Add CLI for analyze element result in a bar figure (#235)

aiida_sssp_workflow/cli/inspect.py

@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 """CLI to inspect the results of the workflow"""
 import json
+import random
 from pathlib import Path
 
 import click
@@ -14,6 +15,100 @@
 from aiida_sssp_workflow.utils import HIGH_DUAL_ELEMENTS, get_protocol
 
 
+def lighten_color(color, amount=0.5):
+    """
+    Lightens the given color by multiplying (1-luminosity) by the given amount.
+    Input can be matplotlib color string, hex string, or RGB tuple.
+    REF from https://stackoverflow.com/questions/37765197/darken-or-lighten-a-color-in-matplotlib
+
+    Examples:
+    >> lighten_color('g', 0.3)
+    >> lighten_color('#F034A3', 0.6)
+    >> lighten_color((.3,.55,.1), 0.5)
+    """
+    import colorsys
+
+    import matplotlib.colors as mc
+
+    try:
+        c = mc.cnames[color]
+    except Exception:
+        c = color
+    c = colorsys.rgb_to_hls(*mc.to_rgb(c))
+    return colorsys.hls_to_rgb(c[0], 1 - amount * (1 - c[1]), c[2])
+
+
+def cmap(pseudo_info: dict) -> str:
+    """Return RGB string of color for given pseudo info
+    Hardcoded at the momment.
+    """
+    if pseudo_info["family"] == "sg15" and pseudo_info["version"] == "v0":
+        return "#000000"
+
+    if pseudo_info["family"] == "gbrv":
+        return "#4682B4"
+
+    if (
+        pseudo_info["family"] == "psl"
+        and pseudo_info["type"] == "us"
+        and pseudo_info["version"] == "v1.0.0-high"
+    ):
+        return "#F50E02"
+
+    if (
+        pseudo_info["family"] == "psl"
+        and pseudo_info["type"] == "us"
+        and pseudo_info["version"] == "v1.0.0-low"
+    ):
+        return lighten_color("#F50E02")
+
+    if (
+        pseudo_info["family"] == "psl"
+        and pseudo_info["type"] == "paw"
+        and pseudo_info["version"] == "v1.0.0-high"
+    ):
+        return "#008B00"
+
+    if (
+        pseudo_info["family"] == "psl"
+        and pseudo_info["type"] == "paw"
+        and pseudo_info["version"] == "v1.0.0-low"
+    ):
+        return lighten_color("#008B00")
+
+    if (
+        pseudo_info["family"] == "psl"
+        and pseudo_info["type"] == "paw"
+        and "v0." in pseudo_info["version"]
+    ):
+        return "#FF00FF"
+
+    if (
+        pseudo_info["family"] == "psl"
+        and pseudo_info["type"] == "us"
+        and "v0." in pseudo_info["version"]
+    ):
+        return lighten_color("#FF00FF")
+
+    if pseudo_info["family"] == "dojo" and pseudo_info["version"] == "v4-str":
+        return "#F9A501"
+
+    if pseudo_info["family"] == "dojo" and pseudo_info["version"] == "v4-std":
+        return lighten_color("#F9A501")
+
+    if pseudo_info["family"] == "jth" and pseudo_info["version"] == "v1.1-str":
+        return "#00C5ED"
+
+    if pseudo_info["family"] == "jth" and pseudo_info["version"] == "v1.1-std":
+        return lighten_color("#00C5ED")
+
+    # TODO: more mapping
+    # if a unknow type generate random color based on ascii sum
+    ascn = sum([ord(c) for c in pseudo_info["representive_label"]])
+    random.seed(ascn)
+    return f"#{random.randint(0, 16777215):06x}"
+
+
 def birch_murnaghan(V, E0, V0, B0, B01):
     """
     Return the energy for given volume (V - it can be a vector) according to
@@ -130,6 +225,80 @@ def convergence_plot(
     ax.set_title(title, fontsize=8)
 
