Merge pull request #82 from luigibonati/fix_plumed_nest_zip

Fixed path to state file timelagged experiment
luigibonati · Jun 5, 2023 · 19c7df3 · 19c7df3
2 parents bf93482 + ed6622a
commit 19c7df3
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Showing 8 changed files with 2 additions and 20,044 deletions.
diff --git a/...ents/results/timelagged/opes-y/State.data → ...s/input_data/timelagged/opes-y/State.data b/...ents/results/timelagged/opes-y/State.data → ...s/input_data/timelagged/opes-y/State.data
diff --git a/docs/notebooks/paper_experiments/paper_3_timelagged.ipynb b/docs/notebooks/paper_experiments/paper_3_timelagged.ipynb
@@ -366,7 +366,7 @@
     "                static_model_path=None,\n",
     "                static_bias_cv='p.y',\n",
     "                file_path=SIMULATION_FOLDER,\n",
-    "                rfile_path=f'input_data/opes-y/State.data', \n",
+    "                rfile_path=f'../../../../input_data/timelagged/opes-y/State.data', \n",
     "                potential_formula=MULLER_BROWN_FORMULA, \n",
     "                opes_mode='OPES_METAD')\n",
     "        gen_input_md(inital_position='-0.7,1.4', file_path=SIMULATION_FOLDER, nsteps=1000000)\n",

diff --git a/docs/notebooks/paper_experiments/paper_experiments.zip b/docs/notebooks/paper_experiments/paper_experiments.zip
diff --git a/docs/notebooks/paper_experiments/results/timelagged/deepTICA/data/plumed.dat b/docs/notebooks/paper_experiments/results/timelagged/deepTICA/data/plumed.dat
@@ -12,12 +12,11 @@ pot: BIASVALUE ARG=ene
 
 # load deep cv pytorch model
 tica: PYTORCH_MODEL FILE=../model_deepTICA.pt ARG=p.x,p.y
-#cv: PYTORCH_MODEL FILE=../../../muller_experiments/deepTDA_bad/model_deepTDA_bad.pt ARG=p.x,p.y 
 
 # apply static bias from previous sim
 static: OPES_METAD ARG=p.y ...
     RESTART=YES
-    STATE_RFILE=../../../muller_experiments/opes-y/State.data
+    STATE_RFILE=../../../../input_data/timelagged/opes-y/State.data
     BARRIER=16
     PACE=10000000
 ...

diff --git a/docs/notebooks/paper_experiments/results/timelagged/opes-y/COLVAR b/docs/notebooks/paper_experiments/results/timelagged/opes-y/COLVAR
diff --git a/docs/notebooks/paper_experiments/results/timelagged/opes-y/md_input b/docs/notebooks/paper_experiments/results/timelagged/opes-y/md_input
diff --git a/docs/notebooks/paper_experiments/results/timelagged/opes-y/md_potential b/docs/notebooks/paper_experiments/results/timelagged/opes-y/md_potential
diff --git a/docs/notebooks/paper_experiments/results/timelagged/opes-y/plumed.dat b/docs/notebooks/paper_experiments/results/timelagged/opes-y/plumed.dat