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Fix directory references in notebooks: 'example' to 'examples' and 'TMP' to '.tmp' #4

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Fix directory references in notebooks: 'example' to 'examples' and 'TMP' to '.tmp' #4

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07f5a02
Initial plan
Copilot Dec 26, 2025
4895d77
Fix directory references from 'example' to 'examples' in all notebooks
Copilot Dec 26, 2025
8e44077
Update fix_cli_paths.py script to use 'examples' directory name
Copilot Dec 26, 2025
a54dd3f
Change TMP directory references to .tmp in notebooks
Copilot Dec 26, 2025
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6 changes: 3 additions & 3 deletions nbs/01_VASP_Tutorial.ipynb
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Expand Up @@ -106,7 +106,7 @@
"source": [
"#| vasp\n",
"# Directory in which our project resides\n",
"base_dir = f'../example/VASP_3C-SiC/{supercell}/'"
"base_dir = f'../examples/VASP_3C-SiC/{supercell}/'"
]
},
{
Expand Down Expand Up @@ -158,7 +158,7 @@
"# Setup the calculator - single point energy calculation\n",
"# The details will change here from case to case\n",
"# We are using run-calc.sh from the main project directory!\n",
"calc.set(directory=f'../TMP/calc_{supercell}/sc')\n",
"calc.set(directory=f'../.tmp/calc_{supercell}/sc')\n",
"calc.set(command=f'{os.getcwd()}/../run-calc.sh \"3C-SiC-{supercell}\"')\n",
"calc.set(nsw=0)\n",
"cryst.calc = calc"
Expand Down Expand Up @@ -214,7 +214,7 @@
"#|vasp\n",
"# Space for results\n",
"xsl = []\n",
"calc_dir = f'../TMP/calc_{supercell}'"
"calc_dir = f'../.tmp/calc_{supercell}'"
]
},
{
Expand Down
40 changes: 20 additions & 20 deletions nbs/02_CLI.ipynb
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Expand Up @@ -74,12 +74,12 @@
"outputs": [],
"source": [
"import os\n",
"os.makedirs('TMP', exist_ok=True)\n",
"os.makedirs('.tmp', exist_ok=True)\n",
"#| hide\n",
"#| vasp\n",
"from tempfile import TemporaryDirectory\n",
"calc_dir = TemporaryDirectory(dir='../TMP')\n",
"calc_dir_2 = TemporaryDirectory(dir='../TMP')"
"calc_dir = TemporaryDirectory(dir='../.tmp')\n",
"calc_dir_2 = TemporaryDirectory(dir='../.tmp')"
]
},
{
Expand Down Expand Up @@ -484,10 +484,10 @@
"name": "stdout",
"output_type": "stream",
"text": [
"$ hecss-sampler -W ../TMP/tmp552lh_fn -T 1000 -N 0 -e 10 -k 0 -c ./run-calc.sh ../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
"$ hecss-sampler -W ../TMP/tmp552lh_fn -T 1000 -N 0 -e 10 -k 0 -c ./run-calc.sh ../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
"\n",
"HECSS (0.5.29)\n",
"Supercell: ../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
"Supercell: ../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
"Temperature: 1000.0K\n",
"Work directory: ../TMP/tmp552lh_fn\n",
"Calculator: VASP\n",
Expand Down Expand Up @@ -536,7 +536,7 @@
" \"-T 1000 -N 0 -e 10 \"\n",
" \"-k 0 \"\n",
" \"-c ./run-calc.sh \"\n",
" \"../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\")"
" \"../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\")"
]
},
{
Expand All @@ -557,10 +557,10 @@
"name": "stdout",
"output_type": "stream",
"text": [
