add support for spin, DeltaSpin and LAMMPS SPIN #728
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WalkthroughWalkthroughThe changes introduce functionality for loading and handling spin data across multiple files in the Changes
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CodSpeed Performance ReportMerging #728 will not alter performanceComparing Summary
|
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## devel #728 +/- ##
==========================================
- Coverage 84.73% 81.56% -3.18%
==========================================
Files 81 84 +3
Lines 7345 7702 +357
==========================================
+ Hits 6224 6282 +58
- Misses 1121 1420 +299 ☔ View full report in Codecov by Sentry. |
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Actionable comments posted: 25
Outside diff range and nitpick comments (5)
dpdata/plugins/vasp_deltaspin.py (2)
75-77: Add a docstring to 'from_labeled_system' methodIncluding a docstring for the
from_labeled_systemmethod enhances code readability and maintainability by documenting its purpose, parameters, and return values.Consider adding a docstring similar to:
def from_labeled_system( self, file_name, begin=0, step=1, convergence_check=True, **kwargs ): """ Load data from a VASP OUTCAR file into a labeled system. Parameters ---------- file_name : str The path to the OUTCAR file. begin : int, optional The starting frame index, by default 0. step : int, optional The step size between frames, by default 1. convergence_check : bool, optional Whether to perform convergence checks, by default True. **kwargs : dict Additional keyword arguments. Returns ------- dict The loaded system data. """
18-24: Increase test coverage for critical code pathsSeveral critical sections of the code, including file operations and data processing, are not covered by unit tests. This may lead to undiscovered bugs and reduce code reliability.
Consider adding unit tests for these code paths to improve test coverage and ensure the code behaves as expected. Do you need help in creating these tests or setting up the testing framework?
Also applies to: 40-42, 44-46, 67-68, 78-80, 98-99, 101-107
Tools
GitHub Check: codecov/patch
[warning] 18-24: dpdata/plugins/vasp_deltaspin.py#L18-L24
Added lines #L18 - L24 were not covered by testsdpdata/vasp_deltaspin/poscar.py (1)
59-61: Correct grammatical error in exception messageIn the exception message, 'seem' should be 'seems' for grammatical correctness.
Apply this diff to correct the message:
- raise RuntimeError( - "seem not to be a valid POSCAR of vasp 5.x, may be a POSCAR of vasp 4.x?" - ) + raise RuntimeError( + "seems not to be a valid POSCAR of VASP 5.x, may be a POSCAR of VASP 4.x?" + )dpdata/vasp_deltaspin/outcar.py (1)
119-122: Simplify conditional assignment using a ternary operator.You can replace the
if-elseblock with a single-line conditional expression for brevity.Apply this diff:
- if len(all_virials) == 0: - all_virials = None - else: - all_virials = np.array(all_virials) + all_virials = None if len(all_virials) == 0 else np.array(all_virials)Tools
Ruff
119-122: Use ternary operator
all_virials = None if len(all_virials) == 0 else np.array(all_virials)instead ofif-else-blockReplace
if-else-block withall_virials = None if len(all_virials) == 0 else np.array(all_virials)(SIM108)
dpdata/lammps/lmp.py (1)
130-141: Add unit tests for new spin-handling functionalityThe newly added
get_spinsfunction and the spin processing insystem_dataare not covered by tests, as indicated by the static analysis. Adding unit tests will help ensure correctness and prevent future regressions.Would you like assistance in creating these unit tests or opening a new GitHub issue to track this task?