 
+@cmd_root.command("analyze")
+@click.argument("group")  # The group to inspect, name or pk of the group
+@click.option("--output", "-o", default="output", help="The output file name")
+def analyze(group, output):
+    """Render the plot for the given pseudos and measure type."""
+    from aiida_sssp_workflow.utils import ACWF_CONFIGURATIONS, parse_label
+
+    # landscape mode
+    fig, ax = plt.subplots(1, 1, figsize=(11.69, 8.27), dpi=100)
+
+    group_node = orm.load_group(group)
+
+    # Get all nodes in the output group (EOS workflows)
+    group_node_query = (
+        orm.QueryBuilder()
+        .append(orm.Group, filters={"id": group_node.id}, tag="groups")
+        .append(orm.Node, project="*", with_group="groups")
+    )
+
+    nodes_lst = group_node_query.all(flat=True)
+    width = 0.6 / len(nodes_lst)
+
+    for i, node in enumerate(nodes_lst):
+        pseudo_info = parse_label(node.base.extras.all["label"].split(" ")[-1])
+
+        # TODO assert element should not change
+        element = node.outputs.pseudo_info.get_dict()["element"]
+
+        y_nu = []
+        for configuration in ACWF_CONFIGURATIONS:
+            res = node.outputs.measure.precision[configuration]["output_parameters"]
+
+            nu = res["rel_errors_vec_length"]
+            y_nu.append(nu)
+
+        x = np.arange(len(ACWF_CONFIGURATIONS))
+
+        ax.bar(
+            x + 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
+
+    ax.axhline(y=0.1, linestyle="--", color="green")
+    ax.text(0 - d, 0.1 + d, "0.1 excellent agreement", color="black")
+    ax.axhline(y=0.33, linestyle="--", color="red")
+    ax.text(0 - d, 0.33 + d, "0.33 good agreement", color="black")
+    ax.legend(loc="upper right", prop={"size": 10})
+    ax.set_ylabel("ν -factor")
+    ax.set_ylim([0, 0.5])
+
+    xticks_shift = len(nodes_lst) * width / 2
+    xticks = [i + xticks_shift for i in range(len(ACWF_CONFIGURATIONS))]
+    ax.set_xticks(xticks)
+    ax.set_xticklabels(ACWF_CONFIGURATIONS)
+
+    # fig to pdf
+    fig.tight_layout()
+    # fig.suptitle(
+    #    f"Comparison on {element}",
+    #    fontsize=10,
+    # )
+    fig.subplots_adjust(top=0.92)
+    fpath = Path.cwd() / f"{output}_{element}_fight.pdf"
+    fig.savefig(fpath.name, bbox_inches="tight")
+
+
 @cmd_root.command("inspect")
 @click.argument("node")  # The node to inspect, uuid or pk
 @click.option("--output", "-o", default="output", help="The output file name")

aiida_sssp_workflow/utils.py

@@ -96,6 +96,7 @@ def get_protocol(category, name=None):
 
 OXIDE_CONFIGURATIONS = ["XO", "XO2", "XO3", "X2O", "X2O3", "X2O5"]
 UNARIE_CONFIGURATIONS = ["BCC", "FCC", "SC", "Diamond"]
+ACWF_CONFIGURATIONS = OXIDE_CONFIGURATIONS + UNARIE_CONFIGURATIONS
 
 
 def update_dict(d, u):
@@ -230,6 +231,31 @@ def get_standard_structure(
     return structure
 
 
+def parse_label(label):
+    """parse standard pseudo label to dict of pseudo info"""
+    element, type, z, tool, family, *version = label.split(".")
+    version = ".".join(version)
+
+    if type == "nc":
+        full_type = "NC"
+    if type == "us":
+        full_type = "Ultrasoft"
+    if type == "paw":
+        full_type = "PAW"
+
+    return {
+        "element": element,
+        "type": type,
+        "z": z,
+        "tool": tool,
+        "family": family,
+        "version": version,
+        "representive_label": f"{z}|{full_type}|{family}|{tool}|{version}",
+        "concise_label": f"{z}|{type}|{family}|{version}",
+        "full_label": f"{element}|{z}|{full_type}|{family}|{tool}|{version}",
+    }
+
+
 def parse_upf(upf_content: str) -> dict:
     """
 

setup-yaml/computer-setup-eiger-mem.yaml → setup-yaml/computer-setup-eiger-mr32-mem.yaml

