espresso and thermoelectric features

Dockerfile

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+FROM condaforge/mambaforge:latest
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    git \
+    wget \
+    && rm -rf /var/lib/apt/lists/*
+
+# Create conda environment with all dependencies
+RUN mamba create --yes -n qe-env -c conda-forge \
+    python=3.11 \
+    qe \
+    phonopy \
+    ase \
+    numpy \
+    scipy \
+    matplotlib \
+    spglib \
+    h5py \
+    pyyaml \
+    pip
+
+# Activate environment
+SHELL ["conda", "run", "-n", "qe-env", "/bin/bash", "-c"]
+
+# Install BoltzTraP2 - essential for transport property calculations
+# Try conda-forge first (pre-built binaries), fallback to pip if needed
+RUN mamba install -n qe-env -c conda-forge boltztrap2 || \
+    echo "BoltzTraP2 conda package not available, continuing without it for demo purposes"
+
+
+RUN mamba install -n qe-env -c conda-forge pymatgen
+
+# Set up working directory
+WORKDIR /app
+
+# Copy the atomate2 source code
+COPY . .
+
+# Install atomate2 with phonon dependencies
+RUN conda run -n qe-env pip install -e .[phonons]
+
+# Create pseudopotential directory and download basic pseudopotentials
+RUN mkdir -p /app/pseudopotentials
+WORKDIR /app/pseudopotentials
+
+# Download basic pseudopotentials for Silicon and Germanium
+# RUN wget -q http://pseudopotentials.quantum-espresso.org/upf_files/Si.pbe-n-rrkjus_psl.1.0.0.UPF || echo "Failed to download Si pseudopotential"
+# RUN wget -q http://pseudopotentials.quantum-espresso.org/upf_files/Ge.pbe-dn-rrkjus_psl.1.0.0.UPF || echo "Failed to download Ge pseudopotential"
+
+RUN cd /app/pseudopotentials && wget https://archive.materialscloud.org/api/records/rcyfm-68h65/files/SSSP_1.3.0_PBE_efficiency.tar.gz/content -O SSSP_1.3.0_PBE_efficiency.tar.gz
+RUN cd /app/pseudopotentials && tar -xzf SSSP_1.3.0_PBE_efficiency.tar.gz
+RUN cd /app/pseudopotentials && wget https://archive.materialscloud.org/api/records/rcyfm-68h65/files/SSSP_1.3.0_PBE_efficiency.json/content -O SSSP_1.3.0_PBE_efficiency.json
+
+# Set environment variables
+ENV ESPRESSO_PSEUDO=/app/pseudopotentials
+ENV PATH="/opt/conda/envs/qe-env/bin:$PATH"
+
+# Go back to app directory
+WORKDIR /app
+
+# Create entry point script
+RUN echo '#!/bin/bash\n\
+source /opt/conda/bin/activate qe-env\n\
+echo "Testing Quantum ESPRESSO installation..."\n\
+pw.x --version 2>/dev/null || echo "QE pw.x not found"\n\
+ph.x --version 2>/dev/null || echo "QE ph.x not found"\n\
+echo ""\n\
+echo "Testing Python dependencies..."\n\
+python3 -c "import atomate2; print(f\"atomate2: OK\")" || echo "atomate2 import failed"\n\
+python3 -c "import phonopy; print(f\"phonopy {phonopy.__version__}: OK\")" || echo "phonopy import failed"\n\
+python3 -c "import ase; print(f\"ASE {ase.__version__}: OK\")" || echo "ASE import failed"\n\
+echo ""\n\
+echo "Running modified ZT example..."\n\
+cd /app && python3 examples/qe_zt_example_runnable.py\n\
+' > /app/run_example.sh && chmod +x /app/run_example.sh
+
+# Default command
+CMD ["/app/run_example.sh"]

Makefile

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+# Makefile for Atomate2 Thermoelectric Calculations with Docker
+
+.PHONY: help build rebuild build-if-needed run-zt run-zt-production run-zt-highthroughput zt-help run-shell test clean
+
+help:
+	@echo "Atomate2 Thermoelectric Docker Commands"
+	@echo "======================================="
+	@echo ""
+	@echo "ZT Calculation Commands:"
+	@echo "  run-zt                - Run ZT calculation (DEMO mode: fast parameters)"
+	@echo "  run-zt-production     - Run ZT calculation (PRODUCTION mode: accurate)"
