use P as control variable in Gibbs free energy for hti #74
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Actionable comments posted: 2
Outside diff range, codebase verification and nitpick comments (8)
dpti/hti_liq.py (4)
480-480: Add a docstring for the new parameter.The
nptparameter should be documented in the function's docstring for clarity.def compute_task(job, free_energy_type="helmholtz", scheme="simpson", manual_pv=None, manual_pv_err=None, npt=None): """ Compute the thermodynamic properties of a job. Parameters: job (str): The job directory. free_energy_type (str): The type of free energy to compute ('helmholtz' or 'gibbs'). scheme (str): The numerical integration scheme. manual_pv (float, optional): Manual pressure-volume value. manual_pv_err (float, optional): Manual pressure-volume error. npt (str, optional): Directory of the NPT task; will use PV from NPT result, where P is the control variable and V varies. """
523-523: Improve logging for manual PV usage.The print statement for
manual_pvshould provide more context to the user.- print(f"# use manual_pv={manual_pv}") + print(f"# Using manual PV value: manual_pv={manual_pv}")
528-528: Improve logging for manual PV error usage.The print statement for
manual_pv_errshould provide more context to the user.- print(f"# use manual_pv_err={manual_pv_err}") + print(f"# Using manual PV error value: manual_pv_err={manual_pv_err}")
658-658: Add a docstring for the new parameter.The
nptparameter should be documented in the function's docstring for clarity.def handle_compute(args): """ Handle the compute command. Parameters: args: Command-line arguments. """dpti/hti.py (4)
1260-1260: Add a docstring for the new parameter.The
nptparameter should be documented in the function's docstring for clarity.def compute_task(job, free_energy_type="helmholtz", method="inte", scheme="simpson", manual_pv=None, manual_pv_err=None, npt=None): """ Compute the thermodynamic properties of a job. Parameters: job (str): The job directory. free_energy_type (str): The type of free energy to compute ('helmholtz' or 'gibbs'). method (str): The method of thermodynamic integration. scheme (str): The numerical integration scheme. manual_pv (float, optional): Manual pressure-volume value. manual_pv_err (float, optional): Manual pressure-volume error. npt (str, optional): Directory of the NPT task; will use PV from NPT result, where P is the control variable and V varies. """
1309-1309: Improve logging for manual PV usage.The print statement for
manual_pvshould provide more context to the user.- print(f"# use manual_pv={manual_pv}") + print(f"# Using manual PV value: manual_pv={manual_pv}")
1314-1314: Improve logging for manual PV error usage.The print statement for
manual_pv_errshould provide more context to the user.- print(f"# use manual_pv_err={manual_pv_err}") + print(f"# Using manual PV error value: manual_pv_err={manual_pv_err}")
1530-1530: Add a docstring for the new parameter.The
nptparameter should be documented in the function's docstring for clarity.def handle_compute(args): """ Handle the compute command. Parameters: args: Command-line arguments. """
dpti/hti_liq.py
Outdated
| if npt is not None: | ||
| npt_in = json.load(open(os.path.join(npt, "jdata.json"))) | ||
| npt_info = json.load(open(os.path.join(npt, "result.json"))) | ||
| p = npt_in["pres"] | ||
| v = npt_info["v"] | ||
| v_err = npt_info["v_err"] | ||
| unit_cvt = 1e5 * (1e-10**3) / pc.electron_volt | ||
| pv = p * v * unit_cvt * 3 | ||
| pv_err = p * v_err * unit_cvt * np.sqrt(3) | ||
| print(f"# use pv from npt task: pv = {pv:.6e} pv_err = {pv_err:.6e}") |
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Ensure error handling for file operations.
The code assumes that the jdata.json and result.json files exist in the npt directory. Add error handling to manage cases where these files are missing or unreadable.
- if npt is not None:
- npt_in = json.load(open(os.path.join(npt, "jdata.json")))
- npt_info = json.load(open(os.path.join(npt, "result.json")))
+ if npt is not None:
+ try:
+ npt_in = json.load(open(os.path.join(npt, "jdata.json")))
+ npt_info = json.load(open(os.path.join(npt, "result.json")))
+ except (FileNotFoundError, json.JSONDecodeError) as e:
+ raise RuntimeError(f"Error loading NPT data: {e}")Committable suggestion was skipped due to low confidence.
dpti/hti.py
Outdated
| if npt is not None: | ||
| npt_in = json.load(open(os.path.join(npt, "jdata.json"))) | ||
| npt_info = json.load(open(os.path.join(npt, "result.json"))) | ||
| p = npt_in["pres"] | ||
| v = npt_info["v"] | ||
| v_err = npt_info["v_err"] | ||
| unit_cvt = 1e5 * (1e-10**3) / pc.electron_volt | ||
| pv = p * v * unit_cvt * 3 | ||
| pv_err = p * v_err * unit_cvt * np.sqrt(3) | ||
| print(f"# use pv from npt task: pv = {pv:.6e} pv_err = {pv_err:.6e}") |
There was a problem hiding this comment.
Ensure error handling for file operations.
The code assumes that the jdata.json and result.json files exist in the npt directory. Add error handling to manage cases where these files are missing or unreadable.
- if npt is not None:
- npt_in = json.load(open(os.path.join(npt, "jdata.json")))
- npt_info = json.load(open(os.path.join(npt, "result.json")))
+ if npt is not None:
+ try:
+ npt_in = json.load(open(os.path.join(npt, "jdata.json")))
+ npt_info = json.load(open(os.path.join(npt, "result.json")))
+ except (FileNotFoundError, json.JSONDecodeError) as e:
+ raise RuntimeError(f"Error loading NPT data: {e}")Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| if npt is not None: | |
| npt_in = json.load(open(os.path.join(npt, "jdata.json"))) | |
| npt_info = json.load(open(os.path.join(npt, "result.json"))) | |
| p = npt_in["pres"] | |
| v = npt_info["v"] | |
| v_err = npt_info["v_err"] | |
| unit_cvt = 1e5 * (1e-10**3) / pc.electron_volt | |
| pv = p * v * unit_cvt * 3 | |
| pv_err = p * v_err * unit_cvt * np.sqrt(3) | |
| print(f"# use pv from npt task: pv = {pv:.6e} pv_err = {pv_err:.6e}") | |
| if npt is not None: | |
| try: | |
| npt_in = json.load(open(os.path.join(npt, "jdata.json"))) | |
| npt_info = json.load(open(os.path.join(npt, "result.json"))) | |
| except (FileNotFoundError, json.JSONDecodeError) as e: | |
| raise RuntimeError(f"Error loading NPT data: {e}") | |
| p = npt_in["pres"] | |
| v = npt_info["v"] | |
| v_err = npt_info["v_err"] | |
| unit_cvt = 1e5 * (1e-10**3) / pc.electron_volt | |
| pv = p * v * unit_cvt * 3 | |
| pv_err = p * v_err * unit_cvt * np.sqrt(3) | |
| print(f"# use pv from npt task: pv = {pv:.6e} pv_err = {pv_err:.6e}") |
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## devel #74 +/- ##
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Coverage 0.00% 0.00%
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Files 24 24
Lines 5829 5862 +33
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- Misses 5829 5862 +33 ☔ View full report in Codecov by Sentry. |
The same as #41 but for
hti.pyandhti_liq.py.Summary by CodeRabbit
New Features
nptparameter for thecompute_taskfunction, allowing users to utilize external pressure-volume data from an NPT simulation directory.--nptoption for enhanced flexibility in data sourcing.User Experience Enhancements