Supported File Formats

ACoord supports molecular, crystallographic, and simulation formats for reading and writing atomic structures. Read-only output formats can be opened and then exported to a writable format with Save As.

Format Overview

Format	Read	Write	Extensions	Description
XYZ	✅	✅	.xyz	Simple atomic coordinates
CIF	✅	✅	.cif	Crystallographic Information File
POSCAR	✅	✅	POSCAR, CONTCAR, .vasp, .poscar	VASP input structure
XDATCAR	✅	❌	XDATCAR, .xdatcar	VASP MD trajectory
OUTCAR	✅	❌	OUTCAR, .outcar	VASP output file
PDB	✅	✅	.pdb	Protein Data Bank
Gaussian	✅	✅	.gjf, .com	Gaussian input
ORCA	✅	✅	.inp	ORCA input
Quantum ESPRESSO	✅	✅	.in, .pwi	QE input
QE Output	✅	❌	.out, .pwo, .log	QE output
ABACUS	✅	✅	.stru	ABACUS STRU
OpenMX	✅	✅	.dat	OpenMX input
CASTEP Cell	✅	✅	.cell	CASTEP input structure
CASTEP Output	✅	❌	.castep	CASTEP output file
SIESTA fdf	✅	✅	.fdf	SIESTA input structure
ACoord Native	✅	✅	.acoord	Native format with full metadata

Format Details

XYZ Format

The simplest format for atomic coordinates.

14
Benzene molecule
C     0.000    1.400    0.000
C     1.212    0.700    0.000
C     1.212   -0.700    0.000
...

Support:

• ✅ Atom positions
• ✅ Element types
• ✅ Comments
• ❌ Unit cell
• ❌ Bonds

CIF Format

Crystallographic Information File for crystal structures.

Support:

• ✅ Atom positions (fractional and Cartesian)
• ✅ Unit cell parameters
• ✅ Space group symmetry operations (applied automatically on read)
• ✅ Atom labels and types

Limitations:

• ❌ Export always uses P 1 space group (symmetry-expanded atoms)

VASP Formats

POSCAR/CONTCAR

Si crystal
1.0
5.43 0.0 0.0
0.0 5.43 0.0
0.0 0.0 5.43
Si
2
Direct
0.00 0.00 0.00
0.25 0.25 0.25

Support:

• ✅ Atom positions (Direct/Cartesian)
• ✅ Unit cell vectors
• ✅ Selective dynamics
• ✅ Multiple atom types

XDATCAR

Molecular dynamics trajectory format.

Support:

• ✅ Multiple frames (trajectory)
• ✅ Frame-by-frame navigation
• ✅ Animation playback
• ❌ Writing (export individual frames as POSCAR)

OUTCAR

VASP output file with structure information.

Support:

• ✅ Final structure extraction
• ✅ Multiple ionic steps
• ✅ Force information (display only)

PDB Format

Protein Data Bank format for biomolecules.

Support:

• ✅ ATOM records
• ✅ HETATM records
• ✅ CRYST1 unit cell
• ✅ Element detection
• ❌ CONECT bonds (not parsed)

Gaussian Input

Quantum chemistry input files.

Support:

• ✅ Atom coordinates
• ✅ Charge and multiplicity
• ✅ TV lattice vectors (for periodic systems)
• ✅ Format preservation (headers, route section preserved on save)

Quantum ESPRESSO

Support:

• ✅ pw.x input format
• ✅ Cell parameters
• ✅ Atomic positions
• ✅ Fixed and partially constrained position flags
• ✅ Output file parsing (final structure)

Save behavior:

• ATOMIC_POSITIONS movement flags are written only when at least one atom has a real constraint. If every atom is unconstrained, ACoord omits redundant 1 1 1 flags.

ABACUS STRU

Support:

• ✅ Atom types and positions
• ✅ Unit cell
• ✅ Numerical orbital info
• ✅ Movement flags, magnetism, velocity, and spin-constraint extras

Save behavior:

• Existing STRU species, orbital, lattice, magnetism, velocity, and spin extras are preserved where possible.
• Movement flags are written only when at least one atom is fixed or partially constrained. If every atom is mobile, ACoord omits redundant 1 1 1 flags.

OpenMX Input (.dat)

OpenMX input files with structure, species, and calculation parameters.

System.Name                   Water
DATA.PATH                     ./

Species.Number                2
<Definition.of.Atomic.Species
  O   O6.0-s2p2d1   O_PBE19
  H   H6.0-s2p1     H_PBE19
Definition.of.Atomic.Species>

Atoms.Number                  3
Atoms.SpeciesAndCoordinates.Unit   Frac
<Atoms.SpeciesAndCoordinates
  1  O  0.5000000  0.5000000  0.5000000  3.0  3.0
  2  H  0.5375000  0.5000000  0.6750000  0.5  0.5
  3  H  0.4625000  0.5000000  0.6750000  0.5  0.5
Atoms.SpeciesAndCoordinates>

Support:

