rep001/std.err → ...sjob_ps_cond000_ss_iter000_rep001/std.err b/...sjob_ps_cond000_ss_iter000_rep001/std.err → ...sjob_ps_cond000_ss_iter000_rep001/std.err
diff --git a/...sjob_ps_cond000_ss_iter000_rep001/std.out → ...sjob_ps_cond000_ss_iter000_rep001/std.out b/...sjob_ps_cond000_ss_iter000_rep001/std.out → ...sjob_ps_cond000_ss_iter000_rep001/std.out
diff --git a/...00_ss_iter001_rep000/energetics_input.dat → ...00_ss_iter001_rep000/energetics_input.dat b/...00_ss_iter001_rep000/energetics_input.dat → ...00_ss_iter001_rep000/energetics_input.dat
diff --git a/...d000_ss_iter001_rep000/general_output.txt → ...d000_ss_iter001_rep000/general_output.txt b/...d000_ss_iter001_rep000/general_output.txt → ...d000_ss_iter001_rep000/general_output.txt
diff --git a/...nd000_ss_iter001_rep000/lattice_input.dat → ...nd000_ss_iter001_rep000/lattice_input.dat b/...nd000_ss_iter001_rep000/lattice_input.dat → ...nd000_ss_iter001_rep000/lattice_input.dat
diff --git a/...000_ss_iter001_rep000/mechanism_input.dat → ...000_ss_iter001_rep000/mechanism_input.dat b/...000_ss_iter001_rep000/mechanism_input.dat → ...000_ss_iter001_rep000/mechanism_input.dat
diff --git a/...lamsjob_ps_cond000_ss_iter001_rep000.dill → ...lamsjob_ps_cond000_ss_iter001_rep000.dill b/...lamsjob_ps_cond000_ss_iter001_rep000.dill → ...lamsjob_ps_cond000_ss_iter001_rep000.dill
diff --git a/..._ps_cond000_ss_iter001_rep000/restart.inf → ..._ps_cond000_ss_iter001_rep000/restart.inf b/..._ps_cond000_ss_iter001_rep000/restart.inf → ..._ps_cond000_ss_iter001_rep000/restart.inf
diff --git a/...00_ss_iter001_rep000/simulation_input.dat → ...00_ss_iter001_rep000/simulation_input.dat b/...00_ss_iter001_rep000/simulation_input.dat → ...00_ss_iter001_rep000/simulation_input.dat
diff --git a/...ob_ps_cond000_ss_iter001_rep000/slurm.run → ...ob_ps_cond000_ss_iter001_rep000/slurm.run b/...ob_ps_cond000_ss_iter001_rep000/slurm.run → ...ob_ps_cond000_ss_iter001_rep000/slurm.run
diff --git a/...d000_ss_iter001_rep000/specnum_output.txt → ...d000_ss_iter001_rep000/specnum_output.txt b/...d000_ss_iter001_rep000/specnum_output.txt → ...d000_ss_iter001_rep000/specnum_output.txt
diff --git a/...sjob_ps_cond000_ss_iter001_rep000/std.err → ...sjob_ps_cond000_ss_iter001_rep000/std.err b/...sjob_ps_cond000_ss_iter001_rep000/std.err → ...sjob_ps_cond000_ss_iter001_rep000/std.err
diff --git a/...sjob_ps_cond000_ss_iter001_rep000/std.out → ...sjob_ps_cond000_ss_iter001_rep000/std.out b/...sjob_ps_cond000_ss_iter001_rep000/std.out → ...sjob_ps_cond000_ss_iter001_rep000/std.out
diff --git a/...00_ss_iter001_rep001/energetics_input.dat → ...00_ss_iter001_rep001/energetics_input.dat b/...00_ss_iter001_rep001/energetics_input.dat → ...00_ss_iter001_rep001/energetics_input.dat
diff --git a/...d000_ss_iter001_rep001/general_output.txt → ...d000_ss_iter001_rep001/general_output.txt b/...d000_ss_iter001_rep001/general_output.txt → ...d000_ss_iter001_rep001/general_output.txt
diff --git a/...nd000_ss_iter001_rep001/lattice_input.dat → ...nd000_ss_iter001_rep001/lattice_input.dat b/...nd000_ss_iter001_rep001/lattice_input.dat → ...nd000_ss_iter001_rep001/lattice_input.dat
diff --git a/...000_ss_iter001_rep001/mechanism_input.dat → ...000_ss_iter001_rep001/mechanism_input.dat b/...000_ss_iter001_rep001/mechanism_input.dat → ...000_ss_iter001_rep001/mechanism_input.dat
diff --git a/...lamsjob_ps_cond000_ss_iter001_rep001.dill → ...lamsjob_ps_cond000_ss_iter001_rep001.dill b/...lamsjob_ps_cond000_ss_iter001_rep001.dill → ...lamsjob_ps_cond000_ss_iter001_rep001.dill
diff --git a/..._ps_cond000_ss_iter001_rep001/restart.inf → ..._ps_cond000_ss_iter001_rep001/restart.inf b/..._ps_cond000_ss_iter001_rep001/restart.inf → ..._ps_cond000_ss_iter001_rep001/restart.inf
diff --git a/...00_ss_iter001_rep001/simulation_input.dat → ...00_ss_iter001_rep001/simulation_input.dat b/...00_ss_iter001_rep001/simulation_input.dat → ...00_ss_iter001_rep001/simulation_input.dat
diff --git a/...ob_ps_cond000_ss_iter001_rep001/slurm.run → ...ob_ps_cond000_ss_iter001_rep001/slurm.run b/...ob_ps_cond000_ss_iter001_rep001/slurm.run → ...ob_ps_cond000_ss_iter001_rep001/slurm.run
diff --git a/...d000_ss_iter001_rep001/specnum_output.txt → ...d000_ss_iter001_rep001/specnum_output.txt b/...d000_ss_iter001_rep001/specnum_output.txt → ...d000_ss_iter001_rep001/specnum_output.txt
diff --git a/...sjob_ps_cond000_ss_iter001_rep001/std.err → ...sjob_ps_cond000_ss_iter001_rep001/std.err b/...sjob_ps_cond000_ss_iter001_rep001/std.err → ...sjob_ps_cond000_ss_iter001_rep001/std.err