"$ hecss-sampler -W ../TMP/tmp552lh_fn -T 300 -N 10 -w 1.85 -c ./run-calc.sh -s scale.dat ../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
"$ hecss-sampler -W ../TMP/tmp552lh_fn -T 300 -N 10 -w 1.85 -c ./run-calc.sh -s scale.dat ../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
"\n",
"HECSS (0.5.29)\n",
"Supercell: ../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
"Supercell: ../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
"Temperature: 300.0K\n",
"Work directory: ../TMP/tmp552lh_fn\n",
"Calculator: VASP\n",
Expand Down Expand Up @@ -613,7 +613,7 @@
" \"-T 300 -N 10 -w 1.85 \"\n",
" \"-c ./run-calc.sh \"\n",
" \"-s scale.dat \"\n",
" \"../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\")"
" \"../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\")"
]
},
{
Expand Down Expand Up @@ -675,7 +675,7 @@
" -V, --version Show the version and exit.\n",
" -h, --help Show this message and exit.\n",
"\n",
"$ calculate-xscale -o ../TMP/tmp552lh_fn/iscale.dat -s 10 ../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR ../TMP/tmp552lh_fn/T_300.0K/scale.dat\n",
"$ calculate-xscale -o ../TMP/tmp552lh_fn/iscale.dat -s 10 ../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR ../TMP/tmp552lh_fn/T_300.0K/scale.dat\n",
"\n",
"Usage: calculate-xscale [OPTIONS] SUPERCELL SCALE\n",
"\n",
Expand Down Expand Up @@ -703,7 +703,7 @@
"run_cli_cmd(calculate_xscale, \"--help\")\n",
"run_cli_cmd(calculate_xscale, \n",
" f\"-o {calc_dir.name}/iscale.dat -s 10 \"\n",
" \"../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR \"\n",
" \"../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR \"\n",
" f\"{calc_dir.name}/T_300.0K/scale.dat\")"
]
},
Expand All @@ -723,10 +723,10 @@
"name": "stdout",
"output_type": "stream",
"text": [
"$ hecss-sampler -W ../TMP/tmpgf1xuhq8 -T 300 -N 10 -w 1.85 -c ./run-calc.sh -s scale.dat -a ../TMP/tmp552lh_fn/iscale.dat ../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
"$ hecss-sampler -W ../TMP/tmpgf1xuhq8 -T 300 -N 10 -w 1.85 -c ./run-calc.sh -s scale.dat -a ../TMP/tmp552lh_fn/iscale.dat ../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
"\n",
"HECSS (0.5.29)\n",
"Supercell: ../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
"Supercell: ../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
"Temperature: 300.0K\n",
"Work directory: ../TMP/tmpgf1xuhq8\n",
"Calculator: VASP\n",
Expand Down Expand Up @@ -778,7 +778,7 @@
"run_cli_cmd(hecss_sampler, \n",
" f\"-W {calc_dir_2.name} -T 300 -N 10 -w 1.85 \"\n",
" f\"-c ./run-calc.sh -s scale.dat -a {calc_dir.name}/iscale.dat\"\n",
" \" ../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\")"
" \" ../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\")"
]
},
{
Expand Down Expand Up @@ -1134,7 +1134,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"$ plot-stats -n -w 7 -h 4 ../example/VASP_3C-SiC_calculated/2x2x2/T_1200K/DFSET.dat 1200\n",
"$ plot-stats -n -w 7 -h 4 ../examples/VASP_3C-SiC_calculated/2x2x2/T_1200K/DFSET.dat 1200\n",
"\n",
"\n"
]
Expand All @@ -1155,7 +1155,7 @@
"run_cli_cmd(plot_stats, \n",
" \"-n \" \n",
" \"-w 7 -h 4 \"\n",
" \"../example/VASP_3C-SiC_calculated/2x2x2/T_1200K/DFSET.dat \"\n",
" \"../examples/VASP_3C-SiC_calculated/2x2x2/T_1200K/DFSET.dat \"\n",