Also applies to: 167-169
Tools
GitHub Check: codecov/patch
[warning] 134-140: dpdata/lammps/lmp.py#L134-L140
Added lines #L134 - L140 were not covered by tests
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (8)
- dpdata/deepmd/comp.py (3 hunks)
- dpdata/deepmd/raw.py (1 hunks)
- dpdata/lammps/dump.py (3 hunks)
- dpdata/lammps/lmp.py (3 hunks)
- dpdata/plugins/vasp_deltaspin.py (1 hunks)
- dpdata/system.py (4 hunks)
- dpdata/vasp_deltaspin/outcar.py (1 hunks)
- dpdata/vasp_deltaspin/poscar.py (1 hunks)
Additional context used
GitHub Check: codecov/patch
dpdata/lammps/dump.py
[warning] 136-141: dpdata/lammps/dump.py#L136-L141
Added lines #L136 - L141 were not covered by tests
[warning] 145-157: dpdata/lammps/dump.py#L145-L157
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[warning] 166-168: dpdata/lammps/dump.py#L166-L168
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[warning] 258-260: dpdata/lammps/dump.py#L258-L260
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[warning] 274-274: dpdata/lammps/dump.py#L274
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[warning] 279-279: dpdata/lammps/dump.py#L279
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[warning] 134-140: dpdata/lammps/lmp.py#L134-L140
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[warning] 169-169: dpdata/lammps/lmp.py#L169
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[warning] 236-236: dpdata/lammps/lmp.py#L236
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[warning] 248-248: dpdata/lammps/lmp.py#L248
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[warning] 251-252: dpdata/lammps/lmp.py#L251-L252
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[warning] 264-264: dpdata/lammps/lmp.py#L264
Added line #L264 was not covered by testsdpdata/plugins/vasp_deltaspin.py
[warning] 18-24: dpdata/plugins/vasp_deltaspin.py#L18-L24
Added lines #L18 - L24 were not covered by tests
[warning] 40-42: dpdata/plugins/vasp_deltaspin.py#L40-L42
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[warning] 44-46: dpdata/plugins/vasp_deltaspin.py#L44-L46
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[warning] 49-50: dpdata/plugins/vasp_deltaspin.py#L49-L50
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[warning] 67-68: dpdata/plugins/vasp_deltaspin.py#L67-L68
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[warning] 78-80: dpdata/plugins/vasp_deltaspin.py#L78-L80
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[warning] 98-99: dpdata/plugins/vasp_deltaspin.py#L98-L99
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[warning] 101-107: dpdata/plugins/vasp_deltaspin.py#L101-L107
Added lines #L101 - L107 were not covered by testsdpdata/vasp_deltaspin/outcar.py
[warning] 10-15: dpdata/vasp_deltaspin/outcar.py#L10-L15
Added lines #L10 - L15 were not covered by tests
[warning] 17-18: dpdata/vasp_deltaspin/outcar.py#L17-L18
Added lines #L17 - L18 were not covered by tests
[warning] 20-20: dpdata/vasp_deltaspin/outcar.py#L20
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[warning] 22-22: dpdata/vasp_deltaspin/outcar.py#L22
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[warning] 24-31: dpdata/vasp_deltaspin/outcar.py#L24-L31
Added lines #L24 - L31 were not covered by tests
[warning] 33-41: dpdata/vasp_deltaspin/outcar.py#L33-L41
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[warning] 43-44: dpdata/vasp_deltaspin/outcar.py#L43-L44
Added lines #L43 - L44 were not covered by tests
[warning] 48-57: dpdata/vasp_deltaspin/outcar.py#L48-L57
Added lines #L48 - L57 were not covered by tests
[warning] 62-63: dpdata/vasp_deltaspin/outcar.py#L62-L63
Added lines #L62 - L63 were not covered by tests
[warning] 65-66: dpdata/vasp_deltaspin/outcar.py#L65-L66
Added lines #L65 - L66 were not covered by tests
Ruff
dpdata/lammps/lmp.py
235-235: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
250-250: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
dpdata/plugins/vasp_deltaspin.py
46-48:
re.subshould passcountandflagsas keyword arguments to avoid confusion due to unintuitive argument positions(B034)
dpdata/system.py
716-719: Use