diff --git a/...sjob_ps_cond000_ss_iter001_rep001/std.out → ...sjob_ps_cond000_ss_iter001_rep001/std.out b/...sjob_ps_cond000_ss_iter001_rep001/std.out → ...sjob_ps_cond000_ss_iter001_rep001/std.out
diff --git a/...00_ss_iter002_rep000/energetics_input.dat → ...00_ss_iter002_rep000/energetics_input.dat b/...00_ss_iter002_rep000/energetics_input.dat → ...00_ss_iter002_rep000/energetics_input.dat
diff --git a/...d000_ss_iter002_rep000/general_output.txt → ...d000_ss_iter002_rep000/general_output.txt b/...d000_ss_iter002_rep000/general_output.txt → ...d000_ss_iter002_rep000/general_output.txt
diff --git a/...nd000_ss_iter002_rep000/lattice_input.dat → ...nd000_ss_iter002_rep000/lattice_input.dat b/...nd000_ss_iter002_rep000/lattice_input.dat → ...nd000_ss_iter002_rep000/lattice_input.dat
diff --git a/...000_ss_iter002_rep000/mechanism_input.dat → ...000_ss_iter002_rep000/mechanism_input.dat b/...000_ss_iter002_rep000/mechanism_input.dat → ...000_ss_iter002_rep000/mechanism_input.dat
diff --git a/...lamsjob_ps_cond000_ss_iter002_rep000.dill → ...lamsjob_ps_cond000_ss_iter002_rep000.dill b/...lamsjob_ps_cond000_ss_iter002_rep000.dill → ...lamsjob_ps_cond000_ss_iter002_rep000.dill
diff --git a/..._ps_cond000_ss_iter002_rep000/restart.inf → ..._ps_cond000_ss_iter002_rep000/restart.inf b/..._ps_cond000_ss_iter002_rep000/restart.inf → ..._ps_cond000_ss_iter002_rep000/restart.inf
diff --git a/...00_ss_iter002_rep000/simulation_input.dat → ...00_ss_iter002_rep000/simulation_input.dat b/...00_ss_iter002_rep000/simulation_input.dat → ...00_ss_iter002_rep000/simulation_input.dat
diff --git a/...ob_ps_cond000_ss_iter002_rep000/slurm.run → ...ob_ps_cond000_ss_iter002_rep000/slurm.run b/...ob_ps_cond000_ss_iter002_rep000/slurm.run → ...ob_ps_cond000_ss_iter002_rep000/slurm.run
diff --git a/...d000_ss_iter002_rep000/specnum_output.txt → ...d000_ss_iter002_rep000/specnum_output.txt b/...d000_ss_iter002_rep000/specnum_output.txt → ...d000_ss_iter002_rep000/specnum_output.txt
diff --git a/...sjob_ps_cond000_ss_iter002_rep000/std.err → ...sjob_ps_cond000_ss_iter002_rep000/std.err b/...sjob_ps_cond000_ss_iter002_rep000/std.err → ...sjob_ps_cond000_ss_iter002_rep000/std.err
diff --git a/...sjob_ps_cond000_ss_iter002_rep000/std.out → ...sjob_ps_cond000_ss_iter002_rep000/std.out b/...sjob_ps_cond000_ss_iter002_rep000/std.out → ...sjob_ps_cond000_ss_iter002_rep000/std.out
diff --git a/...00_ss_iter002_rep001/energetics_input.dat → ...00_ss_iter002_rep001/energetics_input.dat b/...00_ss_iter002_rep001/energetics_input.dat → ...00_ss_iter002_rep001/energetics_input.dat
diff --git a/...d000_ss_iter002_rep001/general_output.txt → ...d000_ss_iter002_rep001/general_output.txt b/...d000_ss_iter002_rep001/general_output.txt → ...d000_ss_iter002_rep001/general_output.txt
diff --git a/...nd000_ss_iter002_rep001/lattice_input.dat → ...nd000_ss_iter002_rep001/lattice_input.dat b/...nd000_ss_iter002_rep001/lattice_input.dat → ...nd000_ss_iter002_rep001/lattice_input.dat
diff --git a/...000_ss_iter002_rep001/mechanism_input.dat → ...000_ss_iter002_rep001/mechanism_input.dat b/...000_ss_iter002_rep001/mechanism_input.dat → ...000_ss_iter002_rep001/mechanism_input.dat
diff --git a/...lamsjob_ps_cond000_ss_iter002_rep001.dill → ...lamsjob_ps_cond000_ss_iter002_rep001.dill b/...lamsjob_ps_cond000_ss_iter002_rep001.dill → ...lamsjob_ps_cond000_ss_iter002_rep001.dill
diff --git a/..._ps_cond000_ss_iter002_rep001/restart.inf → ..._ps_cond000_ss_iter002_rep001/restart.inf b/..._ps_cond000_ss_iter002_rep001/restart.inf → ..._ps_cond000_ss_iter002_rep001/restart.inf
diff --git a/...00_ss_iter002_rep001/simulation_input.dat → ...00_ss_iter002_rep001/simulation_input.dat b/...00_ss_iter002_rep001/simulation_input.dat → ...00_ss_iter002_rep001/simulation_input.dat
diff --git a/...ob_ps_cond000_ss_iter002_rep001/slurm.run → ...ob_ps_cond000_ss_iter002_rep001/slurm.run b/...ob_ps_cond000_ss_iter002_rep001/slurm.run → ...ob_ps_cond000_ss_iter002_rep001/slurm.run
diff --git a/...d000_ss_iter002_rep001/specnum_output.txt → ...d000_ss_iter002_rep001/specnum_output.txt b/...d000_ss_iter002_rep001/specnum_output.txt → ...d000_ss_iter002_rep001/specnum_output.txt
diff --git a/...sjob_ps_cond000_ss_iter002_rep001/std.err → ...sjob_ps_cond000_ss_iter002_rep001/std.err b/...sjob_ps_cond000_ss_iter002_rep001/std.err → ...sjob_ps_cond000_ss_iter002_rep001/std.err
