Fix bug when reading file in "pwmat/movement" format (#599)

PWmat adds `nonperiodic_Position` block to MOVEMENT file, used to output the atomic positions without non periodic boundary conditions. Due to the fact that dpdata previously locates the number of atoms based on the keyword `Position`, when MOVEMENT contains `nonperiodic_Position`, it will cause the number of atoms to double, resulting in a bug. --------- Co-authored-by: Uper <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
deepmodeling · Jan 24, 2024 · 1355f7b · 1355f7b
1 parent f22e66d
commit 1355f7b
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Showing 6 changed files with 976 additions and 2 deletions.
diff --git a/dpdata/pwmat/movement.py b/dpdata/pwmat/movement.py
@@ -18,7 +18,7 @@ def system_info(lines, type_idx_zero=False):
         nelm = 100
     atomic_number = []
     for idx, ii in enumerate(lines):
-        if "Position" in ii:
+        if ("Position" in ii) and ("nonperiodic_Position" not in ii):
             for kk in range(idx + 1, idx + 1 + natoms):
                 min = kk
                 for jj in range(kk + 1, idx + 1 + natoms):
@@ -175,7 +175,7 @@ def analyze_block(lines, ntot, nelm):
         #                    cell.append([float(ss)
         #                                 for ss in tmp_l.split()[0:3]])
         #                virial = np.zeros([3,3])
-        elif "Position" in ii:
+        elif ("Position" in ii) and ("nonperiodic_Position" not in ii):
             for kk in range(idx + 1, idx + 1 + ntot):
                 min = kk
                 for jj in range(kk + 1, idx + 1 + ntot):