From d5c79720354b57e1cb8d36c8fc875ee8d2557f95 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Mon, 4 Jan 2016 17:47:06 -0600
Subject: [PATCH] fixed RB time units (from fs to ns)
---
RigidBody.cu | 5 +++--
RigidBodyType.cu | 15 ++++++++-------
2 files changed, 11 insertions(+), 9 deletions(-)
diff --git a/RigidBody.cu b/RigidBody.cu
index 0477a27..1ea6148 100644
--- a/RigidBody.cu
+++ b/RigidBody.cu
@@ -12,8 +12,9 @@
RigidBody::RigidBody(const Configuration& cref, RigidBodyType& tref)
- : c(&cref), t(&tref), impulse_to_momentum(0.0004184) {
-
+ : c(&cref), t(&tref), impulse_to_momentum(4.184e8f) {
+ // units "(kcal_mol/AA) * ns" "amu AA/ns" * 4.184e+08
+
timestep = c->timestep;
// RBTODO: fix this
Temp = 295;
diff --git a/RigidBodyType.cu b/RigidBodyType.cu
index 88720bb..15c892c 100644
--- a/RigidBodyType.cu
+++ b/RigidBodyType.cu
@@ -70,17 +70,18 @@ void RigidBodyType::setDampingCoeffs(float timestep) { /* MUST ONLY BE CALLED ON
| |
| f[kcal/mol AA] = - dampingCoeff * momentum[amu AA/fs] |
| |
- | units "(1/ps) * (amu AA/fs)" "kcal_mol/AA" * 2.3900574 |
+ | units "(1/ps) * (amu AA/ns)" "kcal_mol/AA" * 2.390e-06 |
`–––––––––––––––––––––––––––––––––––––––––––––––––––––––*/
/*––––––––––––––––––––––––––––––––––––––––––––––––––––.
| < f(t) f(t') > = 2 kT dampingCoeff mass delta(t-t') |
| |
- | units "sqrt( k K (1/ps) amu / fs )" "kcal_mol/AA" |
- | * 0.068916889 |
+ | units "sqrt( k K (1/ps) amu / ns )" "kcal_mol/AA" |
+ | * 6.8916889e-05 |
`––––––––––––––––––––––––––––––––––––––––––––––––––––*/
+ // RBTODO: make units consistent with rest of RB code
float Temp = 295; /* RBTODO: temperature should be read from grid? Or set in uniformly in config file */
- transForceCoeff = 0.068916889 * Vector3::element_sqrt( 2*Temp*mass*transDamping/timestep );
+ transForceCoeff = 6.8916889e-05 * Vector3::element_sqrt( 2*Temp*mass*transDamping/timestep );
// setup for langevin
// langevin = rbParams->langevin;
@@ -88,12 +89,12 @@ void RigidBodyType::setDampingCoeffs(float timestep) { /* MUST ONLY BE CALLED ON
// T = - dampingCoeff * angularMomentum
// < f(t) f(t') > = 2 kT dampingCoeff inertia delta(t-t')
- rotTorqueCoeff = 0.068916889 *
+ rotTorqueCoeff = 6.8916889e-05 *
Vector3::element_sqrt( 2*Temp* Vector3::element_mult(inertia,rotDamping) / timestep );
- transDamping = 2.3900574 * transDamping;
- rotDamping = 2.3900574 * rotDamping;
+ transDamping = 2.3900574e-6 * transDamping;
+ rotDamping = 2.3900574e-6 * rotDamping;
// Also apply scale factors
applyScaleFactors();
--
GitLab