diff --git a/...sjob_ps_cond000_ss_iter002_rep001/std.out → ...sjob_ps_cond000_ss_iter002_rep001/std.out b/...sjob_ps_cond000_ss_iter002_rep001/std.out → ...sjob_ps_cond000_ss_iter002_rep001/std.out
diff --git a/...00_ss_iter003_rep000/energetics_input.dat → ...00_ss_iter003_rep000/energetics_input.dat b/...00_ss_iter003_rep000/energetics_input.dat → ...00_ss_iter003_rep000/energetics_input.dat
diff --git a/...d000_ss_iter003_rep000/general_output.txt → ...d000_ss_iter003_rep000/general_output.txt b/...d000_ss_iter003_rep000/general_output.txt → ...d000_ss_iter003_rep000/general_output.txt
diff --git a/...nd000_ss_iter003_rep000/lattice_input.dat → ...nd000_ss_iter003_rep000/lattice_input.dat b/...nd000_ss_iter003_rep000/lattice_input.dat → ...nd000_ss_iter003_rep000/lattice_input.dat
diff --git a/...000_ss_iter003_rep000/mechanism_input.dat → ...000_ss_iter003_rep000/mechanism_input.dat b/...000_ss_iter003_rep000/mechanism_input.dat → ...000_ss_iter003_rep000/mechanism_input.dat
diff --git a/...lamsjob_ps_cond000_ss_iter003_rep000.dill → ...lamsjob_ps_cond000_ss_iter003_rep000.dill b/...lamsjob_ps_cond000_ss_iter003_rep000.dill → ...lamsjob_ps_cond000_ss_iter003_rep000.dill
diff --git a/..._ps_cond000_ss_iter003_rep000/restart.inf → ..._ps_cond000_ss_iter003_rep000/restart.inf b/..._ps_cond000_ss_iter003_rep000/restart.inf → ..._ps_cond000_ss_iter003_rep000/restart.inf
diff --git a/...00_ss_iter003_rep000/simulation_input.dat → ...00_ss_iter003_rep000/simulation_input.dat b/...00_ss_iter003_rep000/simulation_input.dat → ...00_ss_iter003_rep000/simulation_input.dat
diff --git a/...ob_ps_cond000_ss_iter003_rep000/slurm.run → ...ob_ps_cond000_ss_iter003_rep000/slurm.run b/...ob_ps_cond000_ss_iter003_rep000/slurm.run → ...ob_ps_cond000_ss_iter003_rep000/slurm.run
diff --git a/...d000_ss_iter003_rep000/specnum_output.txt → ...d000_ss_iter003_rep000/specnum_output.txt b/...d000_ss_iter003_rep000/specnum_output.txt → ...d000_ss_iter003_rep000/specnum_output.txt
diff --git a/...sjob_ps_cond000_ss_iter003_rep000/std.err → ...sjob_ps_cond000_ss_iter003_rep000/std.err b/...sjob_ps_cond000_ss_iter003_rep000/std.err → ...sjob_ps_cond000_ss_iter003_rep000/std.err
diff --git a/...sjob_ps_cond000_ss_iter003_rep000/std.out → ...sjob_ps_cond000_ss_iter003_rep000/std.out b/...sjob_ps_cond000_ss_iter003_rep000/std.out → ...sjob_ps_cond000_ss_iter003_rep000/std.out
diff --git a/...00_ss_iter003_rep001/energetics_input.dat → ...00_ss_iter003_rep001/energetics_input.dat b/...00_ss_iter003_rep001/energetics_input.dat → ...00_ss_iter003_rep001/energetics_input.dat
diff --git a/...d000_ss_iter003_rep001/general_output.txt → ...d000_ss_iter003_rep001/general_output.txt b/...d000_ss_iter003_rep001/general_output.txt → ...d000_ss_iter003_rep001/general_output.txt
diff --git a/...nd000_ss_iter003_rep001/lattice_input.dat → ...nd000_ss_iter003_rep001/lattice_input.dat b/...nd000_ss_iter003_rep001/lattice_input.dat → ...nd000_ss_iter003_rep001/lattice_input.dat
diff --git a/...000_ss_iter003_rep001/mechanism_input.dat → ...000_ss_iter003_rep001/mechanism_input.dat b/...000_ss_iter003_rep001/mechanism_input.dat → ...000_ss_iter003_rep001/mechanism_input.dat
diff --git a/...lamsjob_ps_cond000_ss_iter003_rep001.dill → ...lamsjob_ps_cond000_ss_iter003_rep001.dill b/...lamsjob_ps_cond000_ss_iter003_rep001.dill → ...lamsjob_ps_cond000_ss_iter003_rep001.dill
diff --git a/..._ps_cond000_ss_iter003_rep001/restart.inf → ..._ps_cond000_ss_iter003_rep001/restart.inf b/..._ps_cond000_ss_iter003_rep001/restart.inf → ..._ps_cond000_ss_iter003_rep001/restart.inf
diff --git a/...00_ss_iter003_rep001/simulation_input.dat → ...00_ss_iter003_rep001/simulation_input.dat b/...00_ss_iter003_rep001/simulation_input.dat → ...00_ss_iter003_rep001/simulation_input.dat
diff --git a/...ob_ps_cond000_ss_iter003_rep001/slurm.run → ...ob_ps_cond000_ss_iter003_rep001/slurm.run b/...ob_ps_cond000_ss_iter003_rep001/slurm.run → ...ob_ps_cond000_ss_iter003_rep001/slurm.run
diff --git a/...d000_ss_iter003_rep001/specnum_output.txt → ...d000_ss_iter003_rep001/specnum_output.txt b/...d000_ss_iter003_rep001/specnum_output.txt → ...d000_ss_iter003_rep001/specnum_output.txt
diff --git a/...sjob_ps_cond000_ss_iter003_rep001/std.err → ...sjob_ps_cond000_ss_iter003_rep001/std.err b/...sjob_ps_cond000_ss_iter003_rep001/std.err → ...sjob_ps_cond000_ss_iter003_rep001/std.err
diff --git a/...sjob_ps_cond000_ss_iter003_rep001/std.out → ...sjob_ps_cond000_ss_iter003_rep001/std.out b/...sjob_ps_cond000_ss_iter003_rep001/std.out → ...sjob_ps_cond000_ss_iter003_rep001/std.out