contextlib.suppress(Exception)instead oftry-except-passReplace with
contextlib.suppress(Exception)(SIM105)
718-718: Do not use bare
except(E722)
dpdata/vasp_deltaspin/outcar.py
14-14: Local variable
ii_word_listis assigned to but never usedRemove assignment to unused variable
ii_word_list(F841)
39-39: Loop control variable
jjnot used within loop bodyRename unused
jjto_jj(B007)
62-62: Use a context manager for opening files
(SIM115)
115-115: No explicit
stacklevelkeyword argument found(B028)
119-122: Use ternary operator
all_virials = None if len(all_virials) == 0 else np.array(all_virials)instead ofif-else-blockReplace
if-else-block withall_virials = None if len(all_virials) == 0 else np.array(all_virials)(SIM108)
176-176: Use
lines[idx + in_kB_index].split()[0:2] != ["in", "kB"]instead ofnot lines[idx + in_kB_index].split()[0:2] == ["in", "kB"]Replace with
!=operator(SIM201)
dpdata/vasp_deltaspin/poscar.py
32-32: Loop control variable
jjnot used within loop bodyRename unused
jjto_jj(B007)
48-48: Local variable
spins_idxis assigned to but never usedRemove assignment to unused variable
spins_idx(F841)
57-58: Use a single
ifstatement instead of nestedifstatementsCombine
ifstatements usingand(SIM102)
Additional comments not posted (9)
dpdata/deepmd/raw.py (1)
67-67: LGTM! Verify the usage of the "spins" attribute.The addition of the "spins" attribute to the list of handled data elements in the
to_system_datafunction looks good. It enhances the function's capability to process spin-related data during the conversion from deepmd/raw format to system data format.However, please ensure that the rest of the codebase is equipped to handle the "spins" attribute correctly, as this is a new addition.
Run the following script to verify the usage of the "spins" attribute:
Verification successful
Verified: "spins" attribute is consistently used throughout the codebase.
The addition of the "spins" attribute to the list in the
to_system_datafunction is consistent with its usage throughout the codebase. The attribute is well-integrated into various parts of the project, including:
- Test files (e.g.,
test_abacus_spin.py)- VASP-related files (e.g.,
dpdata/vasp_deltaspin/outcar.py)- LAMMPS-related files (e.g.,
dpdata/lammps/lmp.py)- ABACUS-related files (e.g.,
dpdata/abacus/scf.py)The widespread use of the "spins" attribute in data manipulation, testing, and file I/O operations indicates that the codebase is equipped to handle this attribute correctly. The change enhances the functionality of the
to_system_datafunction by ensuring it can process spin-related data, which is consistent with the project's capabilities.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of the "spins" attribute in the codebase. # Test: Search for the usage of the "spins" attribute. Expect: Relevant code snippets handling the "spins" attribute. rg --type python -A 5 $'spins'Length of output: 60
Script:
#!/bin/bash # Description: Verify the usage of the "spins" attribute in the codebase using alternative methods. # Method 1: Use rg without file type specification echo "Method 1: Using rg without file type specification" rg -A 5 'spins' # Method 2: Use fd to find Python files and xargs with rg to search them echo "Method 2: Using fd and xargs with rg" fd -e py | xargs rg -A 5 'spins' # Method 3: Use ast-grep to search for the "spins" attribute in Python files echo "Method 3: Using ast-grep" ast-grep --lang python --pattern '$_ = $_.spins'Length of output: 33142
dpdata/system.py (1)
98-98: LGTM!The new optional data type
"spins"is correctly defined and enhances the data handling capabilities of theSystemclass.dpdata/plugins/vasp_deltaspin.py (1)
101-106: Verify 'virials' scaling calculation for correctnessThe code scales the virials to the unit of eV using a conversion factor and volume calculations. It's important to ensure that the calculation is correct and that potential numerical issues (e.g., division by zero, incorrect array shapes) are handled.
Please review the scaling factor and the volume calculation to confirm their correctness. Additionally, consider adding checks for zero volume or invalid cell shapes to prevent runtime errors.
