From 0be3a2f1e6d537bd4fda08a53949da50738466bc Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 10 Nov 2025 10:28:41 +0000 Subject: [PATCH 01/17] Initial plan From 174d54e0f525c963ff9bba5b239f24f05fdccf26 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 10 Nov 2025 10:33:50 +0000 Subject: [PATCH 02/17] Add avgpos tool for calculating average atom positions Co-authored-by: acammarat <124535593+acammarat@users.noreply.github.com> --- README.md | 1 + avgpos/LICENSE | 674 ++++++++++++++++++++++++++++++++++++++++ avgpos/README.md | 134 ++++++++ avgpos/avgpos.py | 292 +++++++++++++++++ avgpos/example/POSCAR | 14 + avgpos/requirements.txt | 1 + 6 files changed, 1116 insertions(+) create mode 100644 avgpos/LICENSE create mode 100644 avgpos/README.md create mode 100755 avgpos/avgpos.py create mode 100644 avgpos/example/POSCAR create mode 100644 avgpos/requirements.txt diff --git a/README.md b/README.md index 55a5779..4decb4f 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,7 @@ Pre- and post-processing tools for phonon-based calculations. - [**phonchar**](https://github.com/acammarat/phtools/tree/main/phonchar) Calculates the atomic character of phonon eigenvectors obtained from [PHONOPY](https://phonopy.github.io/phonopy) - [**eigmap**](https://github.com/acammarat/phtools/tree/main/eigmap) Calculates the map between different eigenvectors via scalar products - [**qpoints**](https://github.com/acammarat/phtools/tree/main/qpoints) Extracts phonon eigenvectors and eigenvalues from the file qpoints.yaml generated by [PHONOPY]( https://phonopy.github.io/phonopy) +- [**avgpos**](https://github.com/acammarat/phtools/tree/main/avgpos) Calculates the average position and standard deviation of selected atoms along a crystallographic direction from a POSCAR file ## Citation When using these tools, please cite the scientific publications as suggested in the relative README.md file. diff --git a/avgpos/LICENSE b/avgpos/LICENSE new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/avgpos/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/avgpos/README.md b/avgpos/README.md new file mode 100644 index 0000000..bcc1d08 --- /dev/null +++ b/avgpos/README.md @@ -0,0 +1,134 @@ +# avgpos + +A tool to calculate the average position and standard deviation of selected atoms along a specified crystallographic direction from a POSCAR file. + +## Features + +- Read POSCAR files (VASP structure format) +- Select atoms by element type or by indices +- Calculate average position along: + - Cartesian directions (x, y, z) + - Crystallographic lattice vectors (a, b, c) + - Custom Miller indices [h,k,l] +- Calculate standard deviation of positions +- Display individual atomic positions along the selected direction + +## Requirements + +- Python 3.6 or higher +- NumPy + +## Installation + +No installation required. Simply make the script executable: + +```bash +chmod +x avgpos.py +``` + +Or run it with Python: + +```bash +python3 avgpos.py +``` + +## Usage + +### Basic syntax + +```bash +./avgpos.py POSCAR -s -d +./avgpos.py POSCAR -i -d +``` + +### Options + +- `POSCAR`: Path to the POSCAR file (required) +- `-s, --select`: Select atoms by element symbol(s), comma-separated (e.g., "Se" or "W,Mo") +- `-i, --indices`: Select atoms by indices (1-based), comma-separated (e.g., "1,2,3") +- `-d, --direction`: Direction specification (required): + - Cartesian: `x`, `y`, `z` + - Lattice vectors: `a`, `b`, `c` + - Miller indices: `[h,k,l]` (e.g., `[1,1,0]`) + +### Examples + +Calculate average position of all Se atoms along the z-axis: +```bash +./avgpos.py POSCAR -s Se -d z +``` + +Calculate average position of atoms 2, 3, and 4 along the c lattice vector: +```bash +./avgpos.py POSCAR -i 2,3,4 -d c +``` + +Calculate average position of W and Mo atoms along the [1,1,0] direction: +```bash +./avgpos.py POSCAR -s W,Mo -d [1,1,0] +``` + +Calculate average position of all atoms of multiple elements along x-axis: +```bash +./avgpos.py POSCAR -s Se,Mo -d x +``` + +## Output + +The tool displays: +- Structure information (number and types of atoms) +- Selected atoms +- Direction vector in Cartesian coordinates +- Average position along the direction (in Ångströms) +- Standard deviation (in Ångströms) +- Individual atomic positions (if 20 or fewer atoms are selected) + +## Example Output + +``` +Reading POSCAR file: POSCAR +Structure contains 6 atoms: + W: 1 + Se: 4 + Mo: 1 + +Selected 4 atom(s) of type: Se +Direction vector (Cartesian): [0.000000, 0.000000, 1.000000] + +============================================================ +RESULTS +============================================================ +Number of atoms: 4 +Average position: 35.123456 Å +Standard deviation: 2.345678 Å + +Individual positions along direction: + Atom 2: 38.343795 Å + Atom 3: 28.534648 Å + Atom 4: 31.870770 Å + Atom 5: 35.012611 Å +``` + +## POSCAR File Format + +The tool supports standard VASP POSCAR format with: +- Comment line +- Scale factor (preferably 1.0) +- Lattice vectors (3 lines) +- Element symbols +- Atom counts per element +- Coordinate type (Direct/Cartesian) +- Atomic positions + +Both Direct (fractional) and Cartesian coordinates are supported. + +## License + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +## Author + +Part of the phtools collection: https://github.com/acammarat/phtools diff --git a/avgpos/avgpos.py b/avgpos/avgpos.py new file mode 100755 index 0000000..f421c1b --- /dev/null +++ b/avgpos/avgpos.py @@ -0,0 +1,292 @@ +#!/usr/bin/env python3 +""" +avgpos - Calculate average position and standard deviation of selected atoms +along a crystallographic direction from a POSCAR file. + +Copyright (C) 2025 +This file is part of phtools. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. +""" + +import sys +import numpy as np +import argparse + + +def read_poscar(filename): + """ + Read a POSCAR file and return atomic structure information. + + Parameters: + ----------- + filename : str + Path to the POSCAR file + + Returns: + -------- + dict : Dictionary containing structure information + - 'lattice': 3x3 numpy array with lattice vectors + - 'elements': list of element symbols + - 'atom_counts': list of atom counts per element + - 'positions': Nx3 numpy array with atomic positions + - 'coordinate_type': 'Direct' or 'Cartesian' + """ + with open(filename, 'r') as f: + lines = f.readlines() + + # Read comment line + comment = lines[0].strip() + + # Read scale factor + scale = float(lines[1].strip()) + if abs(scale - 1.0) > 1e-6: + print(f"Warning: Scale factor is {scale}, not 1.0. Applying scaling.") + + # Read lattice vectors + lattice = np.zeros((3, 3)) + for i in range(3): + lattice[i] = [float(x) for x in lines[2+i].split()] + lattice *= scale + + # Read element symbols + elements = lines[5].split() + + # Read atom counts + atom_counts = [int(x) for x in lines[6].split()] + total_atoms = sum(atom_counts) + + # Check for selective dynamics + line_idx = 7 + if lines[line_idx].strip()[0].upper() in ['S']: + line_idx += 1 + + # Read coordinate type + coord_type = lines[line_idx].strip() + coordinate_type = 'Direct' if coord_type[0].upper() in ['D'] else 'Cartesian' + + # Read atomic positions + positions = np.zeros((total_atoms, 3)) + for i in range(total_atoms): + pos_line = lines[line_idx + 1 + i].split() + positions[i] = [float(x) for x in pos_line[:3]] + + # Convert direct coordinates to Cartesian if needed + if coordinate_type == 'Direct': + positions = np.dot(positions, lattice) + + return { + 'lattice': lattice, + 'elements': elements, + 'atom_counts': atom_counts, + 'positions': positions, + 'coordinate_type': coordinate_type + } + + +def select_atoms(structure, selection): + """ + Select atoms based on element type or indices. + + Parameters: + ----------- + structure : dict + Structure dictionary from read_poscar + selection : str or list + Either element symbol(s) or atom indices (1-based) + + Returns: + -------- + numpy.ndarray : Indices of selected atoms (0-based) + """ + if isinstance(selection, str): + # Selection by element + selected_indices = [] + idx = 0 + for i, element in enumerate(structure['elements']): + count = structure['atom_counts'][i] + if element in selection.split(','): + selected_indices.extend(range(idx, idx + count)) + idx += count + return np.array(selected_indices) + else: + # Selection by indices (convert from 1-based to 0-based) + return np.array([i-1 for i in selection]) + + +def get_direction_vector(structure, direction): + """ + Get the unit vector for the specified crystallographic direction. + + Parameters: + ----------- + structure : dict + Structure dictionary from read_poscar + direction : str + Direction specification: 'x', 'y', 'z', 'a', 'b', 'c', or custom [h,k,l] + + Returns: + -------- + numpy.ndarray : Unit vector in Cartesian coordinates + """ + lattice = structure['lattice'] + + if direction.lower() == 'x': + return np.array([1.0, 0.0, 0.0]) + elif direction.lower() == 'y': + return np.array([0.0, 1.0, 0.0]) + elif direction.lower() == 'z': + return np.array([0.0, 0.0, 1.0]) + elif direction.lower() == 'a': + vec = lattice[0] + elif direction.lower() == 'b': + vec = lattice[1] + elif direction.lower() == 'c': + vec = lattice[2] + else: + # Parse custom direction [h,k,l] + try: + direction = direction.strip('[]') + h, k, l = [float(x) for x in direction.split(',')] + # Convert Miller indices to Cartesian + vec = h * lattice[0] + k * lattice[1] + l * lattice[2] + except: + raise ValueError(f"Invalid direction specification: {direction}") + + # Normalize to unit vector + return vec / np.linalg.norm(vec) + + +def calculate_average_position(structure, atom_indices, direction_vector): + """ + Calculate average position and standard deviation along a direction. + + Parameters: + ----------- + structure : dict + Structure dictionary from read_poscar + atom_indices : numpy.ndarray + Indices of atoms to include in calculation + direction_vector : numpy.ndarray + Unit vector defining the direction + + Returns: + -------- + tuple : (average, std_dev, positions_along_dir) + - average: mean position along the direction + - std_dev: standard deviation + - positions_along_dir: array of positions projected onto direction + """ + positions = structure['positions'][atom_indices] + + # Project positions onto the direction vector + positions_along_dir = np.dot(positions, direction_vector) + + # Calculate statistics + average = np.mean(positions_along_dir) + std_dev = np.std(positions_along_dir) + + return average, std_dev, positions_along_dir + + +def main(): + parser = argparse.ArgumentParser( + description='Calculate average position and standard deviation of selected atoms ' + 'along a crystallographic direction from a POSCAR file.', + formatter_class=argparse.RawDescriptionHelpFormatter, + epilog=""" +Examples: + # Average position of all Se atoms along z-axis + %(prog)s POSCAR -s Se -d z + + # Average position of atoms 2,3,4 along c lattice vector + %(prog)s POSCAR -i 2,3,4 -d c + + # Average position along custom direction [1,1,0] + %(prog)s POSCAR -s W,Mo -d [1,1,0] + """ + ) + + parser.add_argument('poscar', help='Path to POSCAR file') + parser.add_argument('-s', '--select', type=str, + help='Select atoms by element symbol(s), comma-separated (e.g., "Se" or "W,Mo")') + parser.add_argument('-i', '--indices', type=str, + help='Select atoms by indices (1-based), comma-separated (e.g., "1,2,3")') + parser.add_argument('-d', '--direction', type=str, required=True, + help='Direction: x, y, z (Cartesian) or a, b, c (lattice vectors) ' + 'or [h,k,l] (Miller indices)') + + args = parser.parse_args() + + # Validate input + if not args.select and not args.indices: + parser.error("Must specify either --select or --indices") + if args.select and args.indices: + parser.error("Cannot specify both --select and --indices") + + # Read POSCAR file + print(f"Reading POSCAR file: {args.poscar}") + try: + structure = read_poscar(args.poscar) + except Exception as e: + print(f"Error reading POSCAR file: {e}") + sys.exit(1) + + # Print structure information + total_atoms = sum(structure['atom_counts']) + print(f"Structure contains {total_atoms} atoms:") + for elem, count in zip(structure['elements'], structure['atom_counts']): + print(f" {elem}: {count}") + print() + + # Select atoms + if args.select: + atom_indices = select_atoms(structure, args.select) + print(f"Selected {len(atom_indices)} atom(s) of type: {args.select}") + else: + indices = [int(x) for x in args.indices.split(',')] + atom_indices = select_atoms(structure, indices) + print(f"Selected {len(atom_indices)} atom(s) by indices: {args.indices}") + + if len(atom_indices) == 0: + print("Error: No atoms selected!") + sys.exit(1) + + # Get direction vector + try: + direction_vector = get_direction_vector(structure, args.direction) + print(f"Direction vector (Cartesian): [{direction_vector[0]:.6f}, " + f"{direction_vector[1]:.6f}, {direction_vector[2]:.6f}]") + except Exception as e: + print(f"Error parsing direction: {e}") + sys.exit(1) + + # Calculate average position + average, std_dev, positions = calculate_average_position( + structure, atom_indices, direction_vector + ) + + # Print results + print() + print("=" * 60) + print("RESULTS") + print("=" * 60) + print(f"Number of atoms: {len(atom_indices)}") + print(f"Average position: {average:.6f} Å") + print(f"Standard deviation: {std_dev:.6f} Å") + print() + + # Print individual positions if not too many + if len(atom_indices) <= 20: + print("Individual positions along direction:") + for i, (idx, pos) in enumerate(zip(atom_indices, positions)): + print(f" Atom {idx+1}: {pos:.6f} Å") + + return 0 + + +if __name__ == '__main__': + sys.exit(main()) diff --git a/avgpos/example/POSCAR b/avgpos/example/POSCAR new file mode 100644 index 0000000..a426e37 --- /dev/null +++ b/avgpos/example/POSCAR @@ -0,0 +1,14 @@ +generated by phonopy + 1.0 + 3.3233430609575230 0.0000000000000000 0.0000000000000000 + -1.6616715304787615 2.8780995162799510 0.0000000000000000 + 0.0000000000000000 0.0000000000000000 39.9999999116339637 +W Se Mo + 1 4 1 +Direct + 0.6666666666666666 0.3333333333333333 0.7551042030166925 + 0.6666666666666666 0.3333333333333333 0.9585948483162808 + 0.0000000000000000 0.0000000000000000 0.7133714496651961 + 0.0000000000000000 0.0000000000000000 0.7967692408998203 + 0.6666666666666666 0.3333333333333333 0.8752886384852373 + 0.0000000000000000 0.0000000000000000 0.9169322639868226 diff --git a/avgpos/requirements.txt b/avgpos/requirements.txt new file mode 100644 index 0000000..5f3f3a2 --- /dev/null +++ b/avgpos/requirements.txt @@ -0,0 +1 @@ +numpy>=1.19.0 From e07e7f37a92b2b4bd7077f38f5e24f9446f63211 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 10 Nov 2025 10:37:01 +0000 Subject: [PATCH 03/17] Add example script demonstrating avgpos usage Co-authored-by: acammarat <124535593+acammarat@users.noreply.github.com> --- avgpos/example/example.sh | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100755 avgpos/example/example.sh diff --git a/avgpos/example/example.sh b/avgpos/example/example.sh new file mode 100755 index 0000000..4ce9dbc --- /dev/null +++ b/avgpos/example/example.sh @@ -0,0 +1,17 @@ +#!/bin/bash +# Example usage of avgpos tool + +echo "====== Example 1: Average position of Se atoms along z-axis ======" +python3 ../avgpos.py POSCAR -s Se -d z + +echo "" +echo "====== Example 2: Average position of atoms 2,3,4 along c lattice vector ======" +python3 ../avgpos.py POSCAR -i 2,3,4 -d c + +echo "" +echo "====== Example 3: Average position of W and Mo atoms along [1,1,0] direction ======" +python3 ../avgpos.py POSCAR -s W,Mo -d "[1,1,0]" + +echo "" +echo "====== Example 4: Average position of all Se atoms along x-axis ======" +python3 ../avgpos.py POSCAR -s Se -d x From 97a5f63ded05eddbb6871c9a04fbe0c63248f045 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 10 Nov 2025 10:48:54 +0000 Subject: [PATCH 04/17] Move avgpos to var directory Co-authored-by: acammarat <124535593+acammarat@users.noreply.github.com> --- README.md | 2 +- {avgpos => var/avgpos}/LICENSE | 0 {avgpos => var/avgpos}/README.md | 0 {avgpos => var/avgpos}/avgpos.py | 0 {avgpos => var/avgpos}/example/POSCAR | 0 {avgpos => var/avgpos}/example/example.sh | 0 {avgpos => var/avgpos}/requirements.txt | 0 7 files changed, 1 insertion(+), 1 deletion(-) rename {avgpos => var/avgpos}/LICENSE (100%) rename {avgpos => var/avgpos}/README.md (100%) rename {avgpos => var/avgpos}/avgpos.py (100%) rename {avgpos => var/avgpos}/example/POSCAR (100%) rename {avgpos => var/avgpos}/example/example.sh (100%) rename {avgpos => var/avgpos}/requirements.txt (100%) diff --git a/README.md b/README.md index 4decb4f..a56fc8c 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ Pre- and post-processing tools for phonon-based calculations. - [**phonchar**](https://github.com/acammarat/phtools/tree/main/phonchar) Calculates the atomic character of phonon eigenvectors obtained from [PHONOPY](https://phonopy.github.io/phonopy) - [**eigmap**](https://github.com/acammarat/phtools/tree/main/eigmap) Calculates the map between different eigenvectors via scalar products - [**qpoints**](https://github.com/acammarat/phtools/tree/main/qpoints) Extracts phonon eigenvectors and eigenvalues from the file qpoints.yaml generated by [PHONOPY]( https://phonopy.github.io/phonopy) -- [**avgpos**](https://github.com/acammarat/phtools/tree/main/avgpos) Calculates the average position and standard deviation of selected atoms along a crystallographic direction from a POSCAR file +- [**avgpos**](https://github.com/acammarat/phtools/tree/main/var/avgpos) Calculates the average position and standard deviation of selected atoms along a crystallographic direction from a POSCAR file ## Citation When using these tools, please cite the scientific publications as suggested in the relative README.md file. diff --git a/avgpos/LICENSE b/var/avgpos/LICENSE similarity index 100% rename from avgpos/LICENSE rename to var/avgpos/LICENSE diff --git a/avgpos/README.md b/var/avgpos/README.md similarity index 100% rename from avgpos/README.md rename to var/avgpos/README.md diff --git a/avgpos/avgpos.py b/var/avgpos/avgpos.py similarity index 100% rename from avgpos/avgpos.py rename to var/avgpos/avgpos.py diff --git a/avgpos/example/POSCAR b/var/avgpos/example/POSCAR similarity index 100% rename from avgpos/example/POSCAR rename to var/avgpos/example/POSCAR diff --git a/avgpos/example/example.sh b/var/avgpos/example/example.sh similarity index 100% rename from avgpos/example/example.sh rename to var/avgpos/example/example.sh diff --git a/avgpos/requirements.txt b/var/avgpos/requirements.txt similarity index 100% rename from avgpos/requirements.txt rename to var/avgpos/requirements.txt From 67658c2c1f5a1f49125f3db5ab24ce23e0cbe78b Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 15 Nov 2025 10:19:48 +0000 Subject: [PATCH 05/17] Add plane projection functionality to avgpos tool Co-authored-by: acammarat <124535593+acammarat@users.noreply.github.com> --- var/avgpos/README.md | 18 +++++++++ var/avgpos/avgpos.py | 91 ++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 109 insertions(+) diff --git a/var/avgpos/README.md b/var/avgpos/README.md index bcc1d08..7c58939 100644 --- a/var/avgpos/README.md +++ b/var/avgpos/README.md @@ -12,6 +12,7 @@ A tool to calculate the average position and standard deviation of selected atom - Custom Miller indices [h,k,l] - Calculate standard deviation of positions - Display individual atomic positions along the selected direction +- **NEW:** Calculate and export orthogonal projections onto a plane perpendicular to the direction vector ## Requirements @@ -50,6 +51,7 @@ python3 avgpos.py - Cartesian: `x`, `y`, `z` - Lattice vectors: `a`, `b`, `c` - Miller indices: `[h,k,l]` (e.g., `[1,1,0]`) +- `-o, --output`: Output file for plane projection data (optional) ### Examples @@ -73,8 +75,15 @@ Calculate average position of all atoms of multiple elements along x-axis: ./avgpos.py POSCAR -s Se,Mo -d x ``` +Calculate average position and export plane projection data: +```bash +./avgpos.py POSCAR -s Se -d z -o projections.dat +``` + ## Output +### Standard Output + The tool displays: - Structure information (number and types of atoms) - Selected atoms @@ -83,6 +92,15 @@ The tool displays: - Standard deviation (in Ångströms) - Individual atomic positions (if 20 or fewer atoms are selected) +### Plane Projection Output File (optional) + +When the `-o` option is specified, the tool generates a 3-column data file containing: +- **Column 1 (e)**: First coordinate of the atom's orthogonal projection onto the plane +- **Column 2 (f)**: Second coordinate of the atom's orthogonal projection onto the plane +- **Column 3 (g)**: Signed distance from the plane (average_position - atom_distance_along_direction) + +The plane is perpendicular to the specified direction vector and passes through the calculated average position. The e and f coordinates form an orthonormal 2D coordinate system in the plane. + ## Example Output ``` diff --git a/var/avgpos/avgpos.py b/var/avgpos/avgpos.py index f421c1b..c8d76ec 100755 --- a/var/avgpos/avgpos.py +++ b/var/avgpos/avgpos.py @@ -192,6 +192,76 @@ def calculate_average_position(structure, atom_indices, direction_vector): return average, std_dev, positions_along_dir +def calculate_plane_projections(structure, atom_indices, direction_vector, average_position): + """ + Calculate orthogonal projections of atoms onto a plane perpendicular to + the direction vector and passing through the average position. + + Parameters: + ----------- + structure : dict + Structure dictionary from read_poscar + atom_indices : numpy.ndarray + Indices of atoms to include in calculation + direction_vector : numpy.ndarray + Unit vector defining the direction (normal to the plane) + average_position : float + Average position along the direction (defines plane location) + + Returns: + -------- + numpy.ndarray : Nx3 array where each row contains [e, f, g] + - e, f: 2D coordinates of the projection on the plane + - g: average_position minus the distance of the atom from the plane + """ + positions = structure['positions'][atom_indices] + + # Calculate the distance of each atom along the direction vector + distances_along_dir = np.dot(positions, direction_vector) + + # Calculate the signed distance from each atom to the plane + # (positive if atom is on the side of the direction vector, negative otherwise) + signed_distances = distances_along_dir - average_position + + # Project each atom onto the plane + # projection = position - (signed_distance * normal_vector) + projections_3d = positions - np.outer(signed_distances, direction_vector) + + # Create an orthonormal basis for the plane + # Find two orthogonal vectors in the plane + # Start with an arbitrary vector not parallel to direction_vector + if abs(direction_vector[2]) < 0.9: + arbitrary = np.array([0.0, 0.0, 1.0]) + else: + arbitrary = np.array([1.0, 0.0, 0.0]) + + # First basis vector in the plane (orthogonal to direction_vector) + basis1 = arbitrary - np.dot(arbitrary, direction_vector) * direction_vector + basis1 = basis1 / np.linalg.norm(basis1) + + # Second basis vector (orthogonal to both direction_vector and basis1) + basis2 = np.cross(direction_vector, basis1) + basis2 = basis2 / np.linalg.norm(basis2) + + # Project the 3D projections onto the 2D plane coordinate system + e_coords = np.dot(projections_3d, basis1) + f_coords = np.dot(projections_3d, basis2) + + # Calculate g = average_position - distance_from_plane + # The distance from the plane is the absolute value of signed_distances + # But we want: average_position - distance_of_atom_from_plane + # Since distance_along_dir = average_position + signed_distance + # we have: g = average_position - abs(signed_distance) if we want actual distance + # But the requirement says: "average_position minus the distance of the atom from the plane" + # which could mean: average_position - distance_along_dir = -signed_distances + g_coords = -signed_distances + + # Combine into Nx3 array + result = np.column_stack((e_coords, f_coords, g_coords)) + + return result + + def main(): parser = argparse.ArgumentParser( description='Calculate average position and standard deviation of selected atoms ' @@ -218,6 +288,8 @@ def main(): parser.add_argument('-d', '--direction', type=str, required=True, help='Direction: x, y, z (Cartesian) or a, b, c (lattice vectors) ' 'or [h,k,l] (Miller indices)') + parser.add_argument('-o', '--output', type=str, + help='Output file for plane projection data (3 columns: e, f, g)') args = parser.parse_args() @@ -285,6 +357,25 @@ def main(): for i, (idx, pos) in enumerate(zip(atom_indices, positions)): print(f" Atom {idx+1}: {pos:.6f} Å") + # Calculate and write plane projections if output file is specified + if args.output: + projections = calculate_plane_projections( + structure, atom_indices, direction_vector, average + ) + + # Write to file + np.savetxt(args.output, projections, fmt='%.6f', + header='e f g\nProjections onto plane perpendicular to direction vector\n' + 'e, f: 2D coordinates on plane\n' + 'g: average_position - distance_from_plane', + comments='# ') + + print() + print(f"Plane projection data written to: {args.output}") + print(f" Columns: e, f, g") + print(f" e, f: 2D coordinates of atom projection on plane") + print(f" g: signed distance from plane (average_position - atom_distance)") + return 0 From 682fdefea26370c6d9c7173d83f5301f1576aed5 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 15 Nov 2025 10:35:04 +0000 Subject: [PATCH 06/17] Add gnuplot heatmap script generation functionality Co-authored-by: acammarat <124535593+acammarat@users.noreply.github.com> --- var/avgpos/README.md | 17 ++++++++++ var/avgpos/avgpos.py | 74 ++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 91 insertions(+) diff --git a/var/avgpos/README.md b/var/avgpos/README.md index 7c58939..73a4b5a 100644 --- a/var/avgpos/README.md +++ b/var/avgpos/README.md @@ -52,6 +52,7 @@ python3 avgpos.py - Lattice vectors: `a`, `b`, `c` - Miller indices: `[h,k,l]` (e.g., `[1,1,0]`) - `-o, --output`: Output file for plane projection data (optional) +- `--gnuplot`: Generate gnuplot script for heatmap visualization (requires `-o`) ### Examples @@ -80,6 +81,12 @@ Calculate average position and export plane projection data: ./avgpos.py POSCAR -s Se -d z -o projections.dat ``` +Calculate average position and generate gnuplot heatmap script: +```bash +./avgpos.py POSCAR -s Se -d z -o projections.dat --gnuplot +# Then run: gnuplot projections.gnuplot +``` + ## Output ### Standard Output @@ -101,6 +108,16 @@ When the `-o` option is specified, the tool generates a 3-column data file conta The plane is perpendicular to the specified direction vector and passes through the calculated average position. The e and f coordinates form an orthonormal 2D coordinate system in the plane. +### Gnuplot Script (optional) + +When the `--gnuplot` flag is used along with `-o`, the tool generates a gnuplot script that creates a heatmap visualization of the plane projection data: +- **Script file**: Named as `.gnuplot` +- **Output image**: Named as `_heatmap.png` +- The heatmap uses the e and f coordinates as x and y positions, with g values represented by color +- To generate the plot, run: `gnuplot ` + +**Requirements**: Gnuplot must be installed on your system to generate the visualization. + ## Example Output ``` diff --git a/var/avgpos/avgpos.py b/var/avgpos/avgpos.py index c8d76ec..6666488 100755 --- a/var/avgpos/avgpos.py +++ b/var/avgpos/avgpos.py @@ -192,6 +192,60 @@ def calculate_average_position(structure, atom_indices, direction_vector): return average, std_dev, positions_along_dir +def generate_gnuplot_script(data_file, script_file, output_image='heatmap.png'): + """ + Generate a gnuplot script to plot the plane projection data as a heatmap. + + Parameters: + ----------- + data_file : str + Path to the data file containing projection data + script_file : str + Path where the gnuplot script will be written + output_image : str + Name of the output image file (default: 'heatmap.png') + """ + script_content = f"""#!/usr/bin/gnuplot +# Gnuplot script to visualize plane projection data as a heatmap +# Usage: gnuplot {script_file} + +set terminal pngcairo enhanced size 800,600 font 'Arial,12' +set output '{output_image}' + +# Set color palette +set palette defined (0 "blue", 0.5 "white", 1 "red") +set cblabel "g: Distance from plane (Å)" + +# Labels +set xlabel "e: First plane coordinate (Å)" +set ylabel "f: Second plane coordinate (Å)" +set title "Atomic Projections on Plane - Heatmap" + +# Grid and style +set grid +set size ratio -1 # Equal aspect ratio for x and y axes + +# Plot the data +# Column 1: e, Column 2: f, Column 3: g (color) +plot '{data_file}' using 1:2:3 with points pt 7 ps 2 palette notitle + +# Alternative: If you want to see point labels (atom numbers), uncomment: +# plot '{data_file}' using 1:2:3:(sprintf("%d", \\$0+1)) with labels point pt 7 offset char 1,1 palette notitle + +print "Plot saved to {output_image}" +""" + + with open(script_file, 'w') as f: + f.write(script_content) + + # Make the script executable (Unix-like systems) + import os + try: + os.chmod(script_file, 0o755) + except: + pass # Ignore if chmod fails (e.g., on Windows) + + def calculate_plane_projections(structure, atom_indices, direction_vector, average_position): """ Calculate orthogonal projections of atoms onto a plane perpendicular to @@ -290,6 +344,8 @@ def main(): 'or [h,k,l] (Miller indices)') parser.add_argument('-o', '--output', type=str, help='Output file for plane projection data (3 columns: e, f, g)') + parser.add_argument('--gnuplot', action='store_true', + help='Generate gnuplot script for heatmap visualization (requires -o)') args = parser.parse_args() @@ -375,6 +431,24 @@ def main(): print(f" Columns: e, f, g") print(f" e, f: 2D coordinates of atom projection on plane") print(f" g: signed distance from plane (average_position - atom_distance)") + + # Generate gnuplot script if requested + if args.gnuplot: + import os + # Determine output paths + base_name = os.path.splitext(args.output)[0] + script_file = f"{base_name}.gnuplot" + image_file = f"{base_name}_heatmap.png" + + generate_gnuplot_script(args.output, script_file, image_file) + + print() + print(f"Gnuplot script generated: {script_file}") + print(f"To create the heatmap, run: gnuplot {script_file}") + print(f"Output image will be: {image_file}") + elif args.gnuplot: + print() + print("Warning: --gnuplot flag requires -o/--output to be specified. Ignoring.") return 0 From 21fd0f40ea64c5f9c55154d7048aca1ac1a9b9ba Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 15 Nov 2025 10:48:34 +0000 Subject: [PATCH 07/17] Fix gnuplot script: correct escape sequence and use RGB gradient Co-authored-by: acammarat <124535593+acammarat@users.noreply.github.com> --- var/avgpos/avgpos.