@@ -4,7 +4,7 @@ hostname: "eiger.cscs.ch"
 description: Eiger is the production partition on Alps, the HPE Cray EX Supercomputer large mem nodes.
 transport: "core.ssh"
 scheduler: "core.slurm"
-work_dir: "/scratch/e1000/{username}/aiida/"
+work_dir: "/capstor/scratch/cscs/{username}/aiida/"
 shebang: "#!/bin/bash"
 mpirun_command: "srun -n {tot_num_mpiprocs}"
 mpiprocs_per_machine: 128

setup-yaml/computer-setup-eiger-mr33-mem.yaml

@@ -0,0 +1,22 @@
+---
+label: "eiger-mc-mr33-mem"
+hostname: "eiger.cscs.ch"
+description: Eiger is the production partition on Alps, the HPE Cray EX Supercomputer large mem nodes.
+transport: "core.ssh"
+scheduler: "core.slurm"
+work_dir: "/capstor/scratch/cscs/{username}/aiida/"
+shebang: "#!/bin/bash"
+mpirun_command: "srun -n {tot_num_mpiprocs}"
+mpiprocs_per_machine: 128
+prepend_text: |
+    ### computer prepend_text start ###
+    #SBATCH --partition=normal
+    #SBATCH --account=mr33
+    #SBATCH --constraint=mc
+    #SBATCH --hint=nomultithread
+    #SBATCH --mem=497G
+
+    export OMP_PROC_BIND=close
+    export OMP_PLACES=cores
+    ### computer prepend_text end ###
+append_text: " "

setup-yaml/ph7.0-eiger-mem.yaml → setup-yaml/ph7.0-eiger-mr32-mem.yaml

@@ -3,9 +3,9 @@ label: "ph-7.0"
 description: Quantum ESPRESSO ph.x v7.0 Compiled with CpeIntel v21.12
 default_calc_job_plugin: "quantumespresso.ph"
 computer: "eiger-mc-mr32-mem"
-filepath_executable: "/apps/eiger/UES/jenkins/1.4.0/software/QuantumESPRESSO/7.0-cpeIntel-21.12/bin/ph.x"
+filepath_executable: "/capstor/apps/cscs/eiger/easybuild/software/QuantumESPRESSO/7.0-cpeIntel-22.05/bin/ph.x"
 prepend_text: |
-  module load cpeIntel/21.12
+  module load cray/22.05  cpeIntel/22.05
   module load QuantumESPRESSO/7.0
 
   export OMP_NUM_THREADS=1

setup-yaml/ph7.0-eiger-mr33-mem.yaml

@@ -0,0 +1,12 @@
+---
+label: "ph-7.0"
+description: Quantum ESPRESSO ph.x v7.0 Compiled with CpeIntel v21.12
+default_calc_job_plugin: "quantumespresso.ph"
+computer: "eiger-mc-mr33-mem"
+filepath_executable: "/capstor/apps/cscs/eiger/easybuild/software/QuantumESPRESSO/7.0-cpeIntel-22.05/bin/ph.x"
+prepend_text: |
+  module load cray/22.05  cpeIntel/22.05
+  module load QuantumESPRESSO/7.0
+
+  export OMP_NUM_THREADS=1
+append_text: " "

setup-yaml/pw7.0-eiger-mem.yaml → setup-yaml/pw7.0-eiger-mr32-mem.yaml

@@ -3,9 +3,9 @@ label: "pw-7.0"
 description: Quantum ESPRESSO pw.x v7.0 Compiled with CpeIntel v21.12
 default_calc_job_plugin: "quantumespresso.pw"
 computer: "eiger-mc-mr32-mem"
-filepath_executable: "/apps/eiger/UES/jenkins/1.4.0/software/QuantumESPRESSO/7.0-cpeIntel-21.12/bin/pw.x"
+filepath_executable: "/capstor/apps/cscs/eiger/easybuild/software/QuantumESPRESSO/7.0-cpeIntel-22.05/bin/pw.x"
 prepend_text: |
-  module load cpeIntel/21.12
+  module load cray/22.05  cpeIntel/22.05
   module load QuantumESPRESSO/7.0
 
   export OMP_NUM_THREADS=1

setup-yaml/pw7.0-eiger-mr33-mem.yaml

@@ -0,0 +1,12 @@
+---
+label: "pw-7.0"
+description: Quantum ESPRESSO pw.x v7.0 Compiled with CpeIntel v21.12
+default_calc_job_plugin: "quantumespresso.pw"
+computer: "eiger-mc-mr33-mem"
+filepath_executable: "/capstor/apps/cscs/eiger/easybuild/software/QuantumESPRESSO/7.0-cpeIntel-22.05/bin/pw.x"
+prepend_text: |
+  module load cray/22.05  cpeIntel/22.05
+  module load QuantumESPRESSO/7.0
+
+  export OMP_NUM_THREADS=1
+append_text: " "