Tools
GitHub Check: codecov/patch
[warning] 101-107: dpdata/plugins/vasp_deltaspin.py#L101-L107
Added lines #L101 - L107 were not covered by testsdpdata/deepmd/comp.py (6)
42-42: Initialization ofall_spinslist is appropriate.The
all_spinslist is correctly initialized to collect spins data across datasets.
44-44: Correctly updated call to_load_setwith additional return value.The function call now properly unpacks
cells,coords, andspins, aligning with the updated_load_setfunction.
48-49: Proper handling and reshaping ofspinsdata.The code appropriately checks if
spinsis notNoneand reshapes it similarly to howcoordsare handled. This ensures the spins data is correctly aggregated.
52-53: Conditional addition ofspinsto thedatadictionary is appropriate.By checking if
all_spinshas any data before adding todata, we ensure thatspinsis only included when available, preventing potential KeyErrors or empty data entries.
68-68: Appropriate exclusion ofspinsfrom dtype processing loop.Adding
"spins"to the skip list ensures thatspinsdata is not processed in the generic loop, avoiding unintended behavior sincespinsrequires specific handling.
29-30: Verify handling of the additional return value from_load_set.The
_load_setfunction now returnsspinsalong withcellsandcoords. Please ensure that all calls to_load_setare updated to handle this new return value, and that backward compatibility is maintained.Run the following script to verify all usages of
_load_setare correctly updated:Verification successful
Changes to
_load_sethave been correctly implemented and used.The verification process confirms that the
_load_setfunction is being called with three assigned variables (cells, coords, spins) as expected. There are no instances of outdated usage with only two return values.For improved clarity, consider updating the function definition to explicitly document the return values:
def _load_set(folder, nopbc: bool) -> Tuple[np.ndarray, np.ndarray, Optional[np.ndarray]]: # ... existing implementation ...This change would make the function's interface more self-documenting and help prevent future misuse.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Find all calls to `_load_set` and check the number of assigned variables. # Search for assignments from `_load_set` with three return variables rg --type python -P '(\w+),\s*(\w+),\s*(\w+)\s*=\s*_load_set\(' # Search for assignments from `_load_set` with two return variables (which may need updating) rg --type python -P '(\w+),\s*(\w+)\s*=\s*_load_set\('Length of output: 184
Script:
#!/bin/bash # Description: Find all calls to `_load_set` and its definition, with context # Search for the definition of _load_set echo "Definition of _load_set:" rg -n -C 2 "def _load_set\(" echo "\nCalls to _load_set:" # Search for assignments from _load_set with any number of return variables rg -n -C 2 "\w+(?:,\s*\w+)*\s*=\s*_load_set\(" # Search for any other usage of _load_set echo "\nOther usages of _load_set:" rg -n -C 2 "_load_set\(" | grep -v "def _load_set"Length of output: 1425
| try: | ||
| self.data["spins"][f_idx] = np.matmul(self.data["spins"][f_idx], trans) | ||
| except: | ||
| pass |
There was a problem hiding this comment.
Use contextlib.suppress(Exception) and avoid bare except.
Consider the following improvements:
- Replace the
try-except-passpattern withcontextlib.suppress(Exception)for a more explicit and concise way to handle the specific exception. - Avoid using a bare
exceptas it can catch unintended exceptions and make debugging difficult. Specify the expected exception type instead.
Apply this diff to address the suggestions:
- try:
- self.data["spins"][f_idx] = np.matmul(self.data["spins"][f_idx], trans)
- except:
- pass
+ with contextlib.suppress(KeyError):
+ self.data["spins"][f_idx] = np.matmul(self.data["spins"][f_idx], trans)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.
| try: | |
| self.data["spins"][f_idx] = np.matmul(self.data["spins"][f_idx], trans) | |
| except: | |
| pass | |
| with contextlib.suppress(KeyError): | |
| self.data["spins"][f_idx] = np.matmul(self.data["spins"][f_idx], trans) |
Tools
Ruff
716-719: Use
contextlib.suppress(Exception)instead oftry-except-passReplace with
contextlib.suppress(Exception)(SIM105)
718-718: Do not use bare
except(E722)
| res_incar = re.sub( | ||
| r"MAGMOM[\s\S]*?\n\nM_CONST[\s\S]*?\n\n", m_str, tmp_incar, re.S | ||
| ) |
There was a problem hiding this comment.
