Merge pull request #119 from jvalegre/jv_branch

Merge v1.4.1

Example_workflows/End-to-end_Workflows/1-Strychnine/Inputs/Instructions.txt

@@ -0,0 +1,3 @@
+1. Run all the cells from the end-to-end-example-1.ipynb Jupyter Notebook
+2. Edit and run the workflow_1_SLURM_script.sh script in your HPC
+3. For the command lines version, visit: https://aqme.readthedocs.io/en/latest/Examples/examples_commandline/end_to_end/example_1.html

Example_workflows/End-to-end_Workflows/1-Strychnine/Inputs/Jupyter-Notebook/end-to-end-example-1.ipynb

@@ -59,7 +59,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -88,7 +88,7 @@
     "smi = 'C1CN2CC3=CCO[C@H]4CC(=O)N5[C@H]6[C@H]4[C@H]3C[C@H]2[C@@]61C7=CC=CC=C75'\n",
     "program = 'rdkit'\n",
     "\n",
-    "sdf_path = f'{os.getcwd()}/{name}_sdf-files' # folder where the SDF files are generated\n",
+    "sdf_path = f'{os.getcwd()}/{name}_sdf_files' # folder where the SDF files are generated\n",
     "\n",
     "csearch(destination=sdf_path,program=program,smi=smi,name=name)"
    ]
@@ -112,7 +112,7 @@
     "nprocs=12\n",
     "\n",
     "sdf_rdkit_files = f'{sdf_path}/*.sdf' # SDF files from Step 2\n",
-    "com_path = f'{os.getcwd()}/{name}_com-files' # folder where the COM files are generated\n",
+    "com_path = f'{os.getcwd()}/{name}_com_files' # folder where the COM files are generated\n",
     "\n",
     "qprep(destination=com_path,files=sdf_rdkit_files,program=program,\n",
     "        qm_input=qm_input,mem=mem,nprocs=nprocs)"
@@ -149,10 +149,11 @@
    "source": [
     "log_files=f'{com_path}/*.log' # LOG files from Step 4\n",
     "\n",
-    "qcorr(files=log_files,freq_conv='opt=(calcfc,maxstep=5)',isom_type='com',isom_inputs=com_path,nprocs=24,mem='96GB')"
+    "qcorr(files=log_files,freq_conv='opt=(calcfc,maxstep=5)',isom_type='com',isom_inputs=com_path,nprocs=12,mem='24GB')"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -165,14 +166,39 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Run the generated COM files (in fixed_inp_folder) with Gaussian"
+    "# Run the generated COM files (in fixed_QM_inputs, shown as resub_path in Step 7) with Gaussian"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "id": "c9820843",
+   "metadata": {},
+   "source": [
+    "### Step 7: QCORR analysis of unsuccessful calculations (if any) from Step 6"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f40487ac",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "resub_path = f'{com_path}/failed/run_1/fixed_QM_inputs' # LOG files from Step 6\n",
+    "log_files_resub = f'{resub_path}/*.log'\n",
+    "\n",
+    "# this QCORR analysis skips the freq_conv since we noticed that thermochemistry data barely change after one freq_conv correction\n",
+    "# if there are no files that failed, you will see a PATH error\n",
+    "qcorr(files=log_files_resub,isom_type='com',isom_inputs=com_path,nprocs=12,mem='24GB')"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Step 7: Creating Gaussian input files for NMR calcs with QPREP"
+    "### Step 8: Creating Gaussian input files for NMR calcs with QPREP"
    ]
   },
   {
@@ -188,16 +214,17 @@
     "\n",
     "success_folder = com_path+'/success' # folder where the successful LOG files are stored during the QCORR cycles (Steps 5 and 6)\n",
     "log_files = f'{success_folder}/*.log'\n",
-    "sp_path = f'{os.getcwd()}/{name}_sp-files' # folder to store the new COM inputs for single point NMR calcs\n",
+    "sp_path = f'{os.getcwd()}/{name}_sp_files' # folder to store the new COM inputs for single point NMR calcs\n",
     "\n",
-    "qprep(w_dir_main=success_folder,destination=sp_path,files=log_files,program=program,qm_input=qm_input,mem=mem,nprocs=nprocs,suffix='SP')"
+    "qprep(w_dir_main=success_folder,destination=sp_path,files=log_files,program=program,qm_input=qm_input,mem=mem,nprocs=nprocs,suffix='SP',nprocs=12,mem='24GB')"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Step 8: Running Gaussian NMR calcs"
+    "### Step 9: Running Gaussian NMR calcs"
    ]
   },
   {
@@ -210,10 +237,11 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Step 9: Obtaining Boltzmann weighted NMR shifts with QDESCP"
+    "### Step 10: Obtaining Boltzmann weighted NMR shifts with QDESCP"
    ]
   },
   {
@@ -229,16 +257,17 @@
     "# Analyze the JSON files to calculate the Boltzmann averaged shielding tensors\n",
     "json_folder = sp_path+'/success/SP_calcs/json_files' # folder where the JSON files were just created with QCORR\n",
     "json_files=f'{json_folder}/*.json'\n",
-    "nmr_path = f'{os.getcwd()}/{name}_nmr-files' # folder to store the results from QDESCP\n",
+    "nmr_path = f'{os.getcwd()}/{name}_nmr_files' # folder to store the results from QDESCP\n",
     "\n",
     "qdescp(program='nmr',boltz=True,files=json_files,destination=nmr_path,nmr_slope=[-1.0537, -1.0784],nmr_intercept=[181.7815,31.8723], nmr_experim='Experimental_NMR_shifts.csv')"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Step 10: Calculating conformer populations with GoodVibes"
+    "### Step 11: Calculating conformer populations with GoodVibes"
    ]
   },
   {
@@ -248,6 +277,7 @@
    "outputs": [],
    "source": [
     "log_files = glob.glob(f'{success_folder}/*.log')\n",
+    "log_files += glob.glob(f'{sp_path}/success/SP_calcs/*.log')\n",
     "\n",
     "w_dir_main  = Path(os.getcwd())\n",
     "GV_folder = w_dir_main.joinpath('Strychine_GoodVibes-analysis')\n",
@@ -258,7 +288,7 @@
     "\n",
     "# run GoodVibes\n",
     "os.chdir(GV_folder)\n",
-    "subprocess.run(['python', '-m', 'goodvibes', '--xyz','-c','1', '*.log','--boltz'])\n",
+    "subprocess.run(['python', '-m', 'goodvibes', '--xyz', '-c', '1', '*.log','--boltz', '--spc', 'SP'])\n",
     "os.chdir(w_dir_main)\n"
    ]
   },

Example_workflows/End-to-end_Workflows/2-Diels_Alder_Reaction/Inputs/Instructions.txt

@@ -1,2 +1,2 @@
-1. Activate the Python kernel with AQME installed
-2. Run all the cells from the end-to-end-example-2.ipynb Jupyter Notebook
+1. Run all the cells from the end-to-end-example-2.ipynb Jupyter Notebook
+2. For the command lines version, visit: https://aqme.readthedocs.io/en/latest/Examples/examples_commandline/end_to_end/example_2.html