" \"1200\")"
]
},
Expand Down Expand Up @@ -1253,7 +1253,7 @@
" -V, --version Show the version and exit.\n",
" --help Show this message and exit.\n",
"\n",
"$ plot-bands -w 7 -h 4 -l '300K,600K,3000K' ../example/VASP_3C-SiC_calculated/2x2x2/T_300K/phon/cryst.bands ../example/VASP_3C-SiC_calculated/2x2x2/T_600K/phon/cryst.bands ../example/VASP_3C-SiC_calculated/2x2x2/T_3000K/phon/cryst.bands \n",
"$ plot-bands -w 7 -h 4 -l '300K,600K,3000K' ../examples/VASP_3C-SiC_calculated/2x2x2/T_300K/phon/cryst.bands ../examples/VASP_3C-SiC_calculated/2x2x2/T_600K/phon/cryst.bands ../examples/VASP_3C-SiC_calculated/2x2x2/T_3000K/phon/cryst.bands \n",
"\n",
"\n"
]
Expand All @@ -1274,9 +1274,9 @@
"run_cli_cmd(plot_bands, \"--help\")\n",
"run_cli_cmd(plot_bands, \n",
" \"-w 7 -h 4 -l '300K,600K,3000K' \"\n",
" \"../example/VASP_3C-SiC_calculated/2x2x2/T_300K/phon/cryst.bands \"\n",
" \"../example/VASP_3C-SiC_calculated/2x2x2/T_600K/phon/cryst.bands \"\n",
" \"../example/VASP_3C-SiC_calculated/2x2x2/T_3000K/phon/cryst.bands \")"
" \"../examples/VASP_3C-SiC_calculated/2x2x2/T_300K/phon/cryst.bands \"\n",
" \"../examples/VASP_3C-SiC_calculated/2x2x2/T_600K/phon/cryst.bands \"\n",
" \"../examples/VASP_3C-SiC_calculated/2x2x2/T_3000K/phon/cryst.bands \")"
]
},
{
Expand Down
6 changes: 3 additions & 3 deletions nbs/03_monitor_stats.ipynb
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Expand Up @@ -74,7 +74,7 @@
"source": [
"T = 300\n",
"supercell = '2x2x2'\n",
"plot_stats(load_dfset(f'../example/VASP_3C-SiC_calculated/{supercell}/T_{T:.0f}K/DFSET.dat'), \n",
"plot_stats(load_dfset(f'../examples/VASP_3C-SiC_calculated/{supercell}/T_{T:.0f}K/DFSET.dat'), \n",
" T=T, sqrN=True);"
]
},
Expand Down Expand Up @@ -108,7 +108,7 @@
"T = 600\n",
"supercell = '1x1x1'\n",
"monitor_stats(T=T, \n",
" dfset=f'../example/VASP_3C-SiC_calculated/{supercell}/T_{T:.0f}K/DFSET.dat',\n",
" dfset=f'../examples/VASP_3C-SiC_calculated/{supercell}/T_{T:.0f}K/DFSET.dat',\n",
" once=True # Show the plot and exit\n",
" )"
]
Expand Down Expand Up @@ -146,7 +146,7 @@
"fig, axs = plt.subplots(4,2, figsize=(14,14))\n",
"\n",
"for n, d in enumerate(sorted(\n",
" glob('../example/VASP_3C-SiC_calculated/?x?x?/T_*K'), \n",
" glob('../examples/VASP_3C-SiC_calculated/?x?x?/T_*K'), \n",
" key=lambda s: (s.split('/')[-2],float(s.split('/')[-1][2:-1])))):\n",
" T=float(d.split('/')[-1][2:-1])\n",
" sc = d.split('/')[-2]\n",
Expand Down
4 changes: 2 additions & 2 deletions nbs/04_monitor_phonons.ipynb
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Expand Up @@ -59,7 +59,7 @@
"for sc, ax in zip(('1x1x1', '2x2x2'), axs):\n",
" plt.sca(ax)\n",
" for T in 300, 600, 1200, 3000:\n",
" plot_bands_file(f'../example/VASP_3C-SiC_calculated/{sc}/T_{T}K/phon/cryst.bands', lbl=f'T={T}K')\n",
" plot_bands_file(f'../examples/VASP_3C-SiC_calculated/{sc}/T_{T}K/phon/cryst.bands', lbl=f'T={T}K')\n",
" plt.legend()\n",
" plt.title(f'Supercell: {sc}');"
]
Expand All @@ -84,7 +84,7 @@
"#| interactive\n",
"T = 3000\n",
"supercell = '2x2x2'\n",
"monitor_phonons(directory=f'../example/VASP_3C-SiC_calculated/{supercell}/phon/', \n",
"monitor_phonons(directory=f'../examples/VASP_3C-SiC_calculated/{supercell}/phon/', \n",
