From aacf4cbad219cf0d396809ff9996e93bda2de5b2 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Fri, 21 Feb 2020 14:03:05 -0600
Subject: [PATCH] Added easy commands for ignoring long bonds during
coarse-simulation
---
bin/mrdna | 4 +++-
mrdna/simulate.py | 27 +++++++++++++++++++++------
2 files changed, 24 insertions(+), 7 deletions(-)
diff --git a/bin/mrdna b/bin/mrdna
index 06fd281..bf47058 100755
--- a/bin/mrdna
+++ b/bin/mrdna
@@ -53,7 +53,8 @@ parser.add_argument('--oxdna-steps', type=float, default=None,
help='Perform an oxDNA simulation instead of creating atomic model')
parser.add_argument('--oxdna-output-period', type=float, default=1e4,
help='Simulation steps between oxDNA configuration and energy output')
-
+parser.add_argument('--coarse-bond-cutoff', type=float, default = 0,
+ help='Ignore bonds beyond this cutoff during first step of simulation; a value of 0 implies bonds are not ignored')
parser.add_argument('--backbone-scale', type=float, default=1.0,
help='Factor to scale DNA backbone in atomic model; try 0.25 to avoid clashes for atomistic simulations')
@@ -155,6 +156,7 @@ def main():
minimization_output_period = int(args.output_period),
coarse_local_twist = args.coarse_local_twist,
fix_linking_number = args.fix_linking_number,
+ bond_cutoff = args.coarse_bond_cutoff,
coarse_output_period = int(args.output_period),
fine_output_period = int(args.output_period),
minimization_steps = 0, # int(args.minimization_steps),
diff --git a/mrdna/simulate.py b/mrdna/simulate.py
index c388a4a..b685098 100644
--- a/mrdna/simulate.py
+++ b/mrdna/simulate.py
@@ -4,8 +4,22 @@ from .arbdmodel.coords import readArbdCoords, readAvgArbdCoords
import shutil
from . import get_resource_path
+import numpy as np
+
## TODO: implement replicas, initial conditions specified through some restart, and a custom simulation schedule
+def _remove_bonds_beyond(model, cutoff):
+ bonds = model.get_bonds()
+ new_bonds = []
+ for bond in bonds:
+ n1,n2,b,ex = bond
+ r2 = np.sum( (n1.position - n2.position)**2 )
+ if r2 > cutoff**2:
+ for l in [model] + model.children:
+ try:
+ l.bonds.remove(bond)
+ except:
+ ...
def minimize_and_simulate_oxdna( model,
output_name,
@@ -61,7 +75,7 @@ def multiresolution_simulation( model, output_name,
fine_output_period = 1e5,
coarse_local_twist = False,
fix_linking_number = False,
- remove_long_bonds=False,
+ bond_cutoff = 0,
backbone_scale=1.0,
oxdna_steps = None,
oxdna_output_period = None,
@@ -123,10 +137,11 @@ def multiresolution_simulation( model, output_name,
# TODO: add the output directory in to the readArbdCoords functions or make it an attribute of the model object
""" Prepare coarse model for minimization and coarse simulation """
- if remove_long_bonds:
- raise NotImplementedError("TODO: remove long bonds")
model.clear_beads()
model.generate_bead_model( **coarse_model_args )
+
+ if bond_cutoff > 0:
+ _remove_bonds_beyond(model, bond_cutoff)
""" Minimization """
if minimization_steps > 0:
@@ -137,11 +152,11 @@ def multiresolution_simulation( model, output_name,
""" Coarse simulation """
simargs = dict(timestep=150e-6 if coarse_local_twist else 200e-6, output_period=coarse_output_period, gpu=gpu)
- if remove_long_bonds:
- run_step(num_steps=0.05*coarse_steps, simargs=simargs)
+ if bond_cutoff > 0 and minimization_steps <= 0:
+ run_step(num_steps=0.25*coarse_steps, simargs=simargs)
model.clear_beads()
model.generate_bead_model( **coarse_model_args )
- run_step(num_steps=0.95*coarse_steps, simargs=simargs)
+ run_step(num_steps=0.75*coarse_steps, simargs=simargs)
else:
run_step(num_steps=coarse_steps, simargs=simargs)
--
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