diff --git a/...s_cond000_ss_scaling/energetics_input.dat → ...s_cond000_ss_scaling/energetics_input.dat b/...s_cond000_ss_scaling/energetics_input.dat → ...s_cond000_ss_scaling/energetics_input.dat
diff --git a/..._ps_cond000_ss_scaling/general_output.txt → ..._ps_cond000_ss_scaling/general_output.txt b/..._ps_cond000_ss_scaling/general_output.txt → ..._ps_cond000_ss_scaling/general_output.txt
diff --git a/...b_ps_cond000_ss_scaling/lattice_input.dat → ...b_ps_cond000_ss_scaling/lattice_input.dat b/...b_ps_cond000_ss_scaling/lattice_input.dat → ...b_ps_cond000_ss_scaling/lattice_input.dat
diff --git a/..._ps_cond000_ss_scaling/lattice_output.txt → ..._ps_cond000_ss_scaling/lattice_output.txt b/..._ps_cond000_ss_scaling/lattice_output.txt → ..._ps_cond000_ss_scaling/lattice_output.txt
diff --git a/...ps_cond000_ss_scaling/mechanism_input.dat → ...ps_cond000_ss_scaling/mechanism_input.dat b/...ps_cond000_ss_scaling/mechanism_input.dat → ...ps_cond000_ss_scaling/mechanism_input.dat
diff --git a/...aling/plamsjob_ps_cond000_ss_scaling.dill → ...aling/plamsjob_ps_cond000_ss_scaling.dill b/...aling/plamsjob_ps_cond000_ss_scaling.dill → ...aling/plamsjob_ps_cond000_ss_scaling.dill
diff --git a/...ps_cond000_ss_scaling/procstat_output.txt → ...ps_cond000_ss_scaling/procstat_output.txt b/...ps_cond000_ss_scaling/procstat_output.txt → ...ps_cond000_ss_scaling/procstat_output.txt
diff --git a/...lamsjob_ps_cond000_ss_scaling/restart.inf → ...lamsjob_ps_cond000_ss_scaling/restart.inf b/...lamsjob_ps_cond000_ss_scaling/restart.inf → ...lamsjob_ps_cond000_ss_scaling/restart.inf
diff --git a/...s_cond000_ss_scaling/simulation_input.dat → ...s_cond000_ss_scaling/simulation_input.dat b/...s_cond000_ss_scaling/simulation_input.dat → ...s_cond000_ss_scaling/simulation_input.dat
diff --git a/.../plamsjob_ps_cond000_ss_scaling/slurm.run → .../plamsjob_ps_cond000_ss_scaling/slurm.run b/.../plamsjob_ps_cond000_ss_scaling/slurm.run → .../plamsjob_ps_cond000_ss_scaling/slurm.run
diff --git a/..._ps_cond000_ss_scaling/specnum_output.txt → ..._ps_cond000_ss_scaling/specnum_output.txt b/..._ps_cond000_ss_scaling/specnum_output.txt → ..._ps_cond000_ss_scaling/specnum_output.txt
diff --git a/...00/plamsjob_ps_cond000_ss_scaling/std.err → ...00/plamsjob_ps_cond000_ss_scaling/std.err b/...00/plamsjob_ps_cond000_ss_scaling/std.err → ...00/plamsjob_ps_cond000_ss_scaling/std.err
diff --git a/...00/plamsjob_ps_cond000_ss_scaling/std.out → ...00/plamsjob_ps_cond000_ss_scaling/std.out b/...00/plamsjob_ps_cond000_ss_scaling/std.out → ...00/plamsjob_ps_cond000_ss_scaling/std.out
diff --git a/...msjob_ps_cond001/plamsjob_ps_cond001.dill → ...msjob_ps_cond001/plamsjob_ps_cond001.dill b/...msjob_ps_cond001/plamsjob_ps_cond001.dill → ...msjob_ps_cond001/plamsjob_ps_cond001.dill
diff --git a/...01_ss_iter000_rep000/energetics_input.dat → ...01_ss_iter000_rep000/energetics_input.dat b/...01_ss_iter000_rep000/energetics_input.dat → ...01_ss_iter000_rep000/energetics_input.dat
diff --git a/...d001_ss_iter000_rep000/general_output.txt → ...d001_ss_iter000_rep000/general_output.txt b/...d001_ss_iter000_rep000/general_output.txt → ...d001_ss_iter000_rep000/general_output.txt
diff --git a/...nd001_ss_iter000_rep000/lattice_input.dat → ...nd001_ss_iter000_rep000/lattice_input.dat b/...nd001_ss_iter000_rep000/lattice_input.dat → ...nd001_ss_iter000_rep000/lattice_input.dat
diff --git a/...d001_ss_iter000_rep000/lattice_output.txt → ...d001_ss_iter000_rep000/lattice_output.txt b/...d001_ss_iter000_rep000/lattice_output.txt → ...d001_ss_iter000_rep000/lattice_output.txt
diff --git a/...001_ss_iter000_rep000/mechanism_input.dat → ...001_ss_iter000_rep000/mechanism_input.dat b/...001_ss_iter000_rep000/mechanism_input.dat → ...001_ss_iter000_rep000/mechanism_input.dat
diff --git a/...lamsjob_ps_cond001_ss_iter000_rep000.dill → ...lamsjob_ps_cond001_ss_iter000_rep000.dill b/...lamsjob_ps_cond001_ss_iter000_rep000.dill → ...lamsjob_ps_cond001_ss_iter000_rep000.dill
diff --git a/..._ps_cond001_ss_iter000_rep000/restart.inf → ..._ps_cond001_ss_iter000_rep000/restart.inf b/..._ps_cond001_ss_iter000_rep000/restart.inf → ..._ps_cond001_ss_iter000_rep000/restart.inf
diff --git a/...01_ss_iter000_rep000/simulation_input.dat → ...01_ss_iter000_rep000/simulation_input.dat b/...01_ss_iter000_rep000/simulation_input.dat → ...01_ss_iter000_rep000/simulation_input.dat
diff --git a/...ob_ps_cond001_ss_iter000_rep000/slurm.run → ...ob_ps_cond001_ss_iter000_rep000/slurm.run b/...ob_ps_cond001_ss_iter000_rep000/slurm.run → ...ob_ps_cond001_ss_iter000_rep000/slurm.run
