Resolving the issue with pop_frequency calculation for polar materials

amset/tools/phonon_frequency.py

@@ -3,6 +3,7 @@
 
 import click
 import numpy as np
+import re
 
 __author__ = "Alex Ganose"
 __maintainer__ = "Alex Ganose"
@@ -18,7 +19,6 @@ def phonon_frequency(vasprun, outcar):
     from tabulate import tabulate
 
     vasprun = get_file(vasprun, Vasprun)
-    outcar = get_file(outcar, Outcar)
 
     elements = vasprun.final_structure.composition.elements
     if len(set(elements)) == 1:
@@ -28,9 +28,18 @@ def phonon_frequency(vasprun, outcar):
             "pop_frequency."
         )
 
-    effective_frequency, weights, freqs = effective_phonon_frequency_from_vasp_files(
-        vasprun, outcar
-    )
+    try:
+        effective_frequency, weights, freqs = effective_phonon_frequency_from_vasp_files(
+            vasprun, outcar
+        )
+        click.echo("Found NAC corrected phonon frequencies\n")
+    except ValueError:
+        click.echo("No NAC corrected file provided. Skipping calculation requiring NAC\n")
+
+        outcar = get_file(outcar, Outcar)
+        effective_frequency, weights, freqs = effective_phonon_frequency_from_vasp_files_no_nac(
+            vasprun, outcar
+        )
 
     table = tabulate(
         list(zip(freqs, weights)),
@@ -44,11 +53,20 @@ def phonon_frequency(vasprun, outcar):
 
     return effective_frequency
 
-
 def effective_phonon_frequency_from_vasp_files(vasprun, outcar):
+    frequencies, eigenvectors, born_effective_charges = extract_gamma_point_data(outcar)
+
+    effective_frequency, weights = calculate_effective_phonon_frequency(
+        frequencies, eigenvectors, born_effective_charges, vasprun.final_structure
+    )
+
+    return effective_frequency, weights, frequencies
+
+
+def effective_phonon_frequency_from_vasp_files_no_nac(vasprun, outcar):
     eigenvalues = -vasprun.normalmode_eigenvals[::-1]
     eigenvectors = vasprun.normalmode_eigenvecs[::-1]
-
+    
     # get frequencies from eigenvals (and convert to THz for VASP 5)
     major_version = int(vasprun.vasp_version.split(".")[0])
     frequencies = np.sqrt(np.abs(eigenvalues)) * np.sign(eigenvalues)
@@ -62,10 +80,11 @@ def effective_phonon_frequency_from_vasp_files(vasprun, outcar):
     effective_frequency, weights = calculate_effective_phonon_frequency(
         frequencies, eigenvectors, born_effective_charges, vasprun.final_structure
     )
-
+    
     return effective_frequency, weights, frequencies
 
 
+
 def calculate_effective_phonon_frequency(
     frequencies: np.ndarray,
     eigenvectors: np.ndarray,
@@ -99,23 +118,117 @@ def get_phonon_weight(eigenvector, frequency, born_effective_charges, structure)
         born_effective_charges, eigenvector, structure
     ):
         ze = np.dot(atom_born, atom_vec) / np.sqrt(site.specie.atomic_mass * frequency)
+
         zes.append(ze)
 
     all_weights = []
     for direction in directions:
         # Calculate q.Z*.e(q) / sqrt(M*omega) for each atom
         qze = np.dot(zes, direction)
-
+        
         # sum across all atoms
         all_weights.append(np.abs(np.sum(qze)))
 
     weight = np.average(all_weights * quad_weights)
-
+    
     if np.isnan(weight):
         return 0
     else:
         return weight
 