+	@echo "  run-zt-highthroughput - Run high-throughput ZT screening (multiple materials)"
+	@echo "  zt-help               - Show detailed ZT calculation example help"
+	@echo ""
+	@echo "Docker Build Commands:"
+	@echo "  build                 - Build Docker image (always builds)"
+	@echo "  rebuild               - Force rebuild Docker image (ignore cache)"
+	@echo "  build-if-needed       - Build only if image doesn't exist"
+	@echo ""
+	@echo "Development Commands:"
+	@echo "  run-shell             - Open interactive shell in container"
+	@echo "  test                  - Test all dependencies are working"
+	@echo "  test-workflow         - Test ZT workflow creation"
+	@echo "  dev                   - Start development environment"
+	@echo "  clean                 - Remove Docker images"
+	@echo ""
+	@echo "ZT Calculation Modes:"
+	@echo "  DEMO mode          : Fast testing (4×4×4 k-pts, 30 Ry, Si structure)"
+	@echo "  PRODUCTION mode    : Converged (8×8×8 k-pts, 60 Ry, multiple materials)"
+	@echo "  HIGH-THROUGHPUT    : Screen multiple materials with filtering"
+	@echo ""
+	@echo "Requirements:"
+	@echo "  - Docker with buildx support"
+	@echo "  - AMD64 platform (for BoltzTraP2 compatibility)"
+	@echo ""
+	@echo "Quick Start:"
+	@echo "  make run-zt           # Run a quick ZT demo (builds if needed)"
+	@echo "  make zt-help          # See all ZT calculation options"
+
+# Build the Docker image for AMD64 architecture
+build:
+	@echo "Building Docker image for AMD64 architecture..."
+	@if ! docker buildx ls | grep -q multiarch; then \
+		docker buildx create --name multiarch --use; \
+	else \
+		docker buildx use multiarch; \
+	fi
+	@docker buildx build --platform linux/amd64 -t atomate2-qe-amd64 . --load
+	@echo "✅ Build complete! Image: atomate2-qe-amd64"
+
+# Force rebuild the Docker image (ignores cache)
+rebuild:
+	@echo "Force rebuilding Docker image (ignoring cache)..."
+	@if ! docker buildx ls | grep -q multiarch; then \
+		docker buildx create --name multiarch --use; \
+	else \
+		docker buildx use multiarch; \
+	fi
+	@docker buildx build --platform linux/amd64 -t atomate2-qe-amd64 . --load --no-cache
+	@echo "✅ Rebuild complete! Image: atomate2-qe-amd64"
+
+# Check if image exists and build only if needed
+build-if-needed:
+	@if ! docker images | grep -q atomate2-qe-amd64; then \
+		echo "Image not found, building..."; \
+		$(MAKE) build; \
+	else \
+		echo "✅ Image atomate2-qe-amd64 already exists"; \
+	fi
+
+# Run ZT calculation in demo mode (fast parameters)
+run-zt: build-if-needed
+	@echo "Running ZT Calculation (DEMO mode - fast parameters)..."
+	@echo "======================================================="
+	@docker run --rm --platform linux/amd64 \
+		-v "$(PWD)/examples/zt_calculation.py:/app/examples/zt_calculation.py" \
+		--entrypoint /bin/bash atomate2-qe-amd64 \
+		-c "source /opt/conda/bin/activate qe-env && cd /app && python3 examples/zt_calculation.py --demo"
+
+# Run ZT calculation in production mode (accurate parameters)
+run-zt-production: build-if-needed
+	@echo "Running ZT Calculation (PRODUCTION mode - accurate parameters)..."
+	@echo "=================================================================="
+	@docker run --rm --platform linux/amd64 \
+		-v "$(PWD)/examples/zt_calculation.py:/app/examples/zt_calculation.py" \
+		--entrypoint /bin/bash atomate2-qe-amd64 \
+		-c "source /opt/conda/bin/activate qe-env && cd /app && timeout 1200 python3 examples/zt_calculation.py --production"
+
+# Run high-throughput ZT screening (multiple materials)
+run-zt-highthroughput: build-if-needed
+	@echo "Running High-Throughput ZT Screening (multiple materials)..."
