WIP: removed manual input of weights for lammps speed balancing

libAtoms · Feb 15, 2024 · 027f7ff · 027f7ff
1 parent ffbff8f
commit 027f7ff
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Showing 2 changed files with 3 additions and 5 deletions.
diff --git a/matscipy/fracture_mechanics/thin_strip_utils.py b/matscipy/fracture_mechanics/thin_strip_utils.py
@@ -655,7 +655,7 @@ def write_potential_and_buffer(atoms,lammps_filename):
     #get the potential and buffer array from atoms
     potential = atoms.arrays['potential']
     buffer = atoms.arrays['buffer']
-    ids = atoms.arrays['id']
+    ids = np.arange(1,len(atoms)+1)
 
     #write to file
     #create a vertical array of ids, potential
@@ -677,7 +677,7 @@ def write_potential_and_buffer(atoms,lammps_filename):
 def set_up_simulation_lammps(lmps,tmp_file_path,atomic_mass,calc_commands,
                              sim_tstep=0.001,damping_strength_right=0.1,damping_strength_left=0.1,dump_freq=100, dump_files=True,
                              dump_name='dump.lammpstrj',thermo_freq=100,left_damp_thickness=60,
-                             right_damp_thickness=60,multi_potential=False, pot_speedup=None,y_fixed_length=1):
+                             right_damp_thickness=60,multi_potential=False, y_fixed_length=1):
     """Set up the simulation by passing an active LAMMPS object a number of commands"""
 
     # ---------- Initialize Simulation --------------------- 

diff --git a/scripts/fracture_mechanics/thin_strip_lammps.py b/scripts/fracture_mechanics/thin_strip_lammps.py
@@ -82,7 +82,6 @@
 multi_potential = parameter('multi_potential',False) #if True, use dual potentials, for different regions of the crack
 if multi_potential:
     partition_type = parameter('partition_type') #get the type of partitioning to use between potentials
-    pot_speedup = parameter('pot_speedup') #get the relative speedup between the two potentials
     #if the partition type is strip, then get the strip width
     buffer_thickness = parameter('buffer_thickness',6.0)
     if partition_type == 'strip':
@@ -92,7 +91,6 @@
 else:
     partition_type = None
     partition_width = None
-    pot_speedup = None
 
 y_threshold = parameter('y_threshold',1)
 cpnum = initial_checkpoint_num
@@ -227,7 +225,7 @@
         set_up_simulation_lammps(lmp,temp_path,mass,cmds,sim_tstep=sim_tstep,damping_strength_right=damping_strength_right,damping_strength_left=damping_strength_left
                                  , dump_freq=dump_freq, dump_name=dump_name, thermo_freq=thermo_freq, dump_files=dump_files,
                                  left_damp_thickness=left_damp_thickness, right_damp_thickness=right_damp_thickness,multi_potential=multi_potential,
-                                 pot_speedup=pot_speedup,y_fixed_length=y_fixed_length)
+                                 y_fixed_length=y_fixed_length)
         if (i < initial_damping_time) and (initial_damp):
             #add a lammps command to set a thermostat for all atoms initially
             lmp.command(f'fix therm2 nve_atoms langevin 0.0 0.0 {initial_damping_strengths[i]} 1029')