added configuration B

Author: simongravelle

integration_tests/benchmark/configurationA/nvt.lmp

@@ -18,8 +18,6 @@ atom_style atomic
 pair_style lj/cut ${rc}
 boundary p p p
 
-#read_data twoparticle.data
-
 variable L2 equal ${L}/2
 region myreg block -${L2} ${L2} -${L2} ${L2} -${L2} ${L2}
 create_box 1 myreg

integration_tests/benchmark/configurationB/README.md

@@ -0,0 +1,16 @@
+# Configuration B - Particles in the GCMC ensemble
+
+## Parameters
+
+nmb_1 = 50  # Define inital atom number  
+sig_1 = 3 * ureg.angstrom  # Define LJ parameters (sigma)  
+eps_1 = 0.1 * ureg.kcal/ureg.mol  # Define LJ parameters (epsilon)  
+mss_1 = 10 * ureg.gram/ureg.mol  # Define atom mass          
+L = 20 * ureg.angstrom  # Define box size  
+rc = 2.5 * sig_1  # Define cut_off  
+T = 300 * ureg.kelvin  # Pick the desired temperature  
+mu = - 4 * ureg.kcal/ureg.mol  # Pick the desired chemical potential
+
+## Measurements
+
+density = 0.014 ± 0.000 g/cm3

integration_tests/benchmark/configurationB/gcmc.lmp

@@ -0,0 +1,45 @@
+variable dump equal 50000
+variable thermo equal 50000
+variable steps equal 1000000
+variable eqs equal 100000
+variable av equal ${dump}/10
+
+variable nmb_1 equal 50  # Define atom number
+variable sig_1 equal 3  # Define LJ parameters (sigma)
+variable eps_1 equal 0.1  # Define LJ parameters (epsilon)
+variable mss_1 equal 10  # Define atom mass        
+variable L equal 20  # Define box size
+variable rc equal 2.5*${sig_1}  # Define cut_off (angstrom)
+variable T equal 300  # Pick the desired temperature (kelvin)
+variable mu equal -4 
+
+# main parameters
+units real
+dimension 3
+atom_style atomic
+pair_style lj/cut ${rc}
+boundary p p p
+
+variable L2 equal ${L}/2
+region myreg block -${L2} ${L2} -${L2} ${L2} -${L2} ${L2}
+create_box 1 myreg
+create_atoms 1 random ${nmb_1} 14141 myreg
+
+mass 1 ${mss_1}
+pair_coeff 1 1 ${eps_1} ${sig_1}
+
+timestep 0.1
+fix mygcmc all gcmc 1 1 0 1 29494 ${T} ${mu} 0.01
+
+thermo ${thermo}
+dump mydmp all custom ${dump} dump.lammpstrj id type x y z vx vy vz
+
+run ${eqs}  # equilibration
+
+variable atom atom "type==1"
+group atom dynamic all var atom
+variable n_atom equal count(atom)
+variable density equal v_n_atom/vol
+fix myat1 all ave/time 10 ${av} ${dump} v_density file density.dat
+
+run ${steps}

integration_tests/benchmark/configurationB/update_README.py

@@ -0,0 +1,40 @@
+import numpy as np
+import re
+
+# Function to calculate the average and standard error of the second column in a data file
+def calculate_statistics(filename):
+    try:
+        data = np.loadtxt(filename, usecols=1)  # Load the second column
+        mean = np.mean(data)
+        std_error = np.std(data, ddof=1) / np.sqrt(len(data))  # Standard error of the mean
+        return mean, std_error
+    except Exception as e:
+        print(f"Error reading {filename}: {e}")
+        return None, None
+
+# Filenames
+config_file = "README.md"  # Your configuration file
+density_file = "density.dat"
+
+# Calculate statistics
+average_density, error_density = calculate_statistics(density_file)
+
+if average_density is None or error_density is None:
+    print("Failed to calculate averages or errors. Exiting.")
+    exit(1)
+
+# Update the configuration file
+try:
+    with open(config_file, 'r') as file:
+        config_lines = file.readlines()
+
+    with open(config_file, 'w') as file:
+        for line in config_lines:
+            if re.match(r"^Epot\s*=", line):
+                file.write(f"density = {average_density:.3f} ± {error_density:.3f} g/cm3\n")
+            else:
+                file.write(line)
+
+    print(f"Updated {config_file} with density = {average_density:.3f} ± {error_density:.3f} g/cm3")
+except Exception as e:
+    print(f"Error updating {config_file}: {e}")