diff --git a/...d001_ss_iter000_rep000/specnum_output.txt → ...d001_ss_iter000_rep000/specnum_output.txt b/...d001_ss_iter000_rep000/specnum_output.txt → ...d001_ss_iter000_rep000/specnum_output.txt
diff --git a/...sjob_ps_cond001_ss_iter000_rep000/std.err → ...sjob_ps_cond001_ss_iter000_rep000/std.err b/...sjob_ps_cond001_ss_iter000_rep000/std.err → ...sjob_ps_cond001_ss_iter000_rep000/std.err
diff --git a/...sjob_ps_cond001_ss_iter000_rep000/std.out → ...sjob_ps_cond001_ss_iter000_rep000/std.out b/...sjob_ps_cond001_ss_iter000_rep000/std.out → ...sjob_ps_cond001_ss_iter000_rep000/std.out
diff --git a/...01_ss_iter000_rep001/energetics_input.dat → ...01_ss_iter000_rep001/energetics_input.dat b/...01_ss_iter000_rep001/energetics_input.dat → ...01_ss_iter000_rep001/energetics_input.dat
diff --git a/...d001_ss_iter000_rep001/general_output.txt → ...d001_ss_iter000_rep001/general_output.txt b/...d001_ss_iter000_rep001/general_output.txt → ...d001_ss_iter000_rep001/general_output.txt
diff --git a/...nd001_ss_iter000_rep001/lattice_input.dat → ...nd001_ss_iter000_rep001/lattice_input.dat b/...nd001_ss_iter000_rep001/lattice_input.dat → ...nd001_ss_iter000_rep001/lattice_input.dat
diff --git a/...d001_ss_iter000_rep001/lattice_output.txt → ...d001_ss_iter000_rep001/lattice_output.txt b/...d001_ss_iter000_rep001/lattice_output.txt → ...d001_ss_iter000_rep001/lattice_output.txt
diff --git a/...001_ss_iter000_rep001/mechanism_input.dat → ...001_ss_iter000_rep001/mechanism_input.dat b/...001_ss_iter000_rep001/mechanism_input.dat → ...001_ss_iter000_rep001/mechanism_input.dat
diff --git a/...lamsjob_ps_cond001_ss_iter000_rep001.dill → ...lamsjob_ps_cond001_ss_iter000_rep001.dill b/...lamsjob_ps_cond001_ss_iter000_rep001.dill → ...lamsjob_ps_cond001_ss_iter000_rep001.dill
diff --git a/..._ps_cond001_ss_iter000_rep001/restart.inf → ..._ps_cond001_ss_iter000_rep001/restart.inf b/..._ps_cond001_ss_iter000_rep001/restart.inf → ..._ps_cond001_ss_iter000_rep001/restart.inf
diff --git a/...01_ss_iter000_rep001/simulation_input.dat → ...01_ss_iter000_rep001/simulation_input.dat b/...01_ss_iter000_rep001/simulation_input.dat → ...01_ss_iter000_rep001/simulation_input.dat
diff --git a/...ob_ps_cond001_ss_iter000_rep001/slurm.run → ...ob_ps_cond001_ss_iter000_rep001/slurm.run b/...ob_ps_cond001_ss_iter000_rep001/slurm.run → ...ob_ps_cond001_ss_iter000_rep001/slurm.run
diff --git a/...d001_ss_iter000_rep001/specnum_output.txt → ...d001_ss_iter000_rep001/specnum_output.txt b/...d001_ss_iter000_rep001/specnum_output.txt → ...d001_ss_iter000_rep001/specnum_output.txt
diff --git a/...sjob_ps_cond001_ss_iter000_rep001/std.err → ...sjob_ps_cond001_ss_iter000_rep001/std.err b/...sjob_ps_cond001_ss_iter000_rep001/std.err → ...sjob_ps_cond001_ss_iter000_rep001/std.err
diff --git a/...sjob_ps_cond001_ss_iter000_rep001/std.out → ...sjob_ps_cond001_ss_iter000_rep001/std.out b/...sjob_ps_cond001_ss_iter000_rep001/std.out → ...sjob_ps_cond001_ss_iter000_rep001/std.out
diff --git a/...01_ss_iter001_rep000/energetics_input.dat → ...01_ss_iter001_rep000/energetics_input.dat b/...01_ss_iter001_rep000/energetics_input.dat → ...01_ss_iter001_rep000/energetics_input.dat
diff --git a/...d001_ss_iter001_rep000/general_output.txt → ...d001_ss_iter001_rep000/general_output.txt b/...d001_ss_iter001_rep000/general_output.txt → ...d001_ss_iter001_rep000/general_output.txt
diff --git a/...nd001_ss_iter001_rep000/lattice_input.dat → ...nd001_ss_iter001_rep000/lattice_input.dat b/...nd001_ss_iter001_rep000/lattice_input.dat → ...nd001_ss_iter001_rep000/lattice_input.dat
diff --git a/...001_ss_iter001_rep000/mechanism_input.dat → ...001_ss_iter001_rep000/mechanism_input.dat b/...001_ss_iter001_rep000/mechanism_input.dat → ...001_ss_iter001_rep000/mechanism_input.dat
diff --git a/...lamsjob_ps_cond001_ss_iter001_rep000.dill → ...lamsjob_ps_cond001_ss_iter001_rep000.dill b/...lamsjob_ps_cond001_ss_iter001_rep000.dill → ...lamsjob_ps_cond001_ss_iter001_rep000.dill
diff --git a/..._ps_cond001_ss_iter001_rep000/restart.inf → ..._ps_cond001_ss_iter001_rep000/restart.inf b/..._ps_cond001_ss_iter001_rep000/restart.inf → ..._ps_cond001_ss_iter001_rep000/restart.inf
diff --git a/...01_ss_iter001_rep000/simulation_input.dat → ...01_ss_iter001_rep000/simulation_input.dat b/...01_ss_iter001_rep000/simulation_input.dat → ...01_ss_iter001_rep000/simulation_input.dat