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/var/avgpos/avgpos.py b/var/avgpos/avgpos.py index 6666488..5e803b4 100755 --- a/var/avgpos/avgpos.py +++ b/var/avgpos/avgpos.py @@ -212,8 +212,8 @@ def generate_gnuplot_script(data_file, script_file, output_image='heatmap.png'): set terminal pngcairo enhanced size 800,600 font 'Arial,12' set output '{output_image}' -# Set color palette -set palette defined (0 "blue", 0.5 "white", 1 "red") +# Set RGB gradient color palette +set palette rgbformulae 33,13,10 set cblabel "g: Distance from plane (Å)" # Labels @@ -230,7 +230,7 @@ def generate_gnuplot_script(data_file, script_file, output_image='heatmap.png'): plot '{data_file}' using 1:2:3 with points pt 7 ps 2 palette notitle # Alternative: If you want to see point labels (atom numbers), uncomment: -# plot '{data_file}' using 1:2:3:(sprintf("%d", \\$0+1)) with labels point pt 7 offset char 1,1 palette notitle +# plot '{data_file}' using 1:2:3:(sprintf("%d", $0+1)) with labels point pt 7 offset char 1,1 palette notitle print "Plot saved to {output_image}" """ From 54327ca20b6893f3daea44ac4703975fccbe669e Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 15 Nov 2025 11:02:52 +0000 Subject: [PATCH 08/17] Add atom labels feature with element type and unique ID Co-authored-by: acammarat <124535593+acammarat@users.noreply.github.com> --- var/avgpos/README.md | 14 ++++- var/avgpos/avgpos.py | 125 +++++++++++++++++++++++++++++++++++++------ 2 files changed, 121 insertions(+), 18 deletions(-) diff --git a/var/avgpos/README.md b/var/avgpos/README.md index 73a4b5a..ad954fb 100644 --- a/var/avgpos/README.md +++ b/var/avgpos/README.md @@ -53,6 +53,7 @@ python3 avgpos.py - Miller indices: `[h,k,l]` (e.g., `[1,1,0]`) - `-o, --output`: Output file for plane projection data (optional) - `--gnuplot`: Generate gnuplot script for heatmap visualization (requires `-o`) +- `--labels`: Include atom labels (element+ID, e.g., Ti1, O2) in output and gnuplot visualization (requires `-o`) ### Examples @@ -87,6 +88,13 @@ Calculate average position and generate gnuplot heatmap script: # Then run: gnuplot projections.gnuplot ``` +Calculate average position with atom labels and generate labeled heatmap: +```bash +./avgpos.py POSCAR -s Se -d z -o projections.dat --gnuplot --labels +# Then run: gnuplot projections.gnuplot +# Labels will show atom type and ID (e.g., Se1, Se2, Ti1) +``` + ## Output ### Standard Output @@ -101,10 +109,11 @@ The tool displays: ### Plane Projection Output File (optional) -When the `-o` option is specified, the tool generates a 3-column data file containing: +When the `-o` option is specified, the tool generates a data file containing: - **Column 1 (e)**: First coordinate of the atom's orthogonal projection onto the plane - **Column 2 (f)**: Second coordinate of the atom's orthogonal projection onto the plane - **Column 3 (g)**: Signed distance from the plane (average_position - atom_distance_along_direction) +- **Column 4 (label)**: Atom label with element type and unique ID (e.g., Ti1, O2) - only when `--labels` is used The plane is perpendicular to the specified direction vector and passes through the calculated average position. The e and f coordinates form an orthonormal 2D coordinate system in the plane. @@ -113,7 +122,8 @@ The plane is perpendicular to the specified direction vector and passes through When the `--gnuplot` flag is used along with `-o`, the tool generates a gnuplot script that creates a heatmap visualization of the plane projection data: - **Script file**: Named as `.gnuplot` - **Output image**: Named as `_heatmap.png` -- The heatmap uses the e and f coordinates as x and y positions, with g values represented by color +- The heatmap uses the e and f coordinates as x and y positions, with g values represented by an RGB gradient color +- When `--labels` is also used, atom labels (element+ID) are displayed on the plot - To generate the plot, run: `gnuplot ` **Requirements**: Gnuplot must be installed on your system to generate the visualization. diff --git a/var/avgpos/avgpos.py b/var/avgpos/avgpos.py index 5e803b4..09da4fa 100755 --- a/var/avgpos/avgpos.py +++ b/var/avgpos/avgpos.py @@ -192,7 +192,44 @@ def calculate_average_position(structure, atom_indices, direction_vector): return average, std_dev, positions_along_dir -def generate_gnuplot_script(data_file, script_file, output_image='heatmap.png'): +def get_atom_labels(structure, atom_indices): + """ + Generate atom labels with element type and unique ID for selected atoms. + + Parameters: + ----------- + structure : dict + Structure dictionary from read_poscar + atom_indices : numpy.ndarray + Indices of atoms (0-based) + + Returns: + -------- + list : List of atom labels (e.g., ['Ti1', 'Ti2', 'O1', 'O2']) + """ + labels = [] + + # Create a mapping of atom index to element type + idx = 0 + atom_to_element = [] + for i, element in enumerate(structure['elements']): + count = structure['atom_counts'][i] + atom_to_element.extend([element] * count) + idx += count + + # Count occurrences of each element type among selected atoms + element_counters = {} + for atom_idx in atom_indices: + element = atom_to_element[atom_idx] + if element not in element_counters: + element_counters[element] = 0 + element_counters[element] += 1 + labels.append(f"{element}{element_counters[element]}") + + return labels + + +def generate_gnuplot_script(data_file, script_file, output_image='heatmap.png', labels_file=None): """ Generate a gnuplot script to plot the plane projection data as a heatmap. @@ -204,8 +241,40 @@ def generate_gnuplot_script(data_file, script_file, output_image='heatmap.png'): Path where the gnuplot script will be written output_image : str Name of the output image file (default: 'heatmap.png') + labels_file : str, optional + Path to the file containing atom labels """ - script_content = f"""#!/usr/bin/gnuplot + if labels_file: + # Plot with labels + script_content = f"""#!/usr/bin/gnuplot +# Gnuplot script to visualize plane projection data as a heatmap with atom labels +# Usage: gnuplot {script_file} + +set terminal pngcairo enhanced size 800,600 font 'Arial,12' +set output '{output_image}' + +# Set RGB gradient color palette +set palette rgbformulae 33,13,10 +set cblabel "g: Distance from plane (Å)" + +# Labels +set xlabel "e: First plane coordinate (Å)" +set ylabel "f: Second plane coordinate (Å)" +set title "Atomic Projections on Plane - Heatmap with Labels" + +# Grid and style +set grid +set size ratio -1 # Equal aspect ratio for x and y axes + +# Plot the data with labels +# Column 1: e, Column 2: f, Column 3: g (color), Column 4: label +plot '{data_file}' using 1:2:3:4 with labels point pt 7 ps 2 offset char 1,1 palette + +print "Plot saved to {output_image}" +""" + else: + # Plot without labels + script_content = f"""#!/usr/bin/gnuplot # Gnuplot script to visualize plane projection data as a heatmap # Usage: gnuplot {script_file} @@ -229,8 +298,7 @@ def generate_gnuplot_script(data_file, script_file, output_image='heatmap.png'): # Column 1: e, Column 2: f, Column 3: g (color) plot '{data_file}' using 1:2:3 with points pt 7 ps 2 palette notitle -# Alternative: If you want to see point labels (atom numbers), uncomment: -# plot '{data_file}' using 1:2:3:(sprintf("%d", $0+1)) with labels point pt 7 offset char 1,1 palette notitle +# Alternative: To plot with atom labels, use the --labels option when generating the script print "Plot saved to {output_image}" """ @@ -346,6 +414,8 @@ def main(): help='Output file for plane projection data (3 columns: e, f, g)') parser.add_argument('--gnuplot', action='store_true', help='Generate gnuplot script for heatmap visualization (requires -o)') + parser.add_argument('--labels', action='store_true', + help='Include atom labels (element+ID) in output and gnuplot script (requires -o)') args = parser.parse_args() @@ -419,16 +489,35 @@ def main(): structure, atom_indices, direction_vector, average ) - # Write to file - np.savetxt(args.output, projections, fmt='%.6f', - header='e f g\nProjections onto plane perpendicular to direction vector\n' - 'e, f: 2D coordinates on plane\n' - 'g: average_position - distance_from_plane', - comments='# ') + # Get atom labels if requested + if args.labels: + labels = get_atom_labels(structure, atom_indices) + # Create a combined array with projections and labels + # Save with labels as 4th column + with open(args.output, 'w') as f: + f.write('# e f g label\n') + f.write('# Projections onto plane perpendicular to direction vector\n') + f.write('# e, f: 2D coordinates on plane\n') + f.write('# g: average_position - distance_from_plane\n') + f.write('# label: atom type and ID (e.g., Ti1, O2)\n') + for i, label in enumerate(labels): + f.write(f"{projections[i, 0]:.6f} {projections[i, 1]:.6f} {projections[i, 2]:.6f} {label}\n") + + print() + print(f"Plane projection data with labels written to: {args.output}") + print(f" Columns: e, f, g, label") + else: + # Write to file without labels + np.savetxt(args.output, projections, fmt='%.6f', + header='e f g\nProjections onto plane perpendicular to direction vector\n' + 'e, f: 2D coordinates on plane\n' + 'g: average_position - distance_from_plane', + comments='# ') + + print() + print(f"Plane projection data written to: {args.output}") + print(f" Columns: e, f, g") - print() - print(f"Plane projection data written to: {args.output}") - print(f" Columns: e, f, g") print(f" e, f: 2D coordinates of atom projection on plane") print(f" g: signed distance from plane (average_position - atom_distance)") @@ -440,15 +529,19 @@ def main(): script_file = f"{base_name}.gnuplot" image_file = f"{base_name}_heatmap.png" - generate_gnuplot_script(args.output, script_file, image_file) + # Pass labels_file parameter if labels were requested + labels_file = args.output if args.labels else None + generate_gnuplot_script(args.output, script_file, image_file, labels_file) print() print(f"Gnuplot script generated: {script_file}") print(f"To create the heatmap, run: gnuplot {script_file}") print(f"Output image will be: {image_file}") - elif args.gnuplot: + if args.labels: + print(f" (with atom labels)") + elif args.gnuplot or args.labels: print() - print("Warning: --gnuplot flag requires -o/--output to be specified. Ignoring.") + print("Warning: --gnuplot and --labels flags require -o/--output to be specified. Ignoring.") return 0 From 542769575d529d72781d9e46a9637c47cbf627f3 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 15 Nov 2025 11:26:25 +0000 Subject: [PATCH 09/17] Fix atom labels to use POSCAR file indices and gnuplot range error Co-authored-by: acammarat <124535593+acammarat@users.noreply.github.com> --- var/avgpos/avgpos.py | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/var/avgpos/avgpos.py b/var/avgpos/avgpos.py index 09da4fa..1522c99 100755 --- a/var/avgpos/avgpos.py +++ b/var/avgpos/avgpos.py @@ -194,7 +194,7 @@ def calculate_average_position(structure, atom_indices, direction_vector): def get_atom_labels(structure, atom_indices): """ - Generate atom labels with element type and unique ID for selected atoms. + Generate atom labels with element type and POSCAR file ID for selected atoms. Parameters: ----------- @@ -205,7 +205,8 @@ def get_atom_labels(structure, atom_indices): Returns: -------- - list : List of atom labels (e.g., ['Ti1', 'Ti2', 'O1', 'O2']) + list : List of atom labels (e.g., ['Ti1', 'Ti2', 'O3', 'O4']) + where the number corresponds to the atom's position in the POSCAR file (1-based) """ labels = [] @@ -217,14 +218,11 @@ def get_atom_labels(structure, atom_indices): atom_to_element.extend([element] * count) idx += count - # Count occurrences of each element type among selected atoms - element_counters = {} + # Use the POSCAR file index (1-based) as the atom ID for atom_idx in atom_indices: element = atom_to_element[atom_idx] - if element not in element_counters: - element_counters[element] = 0 - element_counters[element] += 1 - labels.append(f"{element}{element_counters[element]}") + # atom_idx is 0-based, so add 1 to get POSCAR file position + labels.append(f"{element}{atom_idx + 1}") return labels @@ -266,6 +264,9 @@ def generate_gnuplot_script(data_file, script_file, output_image='heatmap.png', set grid set size ratio -1 # Equal aspect ratio for x and y axes +# Set autoscale to ensure proper range calculation +set autoscale + # Plot the data with labels # Column 1: e, Column 2: f, Column 3: g (color), Column 4: label plot '{data_file}' using 1:2:3:4 with labels point pt 7 ps 2 offset char 1,1 palette From 9e7a735c3446de6c112151bc23e5c0026208b174 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 15 Nov 2025 11:53:42 +0000 Subject: [PATCH 10/17] Replace gnuplot with matplotlib for heatmap visualization Co-authored-by: acammarat <124535593+acammarat@users.noreply.github.com> --- var/avgpos/README.md | 31 +++++---- var/avgpos/avgpos.py | 134 ++++++++++++++++++------------------ var/avgpos/requirements.txt | 1 + 3 files changed, 85 insertions(+), 81 deletions(-) diff --git a/var/avgpos/README.md b/var/avgpos/README.md index ad954fb..a4e84e6 100644 --- a/var/avgpos/README.md +++ b/var/avgpos/README.md @@ -18,6 +18,7 @@ A tool to calculate the average position and standard deviation of selected atom - Python 3.6 or higher - NumPy +- Matplotlib (for generating heatmap visualizations) ## Installation @@ -52,8 +53,8 @@ python3 avgpos.py - Lattice vectors: `a`, `b`, `c` - Miller indices: `[h,k,l]` (e.g., `[1,1,0]`) - `-o, --output`: Output file for plane projection data (optional) -- `--gnuplot`: Generate gnuplot script for heatmap visualization (requires `-o`) -- `--labels`: Include atom labels (element+ID, e.g., Ti1, O2) in output and gnuplot visualization (requires `-o`) +- `--plot`: Generate Python matplotlib script for heatmap visualization (requires `-o`) +- `--labels`: Include atom labels (element+ID, e.g., Se2, Ti4) in output and plot (requires `-o`) ### Examples @@ -82,17 +83,17 @@ Calculate average position and export plane projection data: ./avgpos.py POSCAR -s Se -d z -o projections.dat ``` -Calculate average position and generate gnuplot heatmap script: +Calculate average position and generate matplotlib heatmap script: ```bash -./avgpos.py POSCAR -s Se -d z -o projections.dat --gnuplot -# Then run: gnuplot projections.gnuplot +./avgpos.py POSCAR -s Se -d z -o projections.dat --plot +# Then run: python3 projections_plot.py ``` Calculate average position with atom labels and generate labeled heatmap: ```bash -./avgpos.py POSCAR -s Se -d z -o projections.dat --gnuplot --labels -# Then run: gnuplot projections.gnuplot -# Labels will show atom type and ID (e.g., Se1, Se2, Ti1) +./avgpos.py POSCAR -s Se -d z -o projections.dat --plot --labels +# Then run: python3 projections_plot.py +# Labels will show atom type and POSCAR file ID (e.g., Se2, Se3, Ti1) ``` ## Output @@ -117,16 +118,16 @@ When the `-o` option is specified, the tool generates a data file containing: The plane is perpendicular to the specified direction vector and passes through the calculated average position. The e and f coordinates form an orthonormal 2D coordinate system in the plane. -### Gnuplot Script (optional) +### Matplotlib Plotting Script (optional) -When the `--gnuplot` flag is used along with `-o`, the tool generates a gnuplot script that creates a heatmap visualization of the plane projection data: -- **Script file**: Named as `.gnuplot` +When the `--plot` flag is used along with `-o`, the tool generates a Python script using matplotlib that creates a heatmap visualization of the plane projection data: +- **Script file**: Named as `_plot.py` - **Output image**: Named as `_heatmap.png` -- The heatmap uses the e and f coordinates as x and y positions, with g values represented by an RGB gradient color -- When `--labels` is also used, atom labels (element+ID) are displayed on the plot -- To generate the plot, run: `gnuplot ` +- The heatmap uses the e and f coordinates as x and y positions, with g values represented by a color gradient +- When `--labels` is also used, atom labels (element+POSCAR file ID) are displayed on the plot +- To generate the plot, run: `python3 ` -**Requirements**: Gnuplot must be installed on your system to generate the visualization. +**Requirements**: Matplotlib must be installed on your system to generate the visualization. ## Example Output diff --git a/var/avgpos/avgpos.py b/var/avgpos/avgpos.py index 1522c99..1fd16de 100755 --- a/var/avgpos/avgpos.py +++ b/var/avgpos/avgpos.py @@ -227,81 +227,84 @@ def get_atom_labels(structure, atom_indices): return labels -def generate_gnuplot_script(data_file, script_file, output_image='heatmap.png', labels_file=None): +def generate_plot_script(data_file, script_file, output_image='heatmap.png', with_labels=False): """ - Generate a gnuplot script to plot the plane projection data as a heatmap. + Generate a Python script using matplotlib to plot the plane projection data as a heatmap. Parameters: ----------- data_file : str Path to the data file containing projection data script_file : str - Path where the gnuplot script will be written + Path where the Python plotting script will be written output_image : str Name of the output image file (default: 'heatmap.png') - labels_file : str, optional - Path to the file containing atom labels + with_labels : bool + Whether to include atom labels in the plot """ - if labels_file: - # Plot with labels - script_content = f"""#!/usr/bin/gnuplot -# Gnuplot script to visualize plane projection data as a heatmap with atom labels -# Usage: gnuplot {script_file} + script_content = f"""#!/usr/bin/env python3 +\"\"\" +Matplotlib script to visualize plane projection data as a heatmap. +Generated automatically by avgpos tool. -set terminal pngcairo enhanced size 800,600 font 'Arial,12' -set output '{output_image}' +Usage: python3 {script_file} +\"\"\" -# Set RGB gradient color palette -set palette rgbformulae 33,13,10 -set cblabel "g: Distance from plane (Å)" - -# Labels -set xlabel "e: First plane coordinate (Å)" -set ylabel "f: Second plane coordinate (Å)" -set title "Atomic Projections on Plane - Heatmap with Labels" - -# Grid and style -set grid -set size ratio -1 # Equal aspect ratio for x and y axes +import numpy as np +import matplotlib.pyplot as plt +from matplotlib import cm -# Set autoscale to ensure proper range calculation -set autoscale +# Read data from file +data = np.loadtxt('{data_file}', dtype=str) -# Plot the data with labels -# Column 1: e, Column 2: f, Column 3: g (color), Column 4: label -plot '{data_file}' using 1:2:3:4 with labels point pt 7 ps 2 offset char 1,1 palette +# Extract coordinates and g values +e = data[:, 0].astype(float) +f = data[:, 1].astype(float) +g = data[:, 2].astype(float) -print "Plot saved to {output_image}" -""" - else: - # Plot without labels - script_content = f"""#!