Changing the formatting in the dump comppand so that it can handle dy…

…namic vectors. (#124) Fixing the fact that the property/atoms compute should be a vector of undefined length and not an array. Fixes #114
aiidaplugins · Apr 26, 2024 · bd3d402 · bd3d402
1 parent b2f119b
commit bd3d402
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Showing 14 changed files with 862 additions and 627 deletions.
diff --git a/conftest.py b/conftest.py
@@ -118,6 +118,15 @@ def parameters_minimize() -> AttributeDict:
         "ke/atom": [{"type": [{"keyword": " ", "value": " "}], "group": "all"}],
         "stress/atom": [{"type": ["NULL"], "group": "all"}],
         "pressure": [{"type": ["thermo_temp"], "group": "all"}],
+        "property/atom": [
+            {
+                "type": [
+                    {"keyword": " ", "value": "fx"},
+                    {"keyword": " ", "value": "fy"},
+                ],
+                "group": "all",
+            }
+        ],
     }
 
     parameters.minimize = {
@@ -170,6 +179,15 @@ def parameters_minimize_groups() -> AttributeDict:
         "stress/atom": [{"type": ["NULL"], "group": "all"}],
         "pressure": [{"type": ["thermo_temp"], "group": "all"}],
         "ke": [{"type": [{"keyword": " ", "value": " "}], "group": "test"}],
+        "property/atom": [
+            {
+                "type": [
+                    {"keyword": " ", "value": "fx"},
+                    {"keyword": " ", "value": "fy"},
+                ],
+                "group": "all",
+            }
+        ],
     }
 
     parameters.minimize = {
@@ -217,6 +235,15 @@ def parameters_md_nve() -> AttributeDict:
         "ke/atom": [{"type": [{"keyword": " ", "value": " "}], "group": "all"}],
         "stress/atom": [{"type": ["NULL"], "group": "all"}],
         "pressure": [{"type": ["thermo_temp"], "group": "all"}],
+        "property/atom": [
+            {
+                "type": [
+                    {"keyword": " ", "value": "fx"},
+                    {"keyword": " ", "value": "fy"},
+                ],
+                "group": "all",
+            }
+        ],
     }
     parameters.md = {
         "integration": {
@@ -261,6 +288,15 @@ def parameters_md_nvt() -> AttributeDict:
         "ke/atom": [{"type": [{"keyword": " ", "value": " "}], "group": "all"}],
         "stress/atom": [{"type": ["NULL"], "group": "all"}],
         "pressure": [{"type": ["thermo_temp"], "group": "all"}],
+        "property/atom": [
+            {
+                "type": [
+                    {"keyword": " ", "value": "fx"},
+                    {"keyword": " ", "value": "fy"},
+                ],
+                "group": "all",
+            }
+        ],
     }
     parameters.md = {
         "integration": {
@@ -308,6 +344,15 @@ def parameters_md_npt() -> AttributeDict:
         "ke/atom": [{"type": [{"keyword": " ", "value": " "}], "group": "all"}],
         "stress/atom": [{"type": ["NULL"], "group": "all"}],
         "pressure": [{"type": ["thermo_temp"], "group": "all"}],
+        "property/atom": [
+            {
+                "type": [
+                    {"keyword": " ", "value": "fx"},
+                    {"keyword": " ", "value": "fy"},
+                ],
+                "group": "all",
+            }
+        ],
     }
     parameters.md = {
         "integration": {

diff --git a/src/aiida_lammps/parsers/inputfile.py b/src/aiida_lammps/parsers/inputfile.py
@@ -768,8 +768,8 @@ def write_dump_block(
     dump_block += f'{" ".join(computes_list)}\n'
     dump_block += "dump_modify aiida sort id\n"
     dump_block += f'dump_modify aiida element {" ".join(kind_symbols)}\n'
-    dump_block += "dump_modify aiida format line "
-    dump_block += f'"%6d %4d %4s {" ".join(["%16.10f"]*num_double)}"\n'
+    dump_block += "dump_modify aiida format int ' %d ' \n"
+    dump_block += "dump_modify aiida format float ' %16.10e ' \n"
     dump_block += generate_header("End of the Dump information")
 
     return dump_block

diff --git a/src/aiida_lammps/parsers/variables_types.json b/src/aiida_lammps/parsers/variables_types.json
@@ -79,9 +79,9 @@
         "pressure": {"type": "mixed", "size": 6, "locality": "global", "printable": true},
         "pressure/cylinder": {"type": "array", "size": 0, "locality": "global", "printable": true},
         "pressure/uef": {"type": "scalar", "size": 0, "locality": "global", "printable": true},
-        "property/atom": {"type": "array", "size": 0, "locality": "local", "printable": true},
-        "property/chunk": {"type": "array", "size": 0, "locality": "global", "printable": false},
-        "property/local": {"type": "array", "size": 0, "locality": "global", "printable": true},
+        "property/atom": {"type": "vector", "size": 0, "locality": "local", "printable": true},
+        "property/chunk": {"type": "vector", "size": 0, "locality": "global", "printable": false},
+        "property/local": {"type": "vector", "size": 0, "locality": "global", "printable": true},
         "ptm/atom": {"type": "scalar", "size": 0, "locality": "local", "printable": true},
         "rdf": {"type": "array", "size": 0, "locality": "global", "printable": false},
         "reduce": {"type": "mixed", "size": 0, "locality": "global", "printable": true},