diff --git a/...ob_ps_cond001_ss_iter001_rep000/slurm.run → ...ob_ps_cond001_ss_iter001_rep000/slurm.run b/...ob_ps_cond001_ss_iter001_rep000/slurm.run → ...ob_ps_cond001_ss_iter001_rep000/slurm.run
diff --git a/...d001_ss_iter001_rep000/specnum_output.txt → ...d001_ss_iter001_rep000/specnum_output.txt b/...d001_ss_iter001_rep000/specnum_output.txt → ...d001_ss_iter001_rep000/specnum_output.txt
diff --git a/...sjob_ps_cond001_ss_iter001_rep000/std.err → ...sjob_ps_cond001_ss_iter001_rep000/std.err b/...sjob_ps_cond001_ss_iter001_rep000/std.err → ...sjob_ps_cond001_ss_iter001_rep000/std.err
diff --git a/...sjob_ps_cond001_ss_iter001_rep000/std.out → ...sjob_ps_cond001_ss_iter001_rep000/std.out b/...sjob_ps_cond001_ss_iter001_rep000/std.out → ...sjob_ps_cond001_ss_iter001_rep000/std.out
diff --git a/...01_ss_iter001_rep001/energetics_input.dat → ...01_ss_iter001_rep001/energetics_input.dat b/...01_ss_iter001_rep001/energetics_input.dat → ...01_ss_iter001_rep001/energetics_input.dat
diff --git a/...d001_ss_iter001_rep001/general_output.txt → ...d001_ss_iter001_rep001/general_output.txt b/...d001_ss_iter001_rep001/general_output.txt → ...d001_ss_iter001_rep001/general_output.txt
diff --git a/...nd001_ss_iter001_rep001/lattice_input.dat → ...nd001_ss_iter001_rep001/lattice_input.dat b/...nd001_ss_iter001_rep001/lattice_input.dat → ...nd001_ss_iter001_rep001/lattice_input.dat
diff --git a/...001_ss_iter001_rep001/mechanism_input.dat → ...001_ss_iter001_rep001/mechanism_input.dat b/...001_ss_iter001_rep001/mechanism_input.dat → ...001_ss_iter001_rep001/mechanism_input.dat
diff --git a/...lamsjob_ps_cond001_ss_iter001_rep001.dill → ...lamsjob_ps_cond001_ss_iter001_rep001.dill b/...lamsjob_ps_cond001_ss_iter001_rep001.dill → ...lamsjob_ps_cond001_ss_iter001_rep001.dill
diff --git a/..._ps_cond001_ss_iter001_rep001/restart.inf → ..._ps_cond001_ss_iter001_rep001/restart.inf b/..._ps_cond001_ss_iter001_rep001/restart.inf → ..._ps_cond001_ss_iter001_rep001/restart.inf
diff --git a/...01_ss_iter001_rep001/simulation_input.dat → ...01_ss_iter001_rep001/simulation_input.dat b/...01_ss_iter001_rep001/simulation_input.dat → ...01_ss_iter001_rep001/simulation_input.dat
diff --git a/...ob_ps_cond001_ss_iter001_rep001/slurm.run → ...ob_ps_cond001_ss_iter001_rep001/slurm.run b/...ob_ps_cond001_ss_iter001_rep001/slurm.run → ...ob_ps_cond001_ss_iter001_rep001/slurm.run
diff --git a/...d001_ss_iter001_rep001/specnum_output.txt → ...d001_ss_iter001_rep001/specnum_output.txt b/...d001_ss_iter001_rep001/specnum_output.txt → ...d001_ss_iter001_rep001/specnum_output.txt
diff --git a/...sjob_ps_cond001_ss_iter001_rep001/std.err → ...sjob_ps_cond001_ss_iter001_rep001/std.err b/...sjob_ps_cond001_ss_iter001_rep001/std.err → ...sjob_ps_cond001_ss_iter001_rep001/std.err
diff --git a/...sjob_ps_cond001_ss_iter001_rep001/std.out → ...sjob_ps_cond001_ss_iter001_rep001/std.out b/...sjob_ps_cond001_ss_iter001_rep001/std.out → ...sjob_ps_cond001_ss_iter001_rep001/std.out
diff --git a/...01_ss_iter002_rep000/energetics_input.dat → ...01_ss_iter002_rep000/energetics_input.dat b/...01_ss_iter002_rep000/energetics_input.dat → ...01_ss_iter002_rep000/energetics_input.dat
diff --git a/...d001_ss_iter002_rep000/general_output.txt → ...d001_ss_iter002_rep000/general_output.txt b/...d001_ss_iter002_rep000/general_output.txt → ...d001_ss_iter002_rep000/general_output.txt
diff --git a/...nd001_ss_iter002_rep000/lattice_input.dat → ...nd001_ss_iter002_rep000/lattice_input.dat b/...nd001_ss_iter002_rep000/lattice_input.dat → ...nd001_ss_iter002_rep000/lattice_input.dat
diff --git a/...001_ss_iter002_rep000/mechanism_input.dat → ...001_ss_iter002_rep000/mechanism_input.dat b/...001_ss_iter002_rep000/mechanism_input.dat → ...001_ss_iter002_rep000/mechanism_input.dat
diff --git a/...lamsjob_ps_cond001_ss_iter002_rep000.dill → ...lamsjob_ps_cond001_ss_iter002_rep000.dill b/...lamsjob_ps_cond001_ss_iter002_rep000.dill → ...lamsjob_ps_cond001_ss_iter002_rep000.dill
diff --git a/..._ps_cond001_ss_iter002_rep000/restart.inf → ..._ps_cond001_ss_iter002_rep000/restart.inf b/..._ps_cond001_ss_iter002_rep000/restart.inf → ..._ps_cond001_ss_iter002_rep000/restart.inf
diff --git a/...01_ss_iter002_rep000/simulation_input.dat → ...01_ss_iter002_rep000/simulation_input.dat b/...01_ss_iter002_rep000/simulation_input.dat → ...01_ss_iter002_rep000/simulation_input.dat
diff --git a/...ob_ps_cond001_ss_iter002_rep000/slurm.run → ...ob_ps_cond001_ss_iter002_rep000/slurm.run b/...ob_ps_cond001_ss_iter002_rep000/slurm.run → ...ob_ps_cond001_ss_iter002_rep000/slurm.run