/usr/bin/gnuplot -# Gnuplot script to visualize plane projection data as a heatmap -# Usage: gnuplot {script_file} +# Create figure and axis +fig, ax = plt.subplots(figsize=(10, 8)) -set terminal pngcairo enhanced size 800,600 font 'Arial,12' -set output '{output_image}' +# Create scatter plot with color mapping +scatter = ax.scatter(e, f, c=g, cmap='coolwarm', s=200, edgecolors='black', linewidths=1.5) -# Set RGB gradient color palette -set palette rgbformulae 33,13,10 -set cblabel "g: Distance from plane (Å)" +# Add colorbar +cbar = plt.colorbar(scatter, ax=ax) +cbar.set_label('g: Distance from plane (Å)', fontsize=12) -# Labels -set xlabel "e: First plane coordinate (Å)" -set ylabel "f: Second plane coordinate (Å)" -set title "Atomic Projections on Plane - Heatmap" +# Set labels and title +ax.set_xlabel('e: First plane coordinate (Å)', fontsize=12) +ax.set_ylabel('f: Second plane coordinate (Å)', fontsize=12) +""" + + if with_labels: + script_content += f"""ax.set_title('Atomic Projections on Plane - Heatmap with Labels', fontsize=14) -# Grid and style -set grid -set size ratio -1 # Equal aspect ratio for x and y axes +# Add atom labels +labels = data[:, 3] +for i in range(len(e)): + ax.annotate(labels[i], (e[i], f[i]), + xytext=(5, 5), textcoords='offset points', + fontsize=10, fontweight='bold') +""" + else: + script_content += """ax.set_title('Atomic Projections on Plane - Heatmap', fontsize=14) +""" + + script_content += f""" +# Add grid +ax.grid(True, alpha=0.3) -# Plot the data -# Column 1: e, Column 2: f, Column 3: g (color) -plot '{data_file}' using 1:2:3 with points pt 7 ps 2 palette notitle +# Set equal aspect ratio +ax.set_aspect('equal', adjustable='box') -# Alternative: To plot with atom labels, use the --labels option when generating the script +# Save figure +plt.tight_layout() +plt.savefig('{output_image}', dpi=150, bbox_inches='tight') +print(f"Plot saved to {output_image}") -print "Plot saved to {output_image}" +# Optionally display the plot (comment out if running headless) +# plt.show() """ with open(script_file, 'w') as f: @@ -413,10 +416,10 @@ def main(): 'or [h,k,l] (Miller indices)') parser.add_argument('-o', '--output', type=str, help='Output file for plane projection data (3 columns: e, f, g)') - parser.add_argument('--gnuplot', action='store_true', - help='Generate gnuplot script for heatmap visualization (requires -o)') + parser.add_argument('--plot', action='store_true', + help='Generate Python matplotlib script for heatmap visualization (requires -o)') parser.add_argument('--labels', action='store_true', - help='Include atom labels (element+ID) in output and gnuplot script (requires -o)') + help='Include atom labels (element+ID) in output and plot (requires -o)') args = parser.parse_args() @@ -522,27 +525,26 @@ def main(): print(f" e, f: 2D coordinates of atom projection on plane") print(f" g: signed distance from plane (average_position - atom_distance)") - # Generate gnuplot script if requested - if args.gnuplot: + # Generate matplotlib plot script if requested + if args.plot: import os # Determine output paths base_name = os.path.splitext(args.output)[0] - script_file = f"{base_name}.gnuplot" + script_file = f"{base_name}_plot.py" image_file = f"{base_name}_heatmap.png" - # Pass labels_file parameter if labels were requested - labels_file = args.output if args.labels else None - generate_gnuplot_script(args.output, script_file, image_file, labels_file) + # Generate the plotting script + generate_plot_script(args.output, script_file, image_file, args.labels) print() - print(f"Gnuplot script generated: {script_file}") - print(f"To create the heatmap, run: gnuplot {script_file}") + print(f"Matplotlib plotting script generated: {script_file}") + print(f"To create the heatmap, run: python3 {script_file}") print(f"Output image will be: {image_file}") if args.labels: print(f" (with atom labels)") - elif args.gnuplot or args.labels: + elif args.plot or args.labels: print() - print("Warning: --gnuplot and --labels flags require -o/--output to be specified. Ignoring.") + print("Warning: --plot and --labels flags require -o/--output to be specified. Ignoring.") return 0 diff --git a/var/avgpos/requirements.txt b/var/avgpos/requirements.txt index 5f3f3a2..830bb41 100644 --- a/var/avgpos/requirements.txt +++ b/var/avgpos/requirements.txt @@ -1 +1,2 @@ numpy>=1.19.0 +matplotlib>=3.0.0 From 1621edcf3e6ba7af9083ea94e049714e48485f77 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 15 Nov 2025 12:06:20 +0000 Subject: [PATCH 11/17] Add smooth interpolated heatmap using RBF interpolation Co-authored-by: acammarat <124535593+acammarat@users.noreply.github.com> --- var/avgpos/README.md | 11 ++++++---- var/avgpos/avgpos.py | 42 +++++++++++++++++++++++++++++++++---- var/avgpos/requirements.txt | 1 + 3 files changed, 46 insertions(+), 8 deletions(-) diff --git a/var/avgpos/README.md b/var/avgpos/README.md index a4e84e6..01052f7 100644 --- a/var/avgpos/README.md +++ b/var/avgpos/README.md @@ -19,6 +19,7 @@ A tool to calculate the average position and standard deviation of selected atom - Python 3.6 or higher - NumPy - Matplotlib (for generating heatmap visualizations) +- SciPy (for interpolation in smooth heatmaps) ## Installation @@ -120,14 +121,16 @@ The plane is perpendicular to the specified direction vector and passes through ### Matplotlib Plotting Script (optional) -When the `--plot` flag is used along with `-o`, the tool generates a Python script using matplotlib that creates a heatmap visualization of the plane projection data: +When the `--plot` flag is used along with `-o`, the tool generates a Python script using matplotlib that creates a smooth interpolated heatmap visualization of the plane projection data: - **Script file**: Named as `_plot.py` - **Output image**: Named as `_heatmap.png` -- The heatmap uses the e and f coordinates as x and y positions, with g values represented by a color gradient -- When `--labels` is also used, atom labels (element+POSCAR file ID) are displayed on the plot +- The heatmap uses Radial Basis Function (RBF) interpolation to create a smooth surface covering the entire e,f range +- g values are represented by a color gradient (coolwarm colormap) +- Original data points are overlaid as black dots for reference +- When `--labels` is also used, atom labels (element+POSCAR file ID) are annotated on the plot - To generate the plot, run: `python3 ` -**Requirements**: Matplotlib must be installed on your system to generate the visualization. +**Requirements**: Matplotlib and SciPy must be installed on your system to generate the visualization. ## Example Output diff --git a/var/avgpos/avgpos.py b/var/avgpos/avgpos.py index 1fd16de..d7df095 100755 --- a/var/avgpos/avgpos.py +++ b/var/avgpos/avgpos.py @@ -244,7 +244,7 @@ def generate_plot_script(data_file, script_file, output_image='heatmap.png', wit """ script_content = f"""#!/usr/bin/env python3 \"\"\" -Matplotlib script to visualize plane projection data as a heatmap. +Matplotlib script to visualize plane projection data as a smooth interpolated heatmap. Generated automatically by avgpos tool. Usage: python3 {script_file} @@ -253,6 +253,7 @@ def generate_plot_script(data_file, script_file, output_image='heatmap.png', wit import numpy as np import matplotlib.pyplot as plt from matplotlib import cm +from scipy.interpolate import Rbf # Read data from file data = np.loadtxt('{data_file}', dtype=str) @@ -262,14 +263,47 @@ def generate_plot_script(data_file, script_file, output_image='heatmap.png', wit f = data[:, 1].astype(float) g = data[:, 2].astype(float) +# Create a regular grid for interpolation +# Determine the range of e and f with some padding +e_min, e_max = e.min(), e.max() +f_min, f_max = f.min(), f.max() + +# Add padding to ensure coverage (10% on each side) +e_range = e_max - e_min +f_range = f_max - f_min +padding_e = max(0.1 * e_range, 0.5) if e_range > 0 else 0.5 +padding_f = max(0.1 * f_range, 0.5) if f_range > 0 else 0.5 + +e_grid = np.linspace(e_min - padding_e, e_max + padding_e, 200) +f_grid = np.linspace(f_min - padding_f, f_max + padding_f, 200) +e_mesh, f_mesh = np.meshgrid(e_grid, f_grid) + +# Use Radial Basis Function interpolation which handles duplicate points well +# Try multiquadric first (smooth), fall back to linear if needed +try: + rbf = Rbf(e, f, g, function='multiquadric', smooth=0.1) + g_interp = rbf(e_mesh, f_mesh) +except: + # Fall back to thin_plate interpolation + try: + rbf = Rbf(e, f, g, function='thin_plate', smooth=0.1) + g_interp = rbf(e_mesh, f_mesh) + except: + # Last resort: use linear + rbf = Rbf(e, f, g, function='linear') + g_interp = rbf(e_mesh, f_mesh) + # Create figure and axis fig, ax = plt.subplots(figsize=(10, 8)) -# Create scatter plot with color mapping -scatter = ax.scatter(e, f, c=g, cmap='coolwarm', s=200, edgecolors='black', linewidths=1.5) +# Create smooth heatmap using pcolormesh +heatmap = ax.pcolormesh(e_mesh, f_mesh, g_interp, cmap='coolwarm', shading='auto') + +# Overlay the original data points +ax.scatter(e, f, c='black', s=50, edgecolors='white', linewidths=1, zorder=10, alpha=0.7) # Add colorbar -cbar = plt.colorbar(scatter, ax=ax) +cbar = plt.colorbar(heatmap, ax=ax) cbar.set_label('g: Distance from plane (Å)', fontsize=12) # Set labels and title diff --git a/var/avgpos/requirements.txt b/var/avgpos/requirements.txt index 830bb41..db4d647 100644 --- a/var/avgpos/requirements.txt +++ b/var/avgpos/requirements.txt @@ -1,2 +1,3 @@ numpy>=1.19.0 matplotlib>=3.0.0 +scipy>=1.5.0 From 8073ce79b85a4bd2cd653eb2c6923396a0a8531a Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 15 Nov 2025 12:20:50 +0000 Subject: [PATCH 12/17] Update heatmap: exact atomic values, jet colormap, simplified labels Co-authored-by: acammarat <124535593+acammarat@users.noreply.github.com> --- var/avgpos/avgpos.py | 38 ++++++++++++++++++-------------------- 1 file changed, 18 insertions(+), 20 deletions(-) diff --git a/var/avgpos/avgpos.py b/var/avgpos/avgpos.py index d7df095..74d71ac 100755 --- a/var/avgpos/avgpos.py +++ b/var/avgpos/avgpos.py @@ -278,51 +278,49 @@ def generate_plot_script(data_file, script_file, output_image='heatmap.png', wit f_grid = np.linspace(f_min - padding_f, f_max + padding_f, 200) e_mesh, f_mesh = np.meshgrid(e_grid, f_grid) -# Use Radial Basis Function interpolation which handles duplicate points well -# Try multiquadric first (smooth), fall back to linear if needed +# Use Radial Basis Function interpolation with minimal smoothing +# This passes very close to data points while handling duplicates try: - rbf = Rbf(e, f, g, function='multiquadric', smooth=0.1) + rbf = Rbf(e, f, g, function='thin_plate', smooth=0.001) g_interp = rbf(e_mesh, f_mesh) except: - # Fall back to thin_plate interpolation + # Fall back to multiquadric if thin_plate fails try: - rbf = Rbf(e, f, g, function='thin_plate', smooth=0.1) + rbf = Rbf(e, f, g, function='multiquadric', smooth=0.01) g_interp = rbf(e_mesh, f_mesh) except: - # Last resort: use linear - rbf = Rbf(e, f, g, function='linear') + # Last resort: use linear with small smoothing + rbf = Rbf(e, f, g, function='linear', smooth=0.01) g_interp = rbf(e_mesh, f_mesh) # Create figure and axis fig, ax = plt.subplots(figsize=(10, 8)) -# Create smooth heatmap using pcolormesh -heatmap = ax.pcolormesh(e_mesh, f_mesh, g_interp, cmap='coolwarm', shading='auto') +# Create smooth heatmap using pcolormesh with RGB gradient (jet colormap) +heatmap = ax.pcolormesh(e_mesh, f_mesh, g_interp, cmap='jet', shading='auto') -# Overlay the original data points -ax.scatter(e, f, c='black', s=50, edgecolors='white', linewidths=1, zorder=10, alpha=0.7) +# Overlay the original data points with their EXACT g values colored +# This ensures atomic positions correspond to the real g value +scatter = ax.scatter(e, f, c=g, cmap='jet', s=150, edgecolors='black', linewidths=2, zorder=10, vmin=g_interp.min(), vmax=g_interp.max()) # Add colorbar cbar = plt.colorbar(heatmap, ax=ax) cbar.set_label('g: Distance from plane (Å)', fontsize=12) -# Set labels and title -ax.set_xlabel('e: First plane coordinate (Å)', fontsize=12) -ax.set_ylabel('f: Second plane coordinate (Å)', fontsize=12) +# Set simplified labels (no title) +ax.set_xlabel('x', fontsize=12) +ax.set_ylabel('y', fontsize=12) """ if with_labels: - script_content += f"""ax.set_title('Atomic Projections on Plane - Heatmap with Labels', fontsize=14) - + script_content += f""" # Add atom labels labels = data[:, 3] for i in range(len(e)): ax.annotate(labels[i], (e[i], f[i]), xytext=(5, 5), textcoords='offset points', - fontsize=10, fontweight='bold') -""" - else: - script_content += """ax.set_title('Atomic Projections on Plane - Heatmap', fontsize=14) + fontsize=10, fontweight='bold', color='black', + bbox=dict(boxstyle='round,pad=0.3', facecolor='white', edgecolor='black', alpha=0.7)) """ script_content += f""" From ee9ac57bcdc1a027760d3c47bb2c3cbe788ea2d1 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 15 Nov 2025 12:35:29 +0000 Subject: [PATCH 13/17] Fix color mapping and add replication feature for heatmaps Co-authored-by: acammarat <124535593+acammarat@users.noreply.github.com> --- var/avgpos/README.md | 9 ++++++ var/avgpos/avgpos.py | 66 ++++++++++++++++++++++++++++++++++++++------ 2 files changed, 67 insertions(+), 8 deletions(-) diff --git a/var/avgpos/README.md b/var/avgpos/README.md index 01052f7..f490e65 100644 --- a/var/avgpos/README.md +++ b/var/avgpos/README.md @@ -56,6 +56,8 @@ python3 avgpos.py - `-o, --output`: Output file for plane projection data (optional) - `--plot`: Generate Python matplotlib script for heatmap visualization (requires `-o`) - `--labels`: Include atom labels (element+ID, e.g., Se2, Ti4) in output and plot (requires `-o`) +- `--replicate`: Replicate the plot along e and f axes (format: "ne,nf", default: "1,1") + - Supports non-integer replication (e.g., "2.5,3" for 2.5x3 replication) ### Examples @@ -97,6 +99,13 @@ Calculate average position with atom labels and generate labeled heatmap: # Labels will show atom type and POSCAR file ID (e.g., Se2, Se3, Ti1) ``` +Generate heatmap with 2.5x3 replication along e and f axes: +```bash +./avgpos.py POSCAR -s Se -d z -o projections.dat --plot --replicate 2.5,3 +# Then run: python3 projections_plot.py +# Plot will show 2.5 replications along e-axis and 3 along f-axis +``` + ## Output ### Standard Output diff --git a/var/avgpos/avgpos.py b/var/avgpos/avgpos.py index 74d71ac..bdd6f07 100755 --- a/var/avgpos/avgpos.py +++ b/var/avgpos/avgpos.py @@ -227,7 +227,7 @@ def get_atom_labels(structure, atom_indices): return labels -def generate_plot_script(data_file, script_file, output_image='heatmap.png', with_labels=False): +def generate_plot_script(data_file, script_file, output_image='heatmap.png', with_labels=False, replicate=(1, 1)): """ Generate a Python script using matplotlib to plot the plane projection data as a heatmap. @@ -241,6 +241,8 @@ def generate_plot_script(data_file, script_file, output_image='heatmap.png', wit Name of the output image file (default: 'heatmap.png') with_labels : bool Whether to include atom labels in the plot + replicate : tuple + Number of replications along e and f axes (ne, nf) """ script_content = f"""#!/usr/bin/env python3 \"\"\" @@ -259,9 +261,39 @@ def generate_plot_script(data_file, script_file, output_image='heatmap.png', wit data = np.loadtxt('{data_file}', dtype=str) # Extract coordinates and g values -e = data[:, 0].astype(float) -f = data[:, 1].astype(float) -g = data[:, 2].astype(float) +e_orig = data[:, 0].astype(float) +f_orig = data[:, 1].astype(float) +g_orig = data[:, 2].astype(float) + +# Replication parameters +ne_rep, nf_rep = {replicate[0]}, {replicate[1]} + +# Replicate data along e and f axes +e_list, f_list, g_list = [], [], [] +e_range_orig = e_orig.max() - e_orig.min() if len(e_orig) > 1 else 1.0 +f_range_orig = f_orig.max() - f_orig.min() if len(f_orig) > 1 else 1.0 + +# Determine how many full and partial replications to make +ne_full = int(np.ceil(ne_rep)) +nf_full = int(np.ceil(nf_rep)) + +for ie in range(ne_full): + for jf in range(nf_full): + # Calculate if this replica is fully or partially included + e_factor = min(1.0, ne_rep - ie) if ie < ne_full - 1 else (ne_rep - ie) + f_factor = min(1.0, nf_rep - jf) if jf < nf_full - 1 else (nf_rep - jf) + + # Include this replica if it has non-zero contribution + if e_factor > 0 and f_factor > 0: + e_shift = ie * (e_range_orig + (e_orig.max() - e_orig.min())) + f_shift = jf * (f_range_orig + (f_orig.max() - f_orig.min())) + e_list.append(e_orig + e_shift) + f_list.append(f_orig + f_shift) + g_list.append(g_orig) + +e = np.concatenate(e_list) +f = np.concatenate(f_list) +g = np.concatenate(g_list) # Create a regular grid for interpolation # Determine the range of e and f with some padding @@ -293,15 +325,19 @@ def generate_plot_script(data_file, script_file, output_image='heatmap.png', wit rbf = Rbf(e, f, g, function='linear', smooth=0.01) g_interp = rbf(e_mesh, f_mesh) +# Determine color range from actual data values (not interpolated) +vmin, vmax = g.min(), g.max() + # Create figure and axis fig, ax = plt.subplots(figsize=(10, 8)) # Create smooth heatmap using pcolormesh with RGB gradient (jet colormap) -heatmap = ax.pcolormesh(e_mesh, f_mesh, g_interp, cmap='jet', shading='auto') +# Use the same vmin/vmax as the scatter plot for consistent colors +heatmap = ax.pcolormesh(e_mesh, f_mesh, g_interp, cmap='jet', shading='auto', vmin=vmin, vmax=vmax) # Overlay the original data points with their EXACT g values colored -# This ensures atomic positions correspond to the real g value -scatter = ax.scatter(e, f, c=g, cmap='jet', s=150, edgecolors='black', linewidths=2, zorder=10, vmin=g_interp.min(), vmax=g_interp.max()) +# This ensures atomic positions correspond to the real g value from the data file +scatter = ax.scatter(e, f, c=g, cmap='jet', s=150, edgecolors='black', linewidths=2, zorder=10, vmin=vmin, vmax=vmax) # Add colorbar cbar = plt.colorbar(heatmap, ax=ax) @@ -452,6 +488,8 @@ def main(): help='Generate Python matplotlib script for heatmap visualization (requires -o)') parser.add_argument('--labels', action='store_true', help='Include atom labels (element+ID) in output and plot (requires -o)') + parser.add_argument('--replicate', type=str, default='1,1', + help='Replicate the plot along e and f axes (format: "ne,nf", e.g., "2.5,3" for 2.5x3 replication)') args = parser.parse_args() @@ -565,8 +603,18 @@ def main(): script_file = f"{base_name}_plot.py" image_file = f"{base_name}_heatmap.png" + # Parse replication argument + try: + replicate_parts = args.replicate.split(',') + ne_rep = float(replicate_parts[0]) + nf_rep = float(replicate_parts[1]) if len(replicate_parts) > 1 else ne_rep + replicate = (ne_rep, nf_rep) + except (ValueError, IndexError): + print(f"Warning: Invalid replicate format '{args.replicate}'. Using default 1,1") + replicate = (1, 1) + # Generate the plotting script - generate_plot_script(args.output, script_file, image_file, args.labels) + generate_plot_script(args.output, script_file, image_file, args.labels, replicate) print() print(f"Matplotlib plotting script generated: {script_file}") @@ -574,6 +622,8 @@ def main(): print(f"Output image will be: {image_file}") if args.labels: print(f" (with atom labels)") + if replicate != (1, 1): + print(f" (with {replicate[0]}x{replicate[1]} replication)") elif args.plot or args.labels: print() print("Warning: --plot and --labels flags require -o/--output to be specified. Ignoring.") From 0e54168f5da527efb8097c479c1364774f13a9ee Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 15 Nov 2025 12:45:49 +0000 Subject: [PATCH 14/17] Fix replication with labels and improve interpolation exactness Co-authored-by: acammarat <124535593+acammarat@users.noreply.github.com> --- var/avgpos/avgpos.py | 44 +++++++++++++++++++++++++++----------------- 1 file changed, 27 insertions(+), 17 deletions(-) diff --git a/var/avgpos/avgpos.py b/var/avgpos/avgpos.py index bdd6f07..9f7c0f5 100755 --- a/var/avgpos/avgpos.py +++ b/var/avgpos/avgpos.py @@ -265,11 +265,16 @@ def generate_plot_script(data_file, script_file, output_image='heatmap.png', wit f_orig = data[:, 1].astype(float) g_orig = data[:, 2].astype(float) +# Extract labels if present (4th column) +has_labels = data.shape[1] > 3 +if has_labels: + labels_orig = data[:, 3] + # Replication parameters ne_rep, nf_rep = {replicate[0]}, {replicate[1]} # Replicate data along e and f axes -e_list, f_list, g_list = [], [], [] +e_list, f_list, g_list, labels_list = [], [], [], [] e_range_orig = e_orig.max() - e_orig.min() if len(e_orig) > 1 else 1.0 f_range_orig = f_orig.max() - f_orig.min() if len(f_orig) > 1 else 1.0 @@ -290,10 +295,14 @@ def generate_plot_script(data_file, script_file, output_image='heatmap.png', wit e_list.append(e_orig + e_shift) f_list.append(f_orig + f_shift) g_list.append(g_orig) + if has_labels: + labels_list.append(labels_orig) e = np.concatenate(e_list) f = np.concatenate(f_list) g = np.concatenate(g_list) +if has_labels: + labels = np.concatenate(labels_list) # Create a regular grid for interpolation # Determine the range of e and f with some padding @@ -310,19 +319,20 @@ def generate_plot_script(data_file, script_file, output_image='heatmap.png', wit f_grid = np.linspace(f_min - padding_f, f_max + padding_f, 200) e_mesh, f_mesh = np.meshgrid(e_grid, f_grid) -# Use Radial Basis Function interpolation with minimal smoothing -# This passes very close to data points while handling duplicates +# Use Radial Basis Function interpolation with very small smoothing +# This ensures interpolation passes extremely close to data points while handling duplicates +# smooth value is set to a tiny value to get nearly exact values at data points try: - rbf = Rbf(e, f, g, function='thin_plate', smooth=0.001) + rbf = Rbf(e, f, g, function='thin_plate', smooth=1e-10) g_interp = rbf(e_mesh, f_mesh) except: # Fall back to multiquadric if thin_plate fails try: - rbf = Rbf(e, f, g, function='multiquadric', smooth=0.01) + rbf = Rbf(e, f, g, function='multiquadric', smooth=1e-10) g_interp = rbf(e_mesh, f_mesh) except: # Last resort: use linear with small smoothing - rbf = Rbf(e, f, g, function='linear', smooth=0.01) + rbf = Rbf(e, f, g, function='linear', smooth=1e-8) g_interp = rbf(e_mesh, f_mesh) # Determine color range from actual data values (not interpolated) @@ -341,22 +351,22 @@ def generate_plot_script(data_file, script_file, output_image='heatmap.png', wit # Add colorbar cbar = plt.colorbar(heatmap, ax=ax) -cbar.set_label('g: Distance from plane (Å)', fontsize=12) +cbar.set_label('Distance from plane (Å)', fontsize=12) -# Set simplified labels (no title) -ax.set_xlabel('x', fontsize=12) -ax.set_ylabel('y', fontsize=12) +# Set axis labels with units +ax.set_xlabel('x (Å)', fontsize=12) +ax.set_ylabel('y (Å)', fontsize=12) """ if with_labels: script_content += f""" -# Add atom labels -labels = data[:, 3] -for i in range(len(e)): - ax.annotate(labels[i], (e[i], f[i]), - xytext=(5, 5), textcoords='offset points', - fontsize=10, fontweight='bold', color='black', - bbox=dict(boxstyle='round,pad=0.3', facecolor='white', edgecolor='black', alpha=0.7)) +# Add atom labels (already replicated above if needed) +if has_labels: + for i in range(len(e)): + ax.annotate(labels[i], (e[i], f[i]), + xytext=(5, 5), textcoords='offset points', + fontsize=10, fontweight='bold', color='black', + bbox=dict(boxstyle='round,pad=0.3', facecolor='white', edgecolor='black', alpha=0.7)) """ script_content += f""" From ebfd0257d7bd59792287ffeb9ff4da57533838b3 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 15 Nov 2025 14:18:25 +0000 Subject: [PATCH 15/17] Make colorbar height match plot size Co-authored-by: acammarat <124535593+acammarat@users.noreply.github.com> --- var/avgpos/__pycache__/avgpos.cpython-312.pyc | Bin 0 -> 25494 bytes var/avgpos/avgpos.py | 7 +++++-- 2 files changed, 5 insertions(+), 2 deletions(-) create mode 100644 var/avgpos/__pycache__/avgpos.cpython-312.pyc diff --git a/var/avgpos/__pycache__/avgpos.cpython-312.pyc b/var/avgpos/__pycache__/avgpos.cpython-312.pyc new file mode 100644 index 0000000000000000000000000000000000000000..4f1fe703db8a4feafe287fefd7c62c7e944462f2 GIT binary patch literal 25494 zcmdUXX>c4zc4qZ`;%eLnfx}14GrNQ{!qkDtYae95fG(~@yPzM 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+350,10 @@ def generate_plot_script(data_file, script_file, output_image='heatmap.png', wit # This ensures atomic positions correspond to the real g value from the data file scatter = ax.scatter(e, f, c=g, cmap='jet', s=150, edgecolors='black', linewidths=2, zorder=10, vmin=vmin, vmax=vmax) -# Add colorbar -cbar = plt.colorbar(heatmap, ax=ax) +# Add colorbar with height matching the plot +divider = make_axes_locatable(ax) +cax = divider.append_axes("right", size="5%", pad=0.1) +cbar = plt.colorbar(heatmap, cax=cax) cbar.set_label('Distance from plane (Å)', fontsize=12) # Set axis labels with units From 58f744360516c99495c8834b53c326c5ff080c53 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 15 Nov 2025 14:35:20 +0000 Subject: [PATCH 16/17] Add --no-circles option to hide atom position markers Co-authored-by: acammarat <124535593+acammarat@users.noreply.github.com> --- .gitignore | 6 ++++++ var/avgpos/README.md | 8 +++++++ var/avgpos/__pycache__/avgpos.cpython-312.pyc | Bin 25494 -> 0 bytes var/avgpos/avgpos.py | 20 ++++++++++++++---- 4 files changed, 30 insertions(+), 4 deletions(-) create mode 100644 .gitignore delete mode 100644 var/avgpos/__pycache__/avgpos.cpython-312.pyc diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..7ce23c3 --- /dev/null +++ b/.gitignore @@ -0,0 +1,6 @@ +# Python +__pycache__/ +*.py[cod] +*$py.class +*.so +.Python diff --git a/var/avgpos/README.md b/var/avgpos/README.md index f490e65..aefa7b6 100644 --- a/var/avgpos/README.md +++ b/var/avgpos/README.md @@ -58,6 +58,7 @@ python3 avgpos.py - `--labels`: Include atom labels (element+ID, e.g., Se2, Ti4) in output and plot (requires `-o`) - `--replicate`: Replicate the plot along e and f axes (format: "ne,nf", default: "1,1") - Supports non-integer replication (e.g., "2.5,3" for 2.5x3 replication) +- `--no-circles`: Hide circles representing atom positions in the plot (only effective when `--labels` is not used) ### Examples @@ -106,6 +107,13 @@ Generate heatmap with 2.5x3 replication along e and f axes: # Plot will show 2.5 replications along e-axis and 3 along f-axis ``` +Generate smooth heatmap without atom position circles: +```bash +./avgpos.py POSCAR -s Se -d z -o projections.dat --plot --no-circles +# Then run: python3 projections_plot.py +# Plot will show only the smooth interpolated surface without circles +``` + ## Output ### Standard Output diff --git a/var/avgpos/__pycache__/avgpos.cpython-312.pyc b/var/avgpos/__pycache__/avgpos.cpython-312.pyc deleted file mode 100644 index 4f1fe703db8a4feafe287fefd7c62c7e944462f2..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 25494 zcmdUXX>c4zc4qZ`;%eLnfx}14GrNQ{!qkDtYae95fG(~@yPzM z-^)6>05(OAz2Vp`1gfjDGGD&TeEHtXeDCFdDJXDrxF)|{6;5B|xc@;f+GSNAKEIBK zTb#gM-~^Lkj+ic(*suA5h5cGDSOv?Q+y$Fp#oaF0aCZoH+?|30cbDK5oNt;gxCIy9 zJc1i{uUH^>F8eu7sxot;X`)W6H1~^i?}zH^hbHC0#Lb##&4Gg8DiYkmD`QhJnQ!M0 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z%Nu^=PL=LLtp&}jS$%g7|K+KloJ#e*n0j$IRq>6r;^2B+)1SCdX+iUs@+**ue_dPt zdJFgS9li_o*1xUZf1#QC@7oVnUEF5*q+!r=aVPh8Ev^f-mcMInzEEMwR@m^IZFXI( zv1HqtFP2+=S#HDgFSpq)wmN>fbLZEpEDtJ8xM!Wih}J?#(Qv?$@E8=^qtZ=O8Ys#- zhKGe%Xn0uq0SSK_^Y2o8pT2_xrcp7CNl}rQcJvMUK(4)tYD5y9>LC>ZaOe=L4>)$p z1(W+_JRK1aNPmG(5dEAyh8wtw$@H1kW3ql;!Nz-KYZTAn|z-iHHFQlf`_l!kjaNk5xi}D-NsqH3yFJ{>UAp)`uL;c Vzju7`{I_5E1pY=A&RW9|`9Fg^^2h)H diff --git a/var/avgpos/avgpos.py b/var/avgpos/avgpos.py index b4ed354..e8f7a94 100755 --- a/var/avgpos/avgpos.py +++ b/var/avgpos/avgpos.py @@ -227,7 +227,7 @@ def get_atom_labels(structure, atom_indices): return labels -def generate_plot_script(data_file, script_file, output_image='heatmap.png', with_labels=False, replicate=(1, 1)): +def generate_plot_script(data_file, script_file, output_image='heatmap.png', with_labels=False, replicate=(1, 1), no_circles=False): """ Generate a Python script using matplotlib to plot the plane projection data as a heatmap. @@ -243,6 +243,8 @@ def generate_plot_script(data_file, script_file, output_image='heatmap.png', wit Whether to include atom labels in the plot replicate : tuple Number of replications along e and f axes (ne, nf) + no_circles : bool + Whether to hide the circles representing atom positions (only when labels are not used) """ script_content = f"""#!/usr/bin/env python3 \"\"\" @@ -345,11 +347,17 @@ def generate_plot_script(data_file, script_file, output_image='heatmap.png', wit # Create smooth heatmap using pcolormesh with RGB gradient (jet colormap) # Use the same vmin/vmax as the scatter plot for consistent colors heatmap = ax.pcolormesh(e_mesh, f_mesh, g_interp, cmap='jet', shading='auto', vmin=vmin, vmax=vmax) - +""" + + # Add scatter points conditionally + if with_labels or not no_circles: + script_content += f""" # Overlay the original data points with their EXACT g values colored # This ensures atomic positions correspond to the real g value from the data file scatter = ax.scatter(e, f, c=g, cmap='jet', s=150, edgecolors='black', linewidths=2, zorder=10, vmin=vmin, vmax=vmax) - +""" + + script_content += f""" # Add colorbar with height matching the plot divider = make_axes_locatable(ax) cax = divider.append_axes("right", size="5%", pad=0.1) @@ -503,6 +511,8 @@ def main(): help='Include atom labels (element+ID) in output and plot (requires -o)') parser.add_argument('--replicate', type=str, default='1,1', help='Replicate the plot along e and f axes (format: "ne,nf", e.g., "2.5,3" for 2.5x3 replication)') + parser.add_argument('--no-circles', action='store_true', + help='Hide circles representing atom positions in the plot (only when --labels is not used)') args = parser.parse_args() @@ -627,7 +637,7 @@ def main(): replicate = (1, 1) # Generate the plotting script - generate_plot_script(args.output, script_file, image_file, args.labels, replicate) + generate_plot_script(args.output, script_file, image_file, args.labels, replicate, args.no_circles) print() print(f"Matplotlib plotting script generated: {script_file}") @@ -637,6 +647,8 @@ def main(): print(f" (with atom labels)") if replicate != (1, 1): print(f" (with {replicate[0]}x{replicate[1]} replication)") + if args.no_circles and not args.labels: + print(f" (without atom position circles)") elif args.plot or args.labels: print() print("Warning: --plot and --labels flags require -o/--output to be specified. Ignoring.") From 1af728bf4fc308205426d5456a59118485d5524b Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 15 Nov 2025 14:52:44 +0000 Subject: [PATCH 17/17] Remove padding from plot script grid generation Co-authored-by: acammarat <124535593+acammarat@users.noreply.github.com> --- var/avgpos/avgpos.py | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/var/avgpos/avgpos.py b/var/avgpos/avgpos.py index e8f7a94..b446808 100755 --- a/var/avgpos/avgpos.py +++ b/var/avgpos/avgpos.py @@ -308,18 +308,12 @@ def generate_plot_script(data_file, script_file, output_image='heatmap.png', wit labels = np.concatenate(labels_list) # Create a regular grid for interpolation -# Determine the range of e and f with some padding +# Determine the range of e and f e_min, e_max = e.min(), e.max() f_min, f_max = f.min(), f.max() -# Add padding to ensure coverage (10% on each side) -e_range = e_max - e_min -f_range = f_max - f_min -padding_e = max(0.1 * e_range, 0.5) if e_range > 0 else 0.5 -padding_f = max(0.1 * f_range, 0.5) if f_range > 0 else 0.5 - -e_grid = np.linspace(e_min - padding_e, e_max + padding_e, 200) -f_grid = np.linspace(f_min - padding_f, f_max + padding_f, 200) +e_grid = np.linspace(e_min, e_max, 200) +f_grid = np.linspace(f_min, f_max, 200) e_mesh, f_mesh = np.meshgrid(e_grid, f_grid) # Use Radial Basis Function interpolation with very small smoothing