" dfset=f'../T_3000K/DFSET.dat', \n",
" kpath='3C_SiC', charge='3C_SiC', sc=f'../sc/CONTCAR',\n",
" order=1, # Change to 2 if you want to monitor cubic potential\n",
Expand Down
4 changes: 2 additions & 2 deletions nbs/05_vasp_workflow.ipynb
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Expand Up @@ -97,8 +97,8 @@
"source": [
"#|vasp\n",
"# Directory in which our project resides\n",
"base_dir = f'../example/VASP_3C-SiC/{supercell}/'\n",
"calc_dir = TemporaryDirectory(dir='../TMP')"
"base_dir = f'../examples/VASP_3C-SiC/{supercell}/'\n",
"calc_dir = TemporaryDirectory(dir='../.tmp')"
]
},
{
Expand Down
8 changes: 4 additions & 4 deletions nbs/11_parwidth.ipynb
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Expand Up @@ -324,8 +324,8 @@
"source": [
"#|vasp\n",
"# Directory in which our project resides\n",
"base_dir = f'../example/VASP_3C-SiC_calculated/{supercell}/'\n",
"calc_dir = TemporaryDirectory(dir='../TMP')"
"base_dir = f'../examples/VASP_3C-SiC_calculated/{supercell}/'\n",
"calc_dir = TemporaryDirectory(dir='../.tmp')"
]
},
{
Expand Down Expand Up @@ -454,7 +454,7 @@
},
{
"ename": "CalculationFailed",
"evalue": "vasp in /home/jochym/Projects/hecss_AG/TMP/tmp3w9yovet/w_est/000 returned an error: 1 stderr Error: /home/jochym/Projects/hecss_AG/nbs/example/scripts/run-calc-ssh.sh is missing or not executable.\n",
"evalue": "vasp in /home/jochym/Projects/hecss_AG/.tmp/tmp3w9yovet/w_est/000 returned an error: 1 stderr Error: /home/jochym/Projects/hecss_AG/nbs/example/scripts/run-calc-ssh.sh is missing or not executable.\n",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
Expand All @@ -471,7 +471,7 @@
"File \u001b[0;32m~/miniconda/envs/hecss-dev/lib/python3.10/site-packages/ase/calculators/abc.py:26\u001b[0m, in \u001b[0;36mGetPropertiesMixin.get_potential_energy\u001b[0;34m(self, atoms, force_consistent)\u001b[0m\n\u001b[1;32m 24\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 25\u001b[0m name \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124menergy\u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[0;32m---> 26\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_property\u001b[49m\u001b[43m(\u001b[49m\u001b[43mname\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43matoms\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/miniconda/envs/hecss-dev/lib/python3.10/site-packages/ase/calculators/calculator.py:519\u001b[0m, in \u001b[0;36mBaseCalculator.get_property\u001b[0;34m(self, name, atoms, allow_calculation)\u001b[0m\n\u001b[1;32m 516\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39muse_cache:\n\u001b[1;32m 517\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39matoms \u001b[38;5;241m=\u001b[39m atoms\u001b[38;5;241m.\u001b[39mcopy()\n\u001b[0;32m--> 519\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcalculate\u001b[49m\u001b[43m(\u001b[49m\u001b[43matoms\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[43mname\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msystem_changes\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 521\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m name \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mresults:\n\u001b[1;32m 522\u001b[0m \u001b[38;5;66;03m# For some reason the calculator was not able to do what we want,\u001b[39;00m\n\u001b[1;32m 523\u001b[0m \u001b[38;5;66;03m# and that is OK.