fix xml2xyz function #92
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Merge pull request #85 from jcwang587/dev
merge update of dependencies
WalkthroughThis update involves enhancements and modifications across several components of the project. Key changes include the correction of a typo in a URL, introduction of new functions for energy profiles, updates to function imports reflecting module renamings, and the addition of a new parameter in an existing function to handle free energy data more flexibly. Changes
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| def fes_1d(hillspot_path, hills_count, cv_range, resolution=100): | ||
| """ | ||
| Calculate the 1D free energy profile from a HILLSPOT file. | ||
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| Parameters | ||
| ---------- | ||
| hillspot_path : str | ||
| The path of the HILLSPOT file | ||
| hills_count : int | ||
| The number of hills to be read | ||
| cv_range : list | ||
| The range of the collective variable | ||
| resolution : int (optional) | ||
| The resolution of the free energy profile | ||
| """ | ||
| assert isinstance(cv_range, list) and len(cv_range) == 2, "cv_range must be a list of length 2" | ||
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| f = open(hillspot_path, "r") | ||
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| data = [] | ||
| h = [] | ||
| w = [] | ||
| hills_in = 0 | ||
| for line in f.readlines(): | ||
| line = line.split() | ||
| x = [] | ||
| if len(line) > 2: | ||
| for i in range(len(line) - 2): | ||
| x.append(float(line[i])) | ||
| data.append(x) | ||
| h.append(float(line[-2])) | ||
| w.append(float(line[-1])) | ||
| hills_in += 1 | ||
| if hills_in > hills_count: | ||
| break | ||
| f.close() | ||
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| step = (cv_range[1] - cv_range[0]) / resolution | ||
| cv = cv_range[0] | ||
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| data_list = [] | ||
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| for i in range(1, resolution): | ||
| en = 0.0 | ||
| cv = cv + step | ||
| for j in range(len(data)): | ||
| cv0 = data[j][0] | ||
| en_ = gauss_pot_1d(cv, cv0, h[j], w[j]) | ||
| en += en_ | ||
| data_list.append({"cv": cv, "potential_energy": en}) | ||
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| df = pd.DataFrame(data_list) | ||
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| return df | ||
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There was a problem hiding this comment.
The functions for calculating 1D, 2D, and 3D free energy profiles are well-implemented and documented. Consider adding error handling for file operations and validating input parameters to enhance robustness.
+ try:
+ f = open(hillspot_path, "r")
+ except IOError as e:
+ print(f"Error opening file: {e}")
+ returnCommittable 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.
| def fes_1d(hillspot_path, hills_count, cv_range, resolution=100): | |
| """ | |
| Calculate the 1D free energy profile from a HILLSPOT file. | |
| Parameters | |
| ---------- | |
| hillspot_path : str | |
| The path of the HILLSPOT file | |
| hills_count : int | |
| The number of hills to be read | |
| cv_range : list | |
| The range of the collective variable | |
| resolution : int (optional) | |
| The resolution of the free energy profile | |
| """ | |
| assert isinstance(cv_range, list) and len(cv_range) == 2, "cv_range must be a list of length 2" | |
| f = open(hillspot_path, "r") | |
| data = [] | |
| h = [] | |
| w = [] | |
| hills_in = 0 | |
| for line in f.readlines(): | |
| line = line.split() | |
| x = [] | |
| if len(line) > 2: | |
| for i in range(len(line) - 2): | |
| x.append(float(line[i])) | |
| data.append(x) | |
| h.append(float(line[-2])) | |
| w.append(float(line[-1])) | |
| hills_in += 1 | |
| if hills_in > hills_count: | |
| break | |
| f.close() | |
| step = (cv_range[1] - cv_range[0]) / resolution | |
| cv = cv_range[0] | |
| data_list = [] | |
| for i in range(1, resolution): | |
| en = 0.0 | |
| cv = cv + step | |
| for j in range(len(data)): | |
| cv0 = data[j][0] | |
| en_ = gauss_pot_1d(cv, cv0, h[j], w[j]) | |
| en += en_ | |
| data_list.append({"cv": cv, "potential_energy": en}) | |
| df = pd.DataFrame(data_list) | |
| return df | |
| def fes_1d(hillspot_path, hills_count, cv_range, resolution=100): | |
| """ | |
| Calculate the 1D free energy profile from a HILLSPOT file. | |
| Parameters | |
| ---------- | |
| hillspot_path : str | |
| The path of the HILLSPOT file | |
| hills_count : int | |
| The number of hills to be read | |
| cv_range : list | |
| The range of the collective variable | |
| resolution : int (optional) | |
| The resolution of the free energy profile | |
| """ | |
| assert isinstance(cv_range, list) and len(cv_range) == 2, "cv_range must be a list of length 2" | |
| try: | |
| f = open(hillspot_path, "r") | |
| except IOError as e: | |
| print(f"Error opening file: {e}") | |
| return | |
| data = [] | |
| h = [] | |
| w = [] | |
| hills_in = 0 | |
| for line in f.readlines(): | |
| line = line.split() | |
| x = [] | |
| if len(line) > 2: | |
| for i in range(len(line) - 2): | |
| x.append(float(line[i])) | |
| data.append(x) | |
| h.append(float(line[-2])) | |
| w.append(float(line[-1])) | |
| hills_in += 1 | |
| if hills_in > hills_count: | |
| break | |
| f.close() | |
| step = (cv_range[1] - cv_range[0]) / resolution | |
| cv = cv_range[0] | |
| data_list = [] | |
| for i in range(1, resolution): | |
| en = 0.0 | |
| cv = cv + step | |
| for j in range(len(data)): | |
| cv0 = data[j][0] | |
| en_ = gauss_pot_1d(cv, cv0, h[j], w[j]) | |
| en += en_ | |
| data_list.append({"cv": cv, "potential_energy": en}) | |
| df = pd.DataFrame(data_list) | |
| return df |
Summary by CodeRabbit
Documentation
New Features
Enhancements
xml2xyzconversion function.Version Update