Using Diamond structure for Lanthanides and remove magnitization in c…

…alculation
aiidateam · Mar 27, 2024 · cd125ab · cd125ab
1 parent 6bf69c1
commit cd125ab
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Showing 12 changed files with 43 additions and 79 deletions.
diff --git a/aiida_sssp_workflow/cli/inspect.py b/aiida_sssp_workflow/cli/inspect.py
@@ -260,21 +260,31 @@ def analyze(group, output, ylimit):
         for configuration in ACWF_CONFIGURATIONS:
             res = node.outputs.measure.precision[configuration]["output_parameters"]
 
-            nu = res["rel_errors_vec_length"]
-            y_nu.append(nu)
+            try:
+                nu = res["rel_errors_vec_length"]
+            except KeyError:
+                y_nu.append(None)
+            else:
+                y_nu.append(nu)
+
+        xs = np.arange(len(ACWF_CONFIGURATIONS))
+
+        # Find index where y_nu is None
+        none_index = [i for i, x in enumerate(y_nu) if x is None]
 
-        x = np.arange(len(ACWF_CONFIGURATIONS))
+        # Remove None from y_nu and xs
+        y_nu = np.array([x for x in y_nu if x is not None])
+        xs = np.array([x for i, x in enumerate(xs) if i not in none_index])
 
         ax.bar(
-            x + width * i,
+            xs + width * i,
             y_nu,
             width,
             color=cmap(pseudo_info),
             edgecolor="black",
             linewidth=1,
             label=pseudo_info["representive_label"],
         )
-        ax.set_title(f"X={element}")
 
     d = 0.01  # offset for the text
 
@@ -285,6 +295,7 @@ def analyze(group, output, ylimit):
     ax.legend(loc="upper right", prop={"size": 10})
     ax.set_ylabel("ν -factor")
     ax.set_ylim([0, ylimit])
+    ax.set_title(f"X={element}")
 
     xticks_shift = len(nodes_lst) * width / 2
     xticks = [i + xticks_shift for i in range(len(ACWF_CONFIGURATIONS))]

diff --git a/aiida_sssp_workflow/statics/generatemapping.ipynb b/aiida_sssp_workflow/statics/generatemapping.ipynb
@@ -209,7 +209,7 @@
     "    if e in MAGNETIC_ELEMENTS:\n",
     "        d[e] = {\n",
     "            \"bands\": f\"GS\",\n",
-    "            \"convergence\": f\"GS\",\n",
+    "            \"convergence\": f\"Diamond\",\n",
     "        }\n",
     "        continue\n",
     "\n",
@@ -228,13 +228,6 @@
     "with open(\"./structures/mapping.json\", \"w\") as f:\n",
     "    json.dump(d, f, indent=4)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

diff --git a/aiida_sssp_workflow/statics/structures/mapping.json b/aiida_sssp_workflow/statics/structures/mapping.json
@@ -66,11 +66,11 @@
     },
     "Co": {
         "bands": "GS",
-        "convergence": "GS"
+        "convergence": "Diamond"
     },
     "Cr": {
         "bands": "GS",
-        "convergence": "GS"
+        "convergence": "Diamond"
     },
     "Cs": {
         "bands": "GS",
@@ -94,7 +94,7 @@
     },
     "Fe": {
         "bands": "GS",
-        "convergence": "GS"
+        "convergence": "Diamond"
     },
     "F": {
         "bands": "GS",
@@ -170,7 +170,7 @@
     },
     "Mn": {
         "bands": "GS",
-        "convergence": "GS"
+        "convergence": "Diamond"
     },
     "Mo": {
         "bands": "GS",
@@ -198,11 +198,11 @@
     },
     "Ni": {
         "bands": "GS",
-        "convergence": "GS"
+        "convergence": "Diamond"
     },
     "O": {
         "bands": "GS",
-        "convergence": "GS"
+        "convergence": "Diamond"
     },
     "Os": {
         "bands": "GS",

diff --git a/aiida_sssp_workflow/workflows/common.py b/aiida_sssp_workflow/workflows/common.py
@@ -29,15 +29,16 @@ def get_extra_parameters_for_lanthanides(element, nbnd) -> dict:
     """
     extra_parameters = {
         "SYSTEM": {
-            "nspin": 2,
-            "starting_magnetization": {
-                element: 0.5,
-            },
+            # update on 2024-03-27: remove the magnetization for RE
+            # "nspin": 2,
+            # "starting_magnetization": {
+            #    element: 0.5,
+            # },
             "nbnd": int(nbnd),
         },
         "ELECTRONS": {
+            # It usually takes more steps to converge the SCF for lanthanides and actinides
             "diagonalization": "cg",
-            "mixing_beta": 0.5,
             "electron_maxstep": 200,
         },
     }