Use 'flags' as a keyword argument in 're.sub'
To improve code readability and avoid confusion with positional arguments, pass the flags parameter as a keyword argument in the re.sub function.
Apply this diff to address the concern:
res_incar = re.sub(
r"MAGMOM[\s\S]*?\n\nM_CONST[\s\S]*?\n\n", m_str, tmp_incar, flags=re.S
)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.
| res_incar = re.sub( | |
| r"MAGMOM[\s\S]*?\n\nM_CONST[\s\S]*?\n\n", m_str, tmp_incar, re.S | |
| ) | |
| res_incar = re.sub( | |
| r"MAGMOM[\s\S]*?\n\nM_CONST[\s\S]*?\n\n", m_str, tmp_incar, flags=re.S | |
| ) |
Tools
Ruff
46-48:
re.subshould passcountandflagsas keyword arguments to avoid confusion due to unintuitive argument positions(B034)
| **kwargs : dict | ||
| other parameters | ||
| """ | ||
| assert frame_idx < len(data["coords"]) |
There was a problem hiding this comment.
Replace 'assert' with exception handling for input validation
Using assert statements for input validation is not recommended in production code because assertions can be disabled with optimization flags (-O), potentially skipping critical checks.
Replace the assert statement with explicit exception handling to ensure the validation is always performed.
- assert frame_idx < len(data["coords"])
+ if frame_idx >= len(data["coords"]):
+ raise IndexError(f"frame_idx {frame_idx} is out of range.")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.
| assert frame_idx < len(data["coords"]) | |
| if frame_idx >= len(data["coords"]): | |
| raise IndexError(f"frame_idx {frame_idx} is out of range.") |
Tools
GitHub Check: codecov/patch
[warning] 67-68: dpdata/plugins/vasp_deltaspin.py#L67-L68
Added lines #L67 - L68 were not covered by tests
| with open(file_name[:-6] + "INCAR") as fp: | ||
| tmp_incar = fp.read() | ||
| res_incar = re.sub( |
There was a problem hiding this comment.
Add error handling when reading 'INCAR' file
When opening file_name[:-6] + "INCAR", there is no check to handle situations where the file might not exist or be inaccessible, which could result in an unhandled exception.
Include error handling to gracefully handle potential file access issues.
+ import os
+ incar_path = file_name[:-6] + "INCAR"
+ if not os.path.exists(incar_path):
+ raise FileNotFoundError(f"File not found: {incar_path}")
+
with open(incar_path) as fp:
tmp_incar = fp.read()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.
| with open(file_name[:-6] + "INCAR") as fp: | |
| tmp_incar = fp.read() | |
| res_incar = re.sub( | |
| import os | |
| incar_path = file_name[:-6] + "INCAR" | |
| if not os.path.exists(incar_path): | |
| raise FileNotFoundError(f"File not found: {incar_path}") | |
| with open(incar_path) as fp: | |
| tmp_incar = fp.read() | |
| res_incar = re.sub( |
Tools
GitHub Check: codecov/patch
[warning] 44-46: dpdata/plugins/vasp_deltaspin.py#L44-L46
Added lines #L44 - L46 were not covered by tests
| with open(file_name) as fp: | ||
| lines = [line.rstrip("\n") for line in fp] | ||
| with open(file_name[:-6] + "INCAR") as fp: | ||
| lines_incar = [line.rstrip("\n") for line in fp] | ||
| data = dpdata.vasp_deltaspin.poscar.to_system_data(lines, lines_incar) | ||
| data = uniq_atom_names(data) | ||
| return data |
There was a problem hiding this comment.
Ensure robust error handling when opening files
Currently, the code opens file_name and file_name[:-6] + "INCAR" without handling potential exceptions if the files do not exist or cannot be accessed. This may lead to unhandled exceptions and crash the program.