• ✅ Atoms.UnitVectors lattice vectors
• ✅ Atoms.SpeciesAndCoordinates in Ang or Frac
• ✅ Atoms.UnitVectors.Unit in Ang or Bohr
• ✅ MD.Fixed.XYZ constraints mapped to fixed/selective dynamics state
• ✅ Species.Number and Definition.of.Atomic.Species update on edit
• ✅ Existing species rows are preserved exactly when the species remains
• ✅ New species receive default OpenMX PAO/VPS entries
• ✅ Existing calculation parameters are preserved when saving an edited .dat

Save behavior:

• Opening and saving an existing .dat only updates structure-related sections: Atoms.SpeciesAndCoordinates, Atoms.UnitVectors, MD.Fixed.XYZ, Species.Number, and Definition.of.Atomic.Species.
• MD.Fixed.XYZ is omitted when every atom is unconstrained.
• Exporting from another format to .dat generates default OpenMX SCF/MD/DOS parameters using ACoord's OpenMX defaults.

CASTEP Formats

CASTEP Cell (.cell)

CASTEP input structure file.

Support:

• ✅ LATTICE_CART and LATTICE_ABC blocks
• ✅ POSITIONS_ABS (Cartesian) and POSITIONS_FRAC (fractional)
• ✅ Custom species notation (e.g., Fe:1, O:custom)
• ✅ IONIC_CONSTRAINTS mapping to selective dynamics
• ✅ SPIN, LABEL, SPECIES_MASS metadata
• ✅ Unit conversion (bohr, nm, pm, cm, m)
• ✅ Round-trip serialization preserving all metadata
• ✅ Omits IONIC_CONSTRAINTS when every atom is unconstrained

CASTEP Output (.castep)

CASTEP output file from geometry optimization or MD runs.

Support:

• ✅ Lattice extraction from "Unit Cell" block
• ✅ Atomic positions from "Fractional coordinates of atoms"
• ✅ Trajectory extraction from BFGS and MD iterations
• ❌ Writing (export as .cell format)

SIESTA fdf Format

SIESTA input file format with calculation parameters.

SystemName          Water
SystemLabel         H2O

NumberOfAtoms       3
NumberOfSpecies     2

%block ChemicalSpeciesLabel
  1  8   O
  2  1   H
%endblock ChemicalSpeciesLabel

%block LatticeVectors
  15.0   0.0   0.0
  0.0   15.0   0.0
  0.0    0.0  15.0
%endblock LatticeVectors

AtomicCoordinatesFormat  Fractional

%block AtomicCoordinatesAndAtomicSpecies
  0.5   0.5   0.5   1
  0.5375   0.5   0.675   2
  0.4625   0.5   0.675   2
%endblock AtomicCoordinatesAndAtomicSpecies

# SIESTA calculation parameters
XC.functional          GGA
XC.authors             PBE
Mesh.Cutoff            300.0 Ry
kgrid_Monkhorst_Pack    1  1  1

Support:

• ✅ %block LatticeVectors - unit cell vectors
• ✅ %block AtomicCoordinatesAndAtomicSpecies - atomic positions and species
• ✅ %block ChemicalSpeciesLabel - element mapping
• ✅ Calculation parameters (XC.functional, Mesh.Cutoff, kgrid, etc.)
• ✅ Automatic update of NumberOfAtoms and NumberOfSpecies on edit
• ✅ Format preservation (all non-block parameters preserved on save)
• ❌ Selective Dynamics (per-atom fixed flags)
• ❌ Trajectory parsing (multi-frame)

ACoord Native (.acoord)

Native JSON format preserving atoms, bonds, unit-cell data, and ACoord-specific properties.

{
  "atoms": [
    {
      "id": "atom_abc123",
      "element": "C",
      "x": 0.0,
      "y": 1.4,
      "z": 0.0,
      "color": "#909090",
      "radius": 0.77
    }
  ],
  "bonds": [...],
  "unitCell": {...},
  "metadata": {...}
}

Advantages:

• ✅ Preserves all edits (colors, radii, labels)
• ✅ Fast read/write
• ✅ Human-readable JSON
• ✅ Full fidelity round-trip

Note: ACoord registers .acoord files with the VS Code custom editor, so they can be reopened directly from the editor title action or Reopen With menu.

Format Detection

ACoord automatically detects file formats by:

1. File extension (e.g., .cif, .xyz)
2. Filename pattern (e.g., POSCAR, XDATCAR)
3. Content analysis (for ambiguous cases)

Tips

Converting Between Formats

1. Open a file in ACoord
2. Click Save As button in the toolbar
3. Choose the target format
4. Save the converted file

Trajectory Files

For trajectory files like XDATCAR:

• Use the timeline slider to navigate frames
• Press Play to animate
• Export individual frames as POSCAR or XYZ

Best Practices

• Use .acoord for working projects (preserves edits)
• Use CIF for crystal structures (standard format)
• Use XYZ for simple molecules (universal compatibility)
• Use PDB for biomolecules (standard in structural biology)
• Use SIESTA fdf for SIESTA DFT calculations
• Use OpenMX .dat when you need to keep existing OpenMX calculation settings while editing coordinates, lattice vectors, species, or fixed constraints