diff --git a/...d001_ss_iter002_rep000/specnum_output.txt → ...d001_ss_iter002_rep000/specnum_output.txt b/...d001_ss_iter002_rep000/specnum_output.txt → ...d001_ss_iter002_rep000/specnum_output.txt
diff --git a/...sjob_ps_cond001_ss_iter002_rep000/std.err → ...sjob_ps_cond001_ss_iter002_rep000/std.err b/...sjob_ps_cond001_ss_iter002_rep000/std.err → ...sjob_ps_cond001_ss_iter002_rep000/std.err
diff --git a/...sjob_ps_cond001_ss_iter002_rep000/std.out → ...sjob_ps_cond001_ss_iter002_rep000/std.out b/...sjob_ps_cond001_ss_iter002_rep000/std.out → ...sjob_ps_cond001_ss_iter002_rep000/std.out
diff --git a/...01_ss_iter002_rep001/energetics_input.dat → ...01_ss_iter002_rep001/energetics_input.dat b/...01_ss_iter002_rep001/energetics_input.dat → ...01_ss_iter002_rep001/energetics_input.dat
diff --git a/...d001_ss_iter002_rep001/general_output.txt → ...d001_ss_iter002_rep001/general_output.txt b/...d001_ss_iter002_rep001/general_output.txt → ...d001_ss_iter002_rep001/general_output.txt
diff --git a/...nd001_ss_iter002_rep001/lattice_input.dat → ...nd001_ss_iter002_rep001/lattice_input.dat b/...nd001_ss_iter002_rep001/lattice_input.dat → ...nd001_ss_iter002_rep001/lattice_input.dat
diff --git a/...001_ss_iter002_rep001/mechanism_input.dat → ...001_ss_iter002_rep001/mechanism_input.dat b/...001_ss_iter002_rep001/mechanism_input.dat → ...001_ss_iter002_rep001/mechanism_input.dat
diff --git a/...lamsjob_ps_cond001_ss_iter002_rep001.dill → ...lamsjob_ps_cond001_ss_iter002_rep001.dill b/...lamsjob_ps_cond001_ss_iter002_rep001.dill → ...lamsjob_ps_cond001_ss_iter002_rep001.dill
diff --git a/..._ps_cond001_ss_iter002_rep001/restart.inf → ..._ps_cond001_ss_iter002_rep001/restart.inf b/..._ps_cond001_ss_iter002_rep001/restart.inf → ..._ps_cond001_ss_iter002_rep001/restart.inf
diff --git a/...01_ss_iter002_rep001/simulation_input.dat → ...01_ss_iter002_rep001/simulation_input.dat b/...01_ss_iter002_rep001/simulation_input.dat → ...01_ss_iter002_rep001/simulation_input.dat
diff --git a/...ob_ps_cond001_ss_iter002_rep001/slurm.run → ...ob_ps_cond001_ss_iter002_rep001/slurm.run b/...ob_ps_cond001_ss_iter002_rep001/slurm.run → ...ob_ps_cond001_ss_iter002_rep001/slurm.run
diff --git a/...d001_ss_iter002_rep001/specnum_output.txt → ...d001_ss_iter002_rep001/specnum_output.txt b/...d001_ss_iter002_rep001/specnum_output.txt → ...d001_ss_iter002_rep001/specnum_output.txt
diff --git a/...sjob_ps_cond001_ss_iter002_rep001/std.err → ...sjob_ps_cond001_ss_iter002_rep001/std.err b/...sjob_ps_cond001_ss_iter002_rep001/std.err → ...sjob_ps_cond001_ss_iter002_rep001/std.err
diff --git a/...sjob_ps_cond001_ss_iter002_rep001/std.out → ...sjob_ps_cond001_ss_iter002_rep001/std.out b/...sjob_ps_cond001_ss_iter002_rep001/std.out → ...sjob_ps_cond001_ss_iter002_rep001/std.out
diff --git a/...01_ss_iter003_rep000/energetics_input.dat → ...01_ss_iter003_rep000/energetics_input.dat b/...01_ss_iter003_rep000/energetics_input.dat → ...01_ss_iter003_rep000/energetics_input.dat
diff --git a/...d001_ss_iter003_rep000/general_output.txt → ...d001_ss_iter003_rep000/general_output.txt b/...d001_ss_iter003_rep000/general_output.txt → ...d001_ss_iter003_rep000/general_output.txt
diff --git a/...nd001_ss_iter003_rep000/lattice_input.dat → ...nd001_ss_iter003_rep000/lattice_input.dat b/...nd001_ss_iter003_rep000/lattice_input.dat → ...nd001_ss_iter003_rep000/lattice_input.dat
diff --git a/...001_ss_iter003_rep000/mechanism_input.dat → ...001_ss_iter003_rep000/mechanism_input.dat b/...001_ss_iter003_rep000/mechanism_input.dat → ...001_ss_iter003_rep000/mechanism_input.dat
diff --git a/...lamsjob_ps_cond001_ss_iter003_rep000.dill → ...lamsjob_ps_cond001_ss_iter003_rep000.dill b/...lamsjob_ps_cond001_ss_iter003_rep000.dill → ...lamsjob_ps_cond001_ss_iter003_rep000.dill
diff --git a/..._ps_cond001_ss_iter003_rep000/restart.inf → ..._ps_cond001_ss_iter003_rep000/restart.inf b/..._ps_cond001_ss_iter003_rep000/restart.inf → ..._ps_cond001_ss_iter003_rep000/restart.inf
diff --git a/...01_ss_iter003_rep000/simulation_input.dat → ...01_ss_iter003_rep000/simulation_input.dat b/...01_ss_iter003_rep000/simulation_input.dat → ...01_ss_iter003_rep000/simulation_input.dat
diff --git a/...ob_ps_cond001_ss_iter003_rep000/slurm.run → ...ob_ps_cond001_ss_iter003_rep000/slurm.run b/...ob_ps_cond001_ss_iter003_rep000/slurm.run → ...ob_ps_cond001_ss_iter003_rep000/slurm.run