+#------block to extract data from new outcar-----#
+def parse_frequencies(line):
+    """Extract frequencies from a given line."""
+    return [float(value) for value in re.findall(r"[-+]?\d*\.\d+|\d+", line)]
+
+def extract_real_parts(eigenvector_line):
+    """Extract the real parts of eigenvector components from a given line."""
+    components = re.findall(r"[-+]?\d*\.\d+(?:[eE][-+]?\d+)?", eigenvector_line)
+    real_parts = [
+        float(components[i]) for i in range(0, len(components), 2)
+    ]  # Take every other value starting from 0 (real part)
+    return real_parts
+
+def reshape_to_3x3(real_parts):
+    """Reshape a flat list of real parts into a 3x3 array."""
+    return np.array(real_parts).reshape(3, 3)
+
+def extract_gamma_point_data(file_path):
+    """Extract frequencies and reshaped eigenvectors for the gamma point."""
+    with open(file_path, 'r') as file:
+        content = file.read()
+
+    match = re.findall("PHON_BORN_CHARGES = .*", content)
+
+    if match:
+        born = np.array(list(map(float, match[0].split("=")[1].split()))).reshape(-1, 3, 3)
+    else:
+        raise ValueError("Could not find PHONON_BORN_CHARGES")
+
+    content = content.split("\n")
+    # Identify the phonon section
+    phonon_section = []
+    phonon_started = False
+    for line in content:
+        if "Phonons" in line:
+            phonon_started = True
+        if phonon_started:
+            phonon_section.append(line)
+        if phonon_started and "--------------------------------------------------------------------------------" in line:
+            break
+
+    # Initialize data containers
+    q_points = []
+    frequencies = []
+    eigenvector_3d = []
+
+    current_q_point = None
+    current_frequencies = []
+    current_real_parts = []
+
+    for line in phonon_section:
+        # Detect q-point line
+        if re.match(r"\s*\d+\s+[-+]?\d+\.\d+", line):
+            if current_q_point:  # Save previous q-point data
+                q_points.append(current_q_point)
+                frequencies.append(np.array(current_frequencies))
+                eigenvector_3d.append(np.array(current_real_parts))
+                current_frequencies = []
+                current_real_parts = []
+            current_q_point = [float(x) for x in line.split()[1:4]]
+        # Parse frequencies
+        elif "[THz]" in line:
+            current_frequencies = parse_frequencies(line)
+        # Parse eigenvectors
+        elif re.match(r"\s+[-+]?\d+\.\d+", line):
+            real_parts = extract_real_parts(line.strip())
+            reshaped_vector = reshape_to_3x3(real_parts)
+            current_real_parts.append(reshaped_vector)
+
+    # Save the last q-point's data
+    if current_q_point:
+        q_points.append(current_q_point)
+        frequencies.append(np.array(current_frequencies))
+        eigenvector_3d.append(np.array(current_real_parts))
+
+    # Locate gamma point
+    gamma_index = None
+    for i, q_point in enumerate(q_points):
+        if np.allclose(q_point, [0.0, 0.0, 0.0]):
+            gamma_index = i
+            break
+
+    if gamma_index is None:
+        raise ValueError("Gamma point ([0.0, 0.0, 0.0]) not found in the OUTCAR file.")
+
+    # Extract gamma point data
+    gamma_frequencies = frequencies[gamma_index]
+    gamma_eigenvectors_3d = np.array(eigenvector_3d[gamma_index])
+
+    return gamma_frequencies, gamma_eigenvectors_3d, born
+
+#--------block ends here--------#
+
 
 def get_file(filename, class_type):
     if isinstance(filename, str):

docs/src/inputs.md

@@ -123,13 +123,31 @@ Note, DFPT cannot be used with hybrid exchange-correlation functionals. In these
 cases the [LCALCEPS](https://www.vasp.at/wiki/index.php/LCALCEPS) flag should be
 used in combination with `IBRION = 6`.
 
+**Non-Analytical Term Correction (NAC) for Polar Materials**
+
+In polar materials, LO-TO splitting in the phonon dispersion is significant, and to observe this in phonon dispersion, we have to add a non-analytical term correction (NAC) to the dynamical matrix and re-calculate the phonon frequencies. This treatment is done automatically inside VASP using the [LPHON_POLAR = .TRUE.](https://www.vasp.at/wiki/index.php/LPHON_POLAR) tag and specifying the dielectric tensor using [PHON_DIELECTRIC](https://www.vasp.at/wiki/index.php/PHON_DIELECTRIC) tag along with the Born effective charges using [PHON_BORN_CHARGES](https://www.vasp.at/wiki/index.php/PHON_BORN_CHARGES) tag. This step should be performed after obtaining the Born effective charges and dielectric constants from a previous DFPT calculation.
+
+!!! summary "VASP settings for dielectric constants and phonon frequency "
+    ```python
+    ADDGRID = True
+    EDIFF = 1E-8
+    PREC = Accurate
+    NSW = 1
+    IBRION = 6
+    LPHON_DISPERSION = .TRUE.
+    PHON_NWRITE = -3
+    LPHON_POLAR = .TRUE.
+    PHON_DIELECTRIC = [values]
+    PHON_BORN_CHARGES = [values]
+    ```
+
 The dielectric constants and polar phonon frequency can be extracted from the
 VASP outputs using the command:
 ```bash
 amset phonon-frequency
 ```
-The command should be run in a folder containing the `vasprun.xml` file output
-from the DFPT calculation.
+The command should be run in a folder containing the `vasprun.xml` and `OUTCAR` file output
+from the DFPT calculation. For polar materials, an `OUTCAR` from the NAC calculaiton must be provided. 
 
 The effective phonon frequency is determined from the phonon frequencies
 $`\omega_{\mathbf{q}\nu}`$ (where $`\nu`$ is a phonon branch and $`\mathbf{q}`$