Hello,
I am using QuantumATK version X-2025.06 on Linux. I am trying to run a post-processing analysis script in the Editor to calculate the NematicOrderParameter and OrientationFunction for my molecular dynamics simulation results.
However, I am consistently running into a ModuleNotFoundError. I have tried several different import statements based on documentation for various versions, but none seem to work.
The following import attempts have all failed:
from ATK.ForceField import ... (fails with No module named 'ATK')
from ATK.Analyser import ... (fails with No module named 'ATK')
from quantumatk.analysers... import ... (fails with No module named 'quantumatk')
from Analyser import ... (fails with No module named 'Analyser')
This suggests a fundamental issue with how the atkpython environment is finding its own modules in this version.
I have run a diagnostic script to check sys.path, and the output is included in the log file attached below. It seems the main libraries are located in a QATK.zip file, but I cannot find the correct syntax to import from it.
Could you please advise on the correct import syntax for NematicOrderParameter and OrientationFunction for version X-2025.06?
Below is my full analysis script and the latest error log. Thank you for your help.
# ####################################################################
# # Required Libraries #
# ####################################################################
# This is the import section that is causing a ModuleNotFoundError.
# Trying the most basic import structure for NanoLanguage.
from NanoLanguage import *
from Analyser import NematicOrderParameter, OrientationFunction
from IO import nlread
import numpy
import pylab
# ####################################################################
# # !!! SETTINGS !!! #
# # PLEASE CAREFULLY EDIT THIS SECTION TO MATCH YOUR SIMULATION #
# ####################################################################
# 1. Full name of your results file
results_filename = "PureAndC60_8CB_Resorvuar_Pro_NoE_results.py" # Enter your filename here
# 2. LOCAL indices of atoms defining the molecular axis
# - In the Viewer, select the FIRST 8CB molecule (e.g., atoms with indices 0 to 46).
# - Note the Index of the atom at the start of the axis (e.g., 5).
# - Note the Index of the atom at the end of the axis (e.g., 25).
# - Subtract 1 from these numbers and write them in the list below (e.g., [4, 24]).
axis_atom_indices_local = [4, 24] # THIS IS AN EXAMPLE, YOU MUST ENTER YOUR OWN VALUES!
# 3. Molecule and Atom Counts (Updated based on new information)
first_8cb_atom_index = 0 # 8CB molecules are now at the beginning
atoms_per_8cb_molecule = 47 # Number of atoms in one 8CB molecule (C21H25N)
total_atom_count = 3820 # New total atom count: (80 * 47) + 60
# 4. Temperature range to be analyzed (should be the same as in your simulation)
temperatures = range(293, 315)
# 5. Filenames for the output plots
s_parameter_plot_filename = "S_vs_Temperature_NEW.png"
angular_dist_plot_filename = "Angular_Distribution_NEW.png"
# ####################################################################
# # ANALYSIS SCRIPT (DO NOT MODIFY) #
# ####################################################################
# Create empty lists to store the results
calculated_s_parameters = []
first_temp_data = None
last_temp_data = None
# Create the list of all 8CB atom indices (excluding C60)
last_8cb_atom_index = first_8cb_atom_index + (80 * atoms_per_8cb_molecule)
all_8cb_indices = list(range(first_8cb_atom_index, last_8cb_atom_index))
print("+" + "-"*50 + "+")
print("ANALYSIS SCRIPT STARTED")
print(f"File: {results_filename}")
print(f"Total Atoms: {total_atom_count}, 8CB Atoms: {len(all_8cb_indices)}")
print("+" + "-"*50 + "+")
print(f"{'Temperature (K)':<15} | {'Order Parameter (S)':<25}")
print("-" * 52)
# Loop over temperatures
for T in temperatures:
try:
# Read the final configuration for each temperature from the HDF5 file
object_id = f'last_image_3_md_reservoir_temperature_{float(T)}.0_Kelvin'
configuration = nlread(results_filename, object_id=object_id)[0]
# Calculate Nematic Order Parameter
analysis_s = NematicOrderParameter(
configuration=configuration,
axis_atom_indices=axis_atom_indices_local,
molecule_indices=[all_8cb_indices]
)
s_value = analysis_s.evaluate()
calculated_s_parameters.append(s_value)
print(f"{T:<15.1f} | {s_value:<25.4f}")
# Calculate Orientation Function (only for the first and last temperatures for plotting)
if T == temperatures[0] or T == temperatures[-1]:
molecular_axes = []
for i in range(first_8cb_atom_index, last_8cb_atom_index, atoms_per_8cb_molecule):
atom1_index = i + axis_atom_indices_local[0]
atom2_index = i + axis_atom_indices_local[1]
pos1 = configuration.cartesianCoordinates()[atom1_index]
pos2 = configuration.cartesianCoordinates()[atom2_index]
vector = pos2 - pos1
unit_vector = vector / numpy.linalg.norm(vector)
molecular_axes.append(unit_vector)
analysis_angular = OrientationFunction(vectors=molecular_axes, axis=[0,0,1])
theta, probability = analysis_angular.evaluate()
if T == temperatures[0]:
first_temp_data = (theta, probability, T)
else:
last_temp_data = (theta, probability, T)
except Exception as e:
print(f"ERROR: Could not read or analyze data for T={T}K. Check the object_id. Error: {e}")
calculated_s_parameters.append(None) # Append None in case of an error
print("\nGenerating plots...")
# Plot 1: S Parameter vs. Temperature
pylab.figure()
pylab.plot(temperatures, calculated_s_parameters, 'o-', label='S Parameter')
pylab.xlabel("Temperature (K)")
pylab.ylabel("Nematic Order Parameter (S)")
pylab.title("Order Parameter vs. Temperature")
pylab.ylim(0, 1)
pylab.grid(True)
pylab.legend()
pylab.savefig(s_parameter_plot_filename)
print(f"-> Saved plot: '{s_parameter_plot_filename}'")
# Plot 2: Angular Distribution
pylab.figure()
if first_temp_data:
theta_first, prob_first, T_first = first_temp_data
pylab.plot(theta_first * 180 / numpy.pi, prob_first, label=f'{T_first} K (Low Temperature)')
if last_temp_data:
theta_last, prob_last, T_last = last_temp_data
pylab.plot(theta_last * 180 / numpy.pi, prob_last, label=f'{T_last} K (High Temperature)')
pylab.xlabel("Angle with Z-axis (Degrees)")
pylab.ylabel("Probability Density")
pylab.title("Molecular Orientational Distribution")
pylab.grid(True)
pylab.legend()
pylab.savefig(angular_dist_plot_filename)
print(f"-> Saved plot: '{angular_dist_plot_filename}'")
print("\nANALYSIS COMPLETE!")
