Added geometry optimization script

scripts/qp_cipsi_rsh

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+/home/scemama/qp2/plugins/qp_plugins_lct/stable/rsdft_cipsi/qp_cipsi_rsh

scripts/qp_cipsi_rsh_mu_of_r

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+/home/scemama/qp2/plugins/qp_plugins_lct/stable/rsdft_cipsi/qp_cipsi_rsh_mu_of_r

scripts/qp_geom_opt.py

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+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+Usage:
+       qp_geom_opt [-s state] [-r executable] [-f] [-t tolerance] <EZFIO_FILE>
+
+Options:
+      -s --state=<state>       Excited state to optimize 
+      -f --scf                 Perform an SCF after each geomety change
+      -r --qp_run=executable   Excited state to optimize 
+      -t --tol=tolerance       Convergence criterion on the energy
+"""                  
+
+
+try:
+    from docopt import docopt
+    from module_handler import ModuleHandler, get_dict_child
+    from module_handler import get_l_module_descendant
+    from qp_path import QP_SRC, QP_PLUGINS, QP_DATA, QP_ROOT
+except ImportError:
+    print("Please check if you have sourced the ${QP_ROOT}/quantum_package.rc")
+    print("(`source ${QP_ROOT}/quantum_package.rc`)")
+    print(sys.exit(1))
+
+    
+import numpy as np
+import subprocess
+from scipy.optimize import minimize
+from ezfio import ezfio
+
+import sys
+
+
+def set_unbuffered_output():
+    """Ensure sys.stdout is unbuffered or line-buffered in a portable way."""
+    if hasattr(sys.stdout, "reconfigure"):  # Python 3.7+
+        sys.stdout.reconfigure(line_buffering=True)
+    else:
+        sys.stdout = open(sys.stdout.fileno(), mode='w', buffering=1)
+
+set_unbuffered_output()
+
+
+
+
+def get_energy(file, state, arguments):
+    """Compute the energy of the given state by calling Quantum Package."""
+    if not arguments["--qp_run"]:
+        raise ValueError("--qp_run option missing")
+
+    if arguments["--scf"]:
+        executable = "scf"
+    else:
+        executable = "save_ortho_mos"
+
+    result = subprocess.run(f"qp_run {executable} {file} > {file}.energy.out",
+                            shell=True, capture_output=True, text=True, check=True
+    )
+
+    executable = arguments["--qp_run"]
+    result = subprocess.run( f"qp_run {executable} {file} > {file}.energy.out",
+                             shell=True)
+    
+    energy = None
+    with open(f"{file}.energy.out", 'r') as f:
+        for line in f:
+            if "Energy of state" in line and f"{state}" in line:
+                energy = float(line.split()[-1])  # Extracts the energy value
+    
+    return energy
+    raise ValueError("Energy not found in Quantum Package output. Update script {sys.argv[0]}")
+
+def set_coordinates(coord):
+    """Update the nuclear coordinates in EZFIO."""
+    ezfio.set_nuclei_nucl_coord(coord)
+
+
+def get_coordinates():
+    """Retrieve the current nuclear coordinates from EZFIO."""
+    return np.array(ezfio.get_nuclei_nucl_coord())
+
+
+def energy_function(coord, file, state, arguments):
+    """Wrapper for the energy calculation, ensuring coordinates are updated."""
+    set_coordinates(coord)
+    energy = get_energy(file, state, arguments)
+
+    label = ezfio.get_nuclei_nucl_label()
+    num_atoms = len(label)
+    coord = coord.reshape(3, num_atoms).T  # Reshape into (num_atoms, 3)
+    coord_angstrom = coord * 0.529177  # Convert atomic units to angstroms
+    
+    print(num_atoms)
+    print(f"Energy: {energy:15.10f}")
+    for i, (x, y, z) in enumerate(coord_angstrom):
+        print(f"{label[i]:3s} {x:15.8f} {y:15.8f} {z:15.8f}")  # Replace 'X' with actual atomic symbols
+    return energy
+
+
+def optimize_geometry(file, state, arguments):
+    """Perform geometry optimization using SciPy's minimize function."""
+
+    x0 = get_coordinates().flatten()
+
+    if arguments["--tol"]:
+        tolerance = float(tol=arguments["--tol"])
+    else:
+        tolerance = 1.e-3
+
+    result = minimize(energy_function, x0, args=(file, state, arguments), method='BFGS', jac=None, tol=tolerance, options={'eps': 1.e-3})
+    
+    if result.success:
+        print("Optimization successful!")
+        print("Final energy:", result.fun)
+        print("Optimized coordinates:", result.x)
+    else:
+        print("Optimization failed:", result.message)
+    
+    set_coordinates(result.x)  # Store the optimized geometry
+    return result
+
+
+def main(arguments):
+    if arguments["--state"]:
+        state=arguments["--state"]
+    else:
+        state=1
+    ezfio_filename = arguments["<EZFIO_FILE>"]
+    ezfio.set_file(ezfio_filename)
+
+    optimize_geometry(ezfio_filename, state, arguments)
+
+
+if __name__ == "__main__":
+    ARG = docopt(__doc__)
+    main(ARG)