Consider adding error handling to manage file-related exceptions and provide meaningful error messages.
+ import os
+ if not os.path.exists(file_name):
+ raise FileNotFoundError(f"File not found: {file_name}")
+ if not os.path.exists(file_name[:-6] + "INCAR"):
+ raise FileNotFoundError(f"File not found: {file_name[:-6] + 'INCAR'}")
+
with open(file_name) as fp:
lines = [line.rstrip("\n") for line in fp]
with open(file_name[:-6] + "INCAR") as fp:
lines_incar = [line.rstrip("\n") for line in fp]Committable suggestion was skipped due to low confidence.
Tools
GitHub Check: codecov/patch
[warning] 18-24: dpdata/plugins/vasp_deltaspin.py#L18-L24
Added lines #L18 - L24 were not covered by tests
| def get_spintype(keys): | ||
| key_sp = ["sp", "spx", "spy", "spz"] | ||
| key_csp = ["c_spin[1]", "c_spin[2]", "c_spin[3]", "c_spin[4]"] | ||
| lmp_sp_type = [key_sp, key_csp] | ||
| for k in range(2): | ||
| if all(i in keys for i in lmp_sp_type[k]): | ||
| return lmp_sp_type[k] | ||
|
|
There was a problem hiding this comment.
Add unit tests for the get_spintype function to ensure correctness
The newly added get_spintype function is not covered by unit tests. Implementing tests for this function will help verify that it accurately identifies different spin types based on the provided keys, enhancing the reliability of spin data processing.
Would you like assistance in creating unit tests for this function?
Tools
GitHub Check: codecov/patch
[warning] 136-141: dpdata/lammps/dump.py#L136-L141
Added lines #L136 - L141 were not covered by tests
| def safe_get_spin_force(lines): | ||
| blk, head = _get_block(lines, "ATOMS") | ||
| keys = head.split() | ||
| sp_type = get_spintype(keys) | ||
| assert sp_type is not None, "Dump file does not contain spin!" | ||
| id_idx = keys.index("id") - 2 | ||
| sp = keys.index(sp_type[0]) - 2 | ||
| spx = keys.index(sp_type[1]) - 2 | ||
| spy = keys.index(sp_type[2]) - 2 | ||
| spz = keys.index(sp_type[3]) - 2 | ||
| sp_force = [] | ||
| for ii in blk: | ||
| words = ii.split() | ||
| sp_force.append( | ||
| [ | ||
| float(words[id_idx]), | ||
| float(words[sp]), | ||
| float(words[spx]), | ||
| float(words[spy]), | ||
| float(words[spz]), | ||
| ] | ||
| ) | ||
| sp_force.sort() | ||
| sp_force = np.array(sp_force)[:, 1:] | ||
| return sp_force | ||
|
|
There was a problem hiding this comment.
Add unit tests for safe_get_spin_force to validate spin force extraction
The safe_get_spin_force function is crucial for extracting spin force data from the dump files, but it currently lacks test coverage. Adding unit tests will ensure it handles various spin data formats correctly and robustly detects cases where spin data is missing or malformed.
I can help create unit tests for this function if you'd like.
Tools
GitHub Check: codecov/patch
[warning] 145-157: dpdata/lammps/dump.py#L145-L157
Added lines #L145 - L157 were not covered by tests
[warning] 166-168: dpdata/lammps/dump.py#L166-L168
Added lines #L166 - L168 were not covered by tests
| * safe_get_spin_force(array_lines[ii])[:, 1:4] | ||
| ) | ||
| if contain_spin: | ||
| system["spins"] = np.array(system["spins"]) |
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Add tests to verify spin data array conversion
Converting system["spins"] to a NumPy array is essential for ensuring data consistency, but this line is not covered by tests. Consider adding tests to validate that spin data is correctly aggregated and converted after processing multiple blocks.
Would you like assistance in creating tests for this functionality?