\u001b[39;00m\n\u001b[1;32m 524\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m PropertyNotImplementedError(\n\u001b[1;32m 525\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m not present in this \u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mcalculation\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(name)\n\u001b[1;32m 526\u001b[0m )\n",
"File \u001b[0;32m~/miniconda/envs/hecss-dev/lib/python3.10/site-packages/ase/calculators/vasp/vasp.py:342\u001b[0m, in \u001b[0;36mVasp.calculate\u001b[0;34m(self, atoms, properties, system_changes)\u001b[0m\n\u001b[1;32m 337\u001b[0m errorcode, stderr \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_run(command\u001b[38;5;241m=\u001b[39mcommand,\n\u001b[1;32m 338\u001b[0m out\u001b[38;5;241m=\u001b[39mout,\n\u001b[1;32m 339\u001b[0m directory\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdirectory)\n\u001b[1;32m 341\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m errorcode:\n\u001b[0;32m--> 342\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m calculator\u001b[38;5;241m.\u001b[39mCalculationFailed(\n\u001b[1;32m 343\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m in \u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m returned an error: \u001b[39m\u001b[38;5;132;01m{:d}\u001b[39;00m\u001b[38;5;124m stderr \u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(\n\u001b[1;32m 344\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mname, Path(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdirectory)\u001b[38;5;241m.\u001b[39mresolve(), errorcode,\n\u001b[1;32m 345\u001b[0m stderr))\n\u001b[1;32m 347\u001b[0m \u001b[38;5;66;03m# Read results from calculation\u001b[39;00m\n\u001b[1;32m 348\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mupdate_atoms(atoms)\n",
"\u001b[0;31mCalculationFailed\u001b[0m: vasp in /home/jochym/Projects/hecss_AG/TMP/tmp3w9yovet/w_est/000 returned an error: 1 stderr Error: /home/jochym/Projects/hecss_AG/nbs/example/scripts/run-calc-ssh.sh is missing or not executable.\n"
"\u001b[0;31mCalculationFailed\u001b[0m: vasp in /home/jochym/Projects/hecss_AG/.tmp/tmp3w9yovet/w_est/000 returned an error: 1 stderr Error: /home/jochym/Projects/hecss_AG/nbs/example/scripts/run-calc-ssh.sh is missing or not executable.\n"
]
}
],
Expand Down
4 changes: 2 additions & 2 deletions nbs/15_monitor.ipynb
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Expand Up @@ -447,7 +447,7 @@
}
],
"source": [
"plot_stats(load_dfset('../example/VASP_3C-SiC_calculated/1x1x1/T_300K/DFSET.dat'), \n",
"plot_stats(load_dfset('../examples/VASP_3C-SiC_calculated/1x1x1/T_300K/DFSET.dat'), \n",
" T=300, sqrN=True)"
]
},
Expand Down Expand Up @@ -505,7 +505,7 @@
],
"source": [
"monitor_stats(T=600, \n",
" dfset='../example/VASP_3C-SiC_calculated/1x1x1/T_600K/DFSET.dat', \n",
" dfset='../examples/VASP_3C-SiC_calculated/1x1x1/T_600K/DFSET.dat', \n",
" once=True)"
]
},
Expand Down
10 changes: 5 additions & 5 deletions nbs/16_util.ipynb
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Expand Up @@ -227,7 +227,7 @@