diff --git a/...d001_ss_iter003_rep000/specnum_output.txt → ...d001_ss_iter003_rep000/specnum_output.txt b/...d001_ss_iter003_rep000/specnum_output.txt → ...d001_ss_iter003_rep000/specnum_output.txt
diff --git a/...sjob_ps_cond001_ss_iter003_rep000/std.err → ...sjob_ps_cond001_ss_iter003_rep000/std.err b/...sjob_ps_cond001_ss_iter003_rep000/std.err → ...sjob_ps_cond001_ss_iter003_rep000/std.err
diff --git a/...sjob_ps_cond001_ss_iter003_rep000/std.out → ...sjob_ps_cond001_ss_iter003_rep000/std.out b/...sjob_ps_cond001_ss_iter003_rep000/std.out → ...sjob_ps_cond001_ss_iter003_rep000/std.out
diff --git a/...01_ss_iter003_rep001/energetics_input.dat → ...01_ss_iter003_rep001/energetics_input.dat b/...01_ss_iter003_rep001/energetics_input.dat → ...01_ss_iter003_rep001/energetics_input.dat
diff --git a/...d001_ss_iter003_rep001/general_output.txt → ...d001_ss_iter003_rep001/general_output.txt b/...d001_ss_iter003_rep001/general_output.txt → ...d001_ss_iter003_rep001/general_output.txt
diff --git a/...nd001_ss_iter003_rep001/lattice_input.dat → ...nd001_ss_iter003_rep001/lattice_input.dat b/...nd001_ss_iter003_rep001/lattice_input.dat → ...nd001_ss_iter003_rep001/lattice_input.dat
diff --git a/...001_ss_iter003_rep001/mechanism_input.dat → ...001_ss_iter003_rep001/mechanism_input.dat b/...001_ss_iter003_rep001/mechanism_input.dat → ...001_ss_iter003_rep001/mechanism_input.dat
diff --git a/...lamsjob_ps_cond001_ss_iter003_rep001.dill → ...lamsjob_ps_cond001_ss_iter003_rep001.dill b/...lamsjob_ps_cond001_ss_iter003_rep001.dill → ...lamsjob_ps_cond001_ss_iter003_rep001.dill
diff --git a/..._ps_cond001_ss_iter003_rep001/restart.inf → ..._ps_cond001_ss_iter003_rep001/restart.inf b/..._ps_cond001_ss_iter003_rep001/restart.inf → ..._ps_cond001_ss_iter003_rep001/restart.inf
diff --git a/...01_ss_iter003_rep001/simulation_input.dat → ...01_ss_iter003_rep001/simulation_input.dat b/...01_ss_iter003_rep001/simulation_input.dat → ...01_ss_iter003_rep001/simulation_input.dat
diff --git a/...ob_ps_cond001_ss_iter003_rep001/slurm.run → ...ob_ps_cond001_ss_iter003_rep001/slurm.run b/...ob_ps_cond001_ss_iter003_rep001/slurm.run → ...ob_ps_cond001_ss_iter003_rep001/slurm.run
diff --git a/...d001_ss_iter003_rep001/specnum_output.txt → ...d001_ss_iter003_rep001/specnum_output.txt b/...d001_ss_iter003_rep001/specnum_output.txt → ...d001_ss_iter003_rep001/specnum_output.txt
diff --git a/...sjob_ps_cond001_ss_iter003_rep001/std.err → ...sjob_ps_cond001_ss_iter003_rep001/std.err b/...sjob_ps_cond001_ss_iter003_rep001/std.err → ...sjob_ps_cond001_ss_iter003_rep001/std.err
diff --git a/...sjob_ps_cond001_ss_iter003_rep001/std.out → ...sjob_ps_cond001_ss_iter003_rep001/std.out b/...sjob_ps_cond001_ss_iter003_rep001/std.out → ...sjob_ps_cond001_ss_iter003_rep001/std.out
diff --git a/...s_cond001_ss_scaling/energetics_input.dat → ...s_cond001_ss_scaling/energetics_input.dat b/...s_cond001_ss_scaling/energetics_input.dat → ...s_cond001_ss_scaling/energetics_input.dat
diff --git a/..._ps_cond001_ss_scaling/general_output.txt → ..._ps_cond001_ss_scaling/general_output.txt b/..._ps_cond001_ss_scaling/general_output.txt → ..._ps_cond001_ss_scaling/general_output.txt
diff --git a/...b_ps_cond001_ss_scaling/lattice_input.dat → ...b_ps_cond001_ss_scaling/lattice_input.dat b/...b_ps_cond001_ss_scaling/lattice_input.dat → ...b_ps_cond001_ss_scaling/lattice_input.dat
diff --git a/..._ps_cond001_ss_scaling/lattice_output.txt → ..._ps_cond001_ss_scaling/lattice_output.txt b/..._ps_cond001_ss_scaling/lattice_output.txt → ..._ps_cond001_ss_scaling/lattice_output.txt
diff --git a/...ps_cond001_ss_scaling/mechanism_input.dat → ...ps_cond001_ss_scaling/mechanism_input.dat b/...ps_cond001_ss_scaling/mechanism_input.dat → ...ps_cond001_ss_scaling/mechanism_input.dat
diff --git a/...aling/plamsjob_ps_cond001_ss_scaling.dill → ...aling/plamsjob_ps_cond001_ss_scaling.dill b/...aling/plamsjob_ps_cond001_ss_scaling.dill → ...aling/plamsjob_ps_cond001_ss_scaling.dill
diff --git a/...ps_cond001_ss_scaling/procstat_output.txt → ...ps_cond001_ss_scaling/procstat_output.txt b/...ps_cond001_ss_scaling/procstat_output.txt → ...ps_cond001_ss_scaling/procstat_output.txt
diff --git a/...lamsjob_ps_cond001_ss_scaling/restart.inf → ...lamsjob_ps_cond001_ss_scaling/restart.inf b/...lamsjob_ps_cond001_ss_scaling/restart.inf → ...lamsjob_ps_cond001_ss_scaling/restart.inf
diff --git a/...s_cond001_ss_scaling/simulation_input.dat → ...s_cond001_ss_scaling/simulation_input.dat b/...s_cond001_ss_scaling/simulation_input.dat → ...s_cond001_ss_scaling/simulation_input.dat