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GitHub Check: codecov/patch
[warning] 279-279: dpdata/lammps/dump.py#L279
Added line #L279 was not covered by tests
| contain_spin = False | ||
| blk, head = _get_block(lines, "ATOMS") | ||
| if "sp" in head: | ||
| contain_spin = True | ||
| spin_force = safe_get_spin_force(lines) | ||
| system["spins"] = [spin_force[:, :1] * spin_force[:, 1:4]] |
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Use get_spintype for consistent spin data detection
Currently, the code checks if "sp" in head to determine the presence of spin data. Since spin data may be indicated by different keys (e.g., "sp", "spx", "c_spin[1]"), using the get_spintype function ensures consistent detection across various formats.
Apply this diff to improve spin data detection:
contain_spin = False
blk, head = _get_block(lines, "ATOMS")
+ keys = head.split()
+ sp_type = get_spintype(keys)
+ if sp_type is not None:
contain_spin = True
spin_force = safe_get_spin_force(lines)
system["spins"] = [spin_force[:, :1] * spin_force[:, 1:4]]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.
| contain_spin = False | |
| blk, head = _get_block(lines, "ATOMS") | |
| if "sp" in head: | |
| contain_spin = True | |
| spin_force = safe_get_spin_force(lines) | |
| system["spins"] = [spin_force[:, :1] * spin_force[:, 1:4]] | |
| contain_spin = False | |
| blk, head = _get_block(lines, "ATOMS") | |
| keys = head.split() | |
| sp_type = get_spintype(keys) | |
| if sp_type is not None: | |
| contain_spin = True | |
| spin_force = safe_get_spin_force(lines) | |
| system["spins"] = [spin_force[:, :1] * spin_force[:, 1:4]] |
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GitHub Check: codecov/patch
[warning] 258-260: dpdata/lammps/dump.py#L258-L260
Added lines #L258 - L260 were not covered by tests
| if contain_spin: | ||
| system["spins"].append( | ||
| safe_get_spin_force(array_lines[ii])[:, :1] | ||
| * safe_get_spin_force(array_lines[ii])[:, 1:4] | ||
| ) |
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Optimize by storing the result of safe_get_spin_force
In the loop, safe_get_spin_force(array_lines[ii]) is called twice, leading to unnecessary computation. Storing the result in a variable enhances performance by avoiding redundant function calls.
Apply this diff to optimize the code:
if contain_spin:
+ spin_force = safe_get_spin_force(array_lines[ii])
system["spins"].append(
- safe_get_spin_force(array_lines[ii])[:, :1]
- * safe_get_spin_force(array_lines[ii])[:, 1:4]
+ spin_force[:, :1] * spin_force[:, 1:4]
)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 contain_spin: | |
| system["spins"].append( | |
| safe_get_spin_force(array_lines[ii])[:, :1] | |
| * safe_get_spin_force(array_lines[ii])[:, 1:4] | |
| ) | |
| if contain_spin: | |
| spin_force = safe_get_spin_force(array_lines[ii]) | |
| system["spins"].append( | |
| spin_force[:, :1] * spin_force[:, 1:4] | |
| ) |
Tools
GitHub Check: codecov/patch
[warning] 274-274: dpdata/lammps/dump.py#L274
Added line #L274 was not covered by tests
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- please follow the PR feat: support spin for ABACUS #718 to add spin support for vasp.
- unit tests are missing.
Reference #728 to add the spin information for lammps. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Introduced functions to extract and normalize spin data from LAMMPS dump files. - Added support for registering spin data types in the system. - Created new simulation input and output files for LAMMPS. - Added new compute and dump commands for calculating and outputting spin properties in LAMMPS. - **Tests** - Implemented unit tests for verifying the handling of spin configurations in LAMMPS files, including scenarios with zero spin values and incomplete data. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: root <pxlxingliang> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Han Wang <[email protected]>
Summary by CodeRabbit
Release Notes
New Features
Enhancements
Bug Fixes