+	@echo "============================================================"
+	@docker run --rm --platform linux/amd64 \
+		-v "$(PWD)/examples/zt_calculation.py:/app/examples/zt_calculation.py" \
+		--entrypoint /bin/bash atomate2-qe-amd64 \
+		-c "source /opt/conda/bin/activate qe-env && cd /app && timeout 1800 python3 examples/zt_calculation.py --high-throughput"
+
+# Open interactive shell in the container
+run-shell: build-if-needed
+	@echo "Opening interactive shell in atomate2 container..."
+	@docker run --rm -it --platform linux/amd64 \
+		-v "$(PWD):/app" \
+		--entrypoint /bin/bash atomate2-qe-amd64 \
+		-c "source /opt/conda/bin/activate qe-env && cd /app && exec bash"
+
+# Test that all dependencies are working
+test: build-if-needed
+	@echo "Testing Dependencies..."
+	@echo "======================"
+	@docker run --rm --platform linux/amd64 --entrypoint /bin/bash atomate2-qe-amd64 -c "\
+		source /opt/conda/bin/activate qe-env && \
+		echo '1. Testing Quantum ESPRESSO...' && \
+		(pw.x --version 2>/dev/null | head -1 || echo '❌ QE pw.x failed') && \
+		echo '2. Testing Python packages...' && \
+		python3 -c 'import atomate2; print(\"✅ atomate2:\", \"OK\")' && \
+		python3 -c 'import phonopy; print(\"✅ phonopy:\", phonopy.__version__)' && \
+		python3 -c 'import ase; print(\"✅ ASE:\", ase.__version__)' && \
+		python3 -c 'import BoltzTraP2; print(\"✅ BoltzTraP2: Available\")' && \
+		echo '3. Testing workflow creation...' && \
+		python3 -c 'from atomate2.espresso.flows.thermoelectric import ZTMaker; print(\"✅ ZT workflow: OK\")' && \
+		echo '' && \
+		echo '🎉 All dependencies working!'"
+
+# Clean up Docker images
+clean:
+	@echo "Cleaning up Docker images..."
+	@docker rmi atomate2-qe-amd64 2>/dev/null || echo "Image not found"
+	@docker system prune -f
+	@echo "✅ Cleanup complete"
+
+# Quick test of ZT workflow components
+test-workflow: build-if-needed
+	@echo "Testing ZT Workflow Components..."
+	@echo "================================="
+	@docker run --rm --platform linux/amd64 \
+		-v "$(PWD)/examples/zt_calculation.py:/app/examples/zt_calculation.py" \
+		--entrypoint /bin/bash atomate2-qe-amd64 -c "\
+		source /opt/conda/bin/activate qe-env && \
+		python3 -c \"\
+print('Testing ZT calculation workflow creation...'); \
+from atomate2.espresso.flows.thermoelectric import ZTMaker; \
+from pymatgen.core import Structure; \
+si = Structure([[0,2.73,2.73],[2.73,0,2.73],[2.73,2.73,0]], ['Si','Si'], [[0,0,0],[0.25,0.25,0.25]]); \
+zt_maker = ZTMaker(name='test_zt_workflow'); \
+flow = zt_maker.make(si); \
+print(f'✅ ZT workflow created successfully!'); \
+print(f'   - Total jobs: {len(flow.jobs)}'); \
+print(f'   - Job names: {[job.name for job in flow.jobs]}'); \
+print('✅ Ready for ZT calculations!')\""
+
+# Show ZT calculation example help
+zt-help: build-if-needed
+	@echo "ZT Calculation Example Help..."
+	@echo "=============================="
+	@docker run --rm --platform linux/amd64 \
+		-v "$(PWD)/examples/zt_calculation.py:/app/examples/zt_calculation.py" \
+		--entrypoint /bin/bash atomate2-qe-amd64 \
+		-c "source /opt/conda/bin/activate qe-env && cd /app && python3 examples/zt_calculation.py --help"
+
+# Development mode - mount source code
+dev: build-if-needed
+	@echo "Starting development environment..."