],
"source": [
"#| hide\n",
"confs = load_dfset('../example/VASP_3C-SiC_calculated/2x2x2/T_300K/DFSET.dat')\n",
"confs = load_dfset('../examples/VASP_3C-SiC_calculated/2x2x2/T_300K/DFSET.dat')\n",
"len(confs)"
]
},
Expand Down Expand Up @@ -266,12 +266,12 @@
"outputs": [],
"source": [
"#| hide\n",
"open('../TMP/dfset_test.dat', 'w').close()\n",
"open('../.tmp/dfset_test.dat', 'w').close()\n",
"for s in confs:\n",
" write_dfset('../TMP/dfset_test.dat', s)\n",
" write_dfset('../.tmp/dfset_test.dat', s)\n",
"\n",
"assert allclose(loadtxt('../TMP/dfset_test.dat'), \n",
" loadtxt('../example/VASP_3C-SiC_calculated/2x2x2/T_300K/DFSET.dat'))"
"assert allclose(loadtxt('../.tmp/dfset_test.dat'), \n",
" loadtxt('../examples/VASP_3C-SiC_calculated/2x2x2/T_300K/DFSET.dat'))"
]
},
{
Expand Down
4 changes: 2 additions & 2 deletions nbs/17_xscale.ipynb
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Expand Up @@ -338,7 +338,7 @@
"metadata": {},
"outputs": [],
"source": [
"sc = ase.io.read(f'../example/VASP_3C-SiC/{supercell}/sc_{supercell}/vasprun.xml')"
"sc = ase.io.read(f'../examples/VASP_3C-SiC/{supercell}/sc_{supercell}/vasprun.xml')"
]
},
{
Expand Down Expand Up @@ -383,7 +383,7 @@
"vt = []\n",
"\n",
"# for i, sfn in enumerate(sorted(glob(f'TMP/calc_{supercell}/w_est/*/vasprun.xml'))):\n",
"for i, sfn in enumerate(sorted(glob(f'../example/VASP_3C-SiC_calculated/calc_{supercell}/w_est/*/vasprun.xml'))):\n",
"for i, sfn in enumerate(sorted(glob(f'../examples/VASP_3C-SiC_calculated/calc_{supercell}/w_est/*/vasprun.xml'))):\n",
" s = ase.io.read(sfn)\n",
" dx = normalize_conf(s, sc)[0] - sc.get_positions()\n",
" try :\n",
Expand Down
2 changes: 1 addition & 1 deletion nbs/72_DOF_map.ipynb
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Expand Up @@ -56,7 +56,7 @@
"# cryst = ase.io.read('/home/jochym/cryst/TiO2_hecss/PBE_2x2x4/uc/CONTCAR')\n",
"# cryst = ase.io.read('/home/jochym/cryst/TiO2_hecss/PBE_Tetra/uc/CONTCAR')*(2,2,4)\n",
"# cryst = ase.io.read('/home/pastukh/Czech.calculation/sc/CONTCAR')\n",
"cryst = ase.io.read('../example/VASP_3C-SiC_calculated/2x2x2/sc/CONTCAR')"
"cryst = ase.io.read('../examples/VASP_3C-SiC_calculated/2x2x2/sc/CONTCAR')"
]
},
{
Expand Down
6 changes: 3 additions & 3 deletions nbs/98_ase_smoketest.ipynb
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Expand Up @@ -25,7 +25,7 @@
"output_type": "stream",
"text": [
"Energy: -55.65267549 eV\n",
"Workdir: ../TMP/tmpano7eqne\n"
"Workdir: ../.tmp/tmpano7eqne\n"
]
}
],
Expand All @@ -39,7 +39,7 @@
"from ase.calculators.vasp import Vasp\n",
"\n",
"# Paths\n",
"source_dir = Path('../TMP/sc').resolve()\n",
"source_dir = Path('../.tmp/sc').resolve()\n",
"run_calc = Path('../run-calc.sh').resolve()\n",
"\n",
"if not source_dir.exists():\n",
Expand All @@ -48,7 +48,7 @@
" raise FileNotFoundError(f\"Missing run-calc.sh: {run_calc}\")\n",
"\n",
"# Working directory in TMP\n",
"work_tmp = TemporaryDirectory(dir='../TMP')\n",
"work_tmp = TemporaryDirectory(dir='../.tmp')\n",
"workdir = Path(work_tmp.name)\n",
"\n",
"# Copy required inputs; include local run-calc.conf if present for convenience\n",
Expand Down
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