diff --git a/aiida_sssp_workflow/workflows/convergence/_base.py b/aiida_sssp_workflow/workflows/convergence/_base.py
@@ -297,10 +297,8 @@ def extra_setup_for_lanthanide_element(self):
         Otherwise it is hard to get converged in scf calculation.
         """
         nbnd_factor = self._NBANDS_FACTOR_FOR_REN
-        pseudo_N = get_pseudo_N()
-        self.ctx.pseudos["N"] = pseudo_N
         pseudo_RE = self.inputs.pseudo
-        nbnd = nbnd_factor * (pseudo_N.z_valence + pseudo_RE.z_valence)
+        nbnd = nbnd_factor * pseudo_RE.z_valence
         self.ctx.extra_pw_parameters = get_extra_parameters_for_lanthanides(
             self.ctx.element, nbnd
         )

diff --git a/setup-yaml/computer-setup-daint-mem.yaml b/setup-yaml/computer-setup-daint-mem.yaml
@@ -1,5 +1,5 @@
 ---
-label: "daint-mc-mrcloud-mem"
+label: "daint-psi15-mem"
 hostname: "daint.cscs.ch"
 description: Piz Daint supercomputer at CSCS Lugano, Switzerland, multicore partition.
 transport: "core.ssh"
@@ -13,7 +13,7 @@ prepend_text: |
     #SBATCH --partition=normal
     #SBATCH --constraint=mc
     #SBATCH --cpus-per-task=1
-    #SBATCH --account="mrcloud"
+    #SBATCH --account="psi15"
     #SBATCH --mem=120GB
     export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
     source $MODULESHOME/init/bash

diff --git a/setup-yaml/computer-setup-daint.yaml b/setup-yaml/computer-setup-daint.yaml
diff --git a/setup-yaml/ph7.0-daint-mem.yaml b/setup-yaml/ph7.0-daint-mem.yaml
@@ -2,7 +2,7 @@
 label: "ph-7.0"
 description: "PH compiled for daint-mc"
 default_calc_job_plugin: "quantumespresso.ph"
-computer: "daint-mc-mrcloud-mem"
+computer: "daint-psi15-mem"
 filepath_executable: "/apps/dom/UES/jenkins/7.0.UP03/21.09/dom-mc/software/QuantumESPRESSO/7.0-CrayIntel-21.09/bin/ph.x"
 prepend_text: |
   module load daint-mc

diff --git a/setup-yaml/ph7.0-daint.yaml b/setup-yaml/ph7.0-daint.yaml
diff --git a/setup-yaml/pw7.0-daint-mem.yaml b/setup-yaml/pw7.0-daint-mem.yaml
@@ -2,7 +2,7 @@
 label: "pw-7.0"
 description: "PW compiled for daint-mc"
 default_calc_job_plugin: "quantumespresso.pw"
-computer: "daint-mc-mrcloud-mem"
+computer: "daint-psi15-mem"
 filepath_executable: "/apps/dom/UES/jenkins/7.0.UP03/21.09/dom-mc/software/QuantumESPRESSO/7.0-CrayIntel-21.09/bin/pw.x"
 prepend_text: |
   module load daint-mc

diff --git a/setup-yaml/pw7.0-daint.yaml b/setup-yaml/pw7.0-daint.yaml
diff --git a/tests/test_utils/test_get_standard_structure_Fe_convergence_None_.yml b/tests/test_utils/test_get_standard_structure_Fe_convergence_None_.yml
@@ -5,10 +5,12 @@
   #\n#  For information on this file format, follow the CIF links at\n#  http://www.iucr.org\n\
   ##########################################################################\n\ndata_0\n\
   \nloop_\n  _atom_site_label\n  _atom_site_fract_x\n  _atom_site_fract_y\n  _atom_site_fract_z\n\
-  \  _atom_site_type_symbol\n         Fe1       0.0       0.0       0.0       Fe \
-  \       \n         Fe2       0.5       0.5       0.5       Fe \n_cell_angle_alpha\
-  \                       90.0\n_cell_angle_beta                        90.0\n_cell_angle_gamma\
-  \                       90.0\n_cell_length_a                          2.83351\n\
-  _cell_length_b                          2.83351\n_cell_length_c                \
-  \          2.83351\nloop_\n  _symmetry_equiv_pos_as_xyz\n         'x, y, z' \n_symmetry_int_tables_number\
-  \             1\n_symmetry_space_group_name_H-M          'P 1'"
+  \  _atom_site_type_symbol\n         Fe1       0.5       0.5       0.5       Fe \
+  \       \n         Fe2       0.75      0.75      0.75      Fe \n_cell_angle_alpha\
+  \                       60.00000000000001\n_cell_angle_beta                    \
+  \    60.00000000000001\n_cell_angle_gamma                       60.00000000000001\n\
+  _cell_length_a                          3.4460197248582936\n_cell_length_b     \
+  \                     3.4460197248582936\n_cell_length_c                       \
+  \   3.4460197248582936\nloop_\n  _symmetry_equiv_pos_as_xyz\n         'x, y, z'\
+  \ \n_symmetry_int_tables_number             1\n_symmetry_space_group_name_H-M  \
+  \        'P 1'"