+	@docker run --rm -it --platform linux/amd64 \
+		-v "$(PWD):/app" \
+		-p 8888:8888 \
+		--entrypoint /bin/bash atomate2-qe-amd64 \
+		-c "source /opt/conda/bin/activate qe-env && cd /app && exec bash"
+
+qe_example: build-if-needed
+	@docker run -v "$(PWD):/src" --platform linux/amd64 --rm atomate2-qe-amd64 bash -c "cd /src && export OMPI_MCA_plm_rsh_agent= && export

examples/qe_bandgap_example.py

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+"""
+Example usage of Quantum ESPRESSO band gap workflow in atomate2.
+
+This example demonstrates how to use the new QE band gap calculation workflow
+that combines SCF and bands calculations to compute accurate band gaps.
+"""
+
+from jobflow import run_locally
+from pymatgen.core import Lattice, Structure
+
+from atomate2.espresso import BandGapMaker, RelaxBandGapMaker
+
+
+def create_silicon_structure():
+    """Create a silicon diamond structure."""
+    lattice = Lattice.cubic(5.43)  # Silicon lattice parameter in Angstroms
+    species = ["Si"] * 2
+    coords = [[0.0, 0.0, 0.0], [0.25, 0.25, 0.25]]
+    return Structure(lattice, species, coords)
+
+
+def main():
+    """Run QE band gap calculation examples."""
+
+    # Create silicon structure
+    structure = create_silicon_structure()
+    print(f"Created structure: {structure.formula}")
+
+    # Example 1: Basic band gap calculation
+    print("\n=== Example 1: Basic Band Gap Calculation ===")
+
+    # Create band gap workflow maker
+    bg_maker = BandGapMaker(
+        name="Si band gap calculation"
+    )
+
+    # Generate the workflow
+    bg_flow = bg_maker.make(structure)
+    print(f"Created workflow: {bg_flow.name}")
+    print(f"Number of jobs: {len(bg_flow.jobs)}")
+    print(f"Job names: {[job.name for job in bg_flow.jobs]}")
+
+    # Example 2: Customized band gap calculation
+    print("\n=== Example 2: Customized Band Gap Calculation ===")
+
+    # Customize SCF and bands settings
+    from atomate2.espresso.jobs.core import SCFMaker, BandsMaker
+
+    custom_scf = SCFMaker(
+        name="custom scf",
+        input_settings={
+            'pseudopotentials': {'Si': 'Si.pbe-n-rrkjus_psl.1.0.0.UPF'},
+            'kpts': (12, 12, 12),  # Denser k-points
+            'ecutwfc': 60.0,       # Higher cutoff
+            'conv_thr': 1e-10,     # Tighter convergence
+            'mixing_beta': 0.5,
+            'occupations': 'fixed',
+        }
+    )
+
+    custom_bands = BandsMaker(
+        name="custom bands",
+        input_settings={
+            'kpts': (16, 16, 16),  # Very dense k-points for bands
+            'nbnd': 30,            # More bands
+        }
+    )
+
+    custom_bg_maker = BandGapMaker(
+        name="Custom Si band gap",
+        scf_maker=custom_scf,
+        bands_maker=custom_bands
+    )
+
+    custom_flow = custom_bg_maker.make(structure)
+    print(f"Custom workflow: {custom_flow.name}")
+
+    # Example 3: Relax + band gap calculation
+    print("\n=== Example 3: Relaxation + Band Gap Calculation ===")
+
+    # This would use a force field for relaxation first
+    relax_bg_maker = RelaxBandGapMaker(
+        name="Relax and band gap",
+        # relax_maker could be added here if needed
+        band_gap_maker=bg_maker
+    )
+
+    relax_flow = relax_bg_maker.make(structure)
+    print(f"Relax + band gap workflow: {relax_flow.name}")
+
+    print("\n=== Workflow Information ===")
+    print("The workflows are now ready to be submitted to a job manager.")
+    print("They will:")
+    print("1. Run SCF calculation to get ground state")
+    print("2. Run bands calculation with denser k-points")
+    print("3. Extract band gap from the results")
+    print("\nRequirements:")
+    print("- Quantum ESPRESSO installation")
+    print("- ASE with QE calculator support")
+    print("- Appropriate pseudopotentials")
+
+    result = run_locally(relax_flow)
+    breakpoint()
+
+
+if __name__ == "__main__":
+    main()