From b4dd2d6ecdc0b0d7815a7c25a94cd2c4f6a89669 Mon Sep 17 00:00:00 2001
From: Andrew White <white.d.andrew@gmail.com>
Date: Wed, 22 Mar 2017 13:03:52 -0400
Subject: [PATCH] EDS: Added ability to tune how often CVs are updated in
multidimensional case
---
regtest/eds/rt-eds-covar/config | 2 +-
.../eds/rt-eds-covar/eds_restart.reference | 6 ++--
regtest/eds/rt-eds-covar/plumed.dat | 2 +-
src/eds/EDS.cpp | 32 +++++++++++++++----
4 files changed, 30 insertions(+), 12 deletions(-)
diff --git a/regtest/eds/rt-eds-covar/config b/regtest/eds/rt-eds-covar/config
index d8580acf3..d524a9db4 100644
--- a/regtest/eds/rt-eds-covar/config
+++ b/regtest/eds/rt-eds-covar/config
@@ -1,5 +1,5 @@
type=driver
plumed_modules=eds
-arg="--plumed plumed.dat --trajectory-stride 1 --ixyz trajectory.xyz"
+arg="--plumed plumed.dat --ixyz trajectory.xyz"
extra_files="../../trajectories/trajectory.xyz"
diff --git a/regtest/eds/rt-eds-covar/eds_restart.reference b/regtest/eds/rt-eds-covar/eds_restart.reference
index 8163b14f0..94b7bf8a2 100644
--- a/regtest/eds/rt-eds-covar/eds_restart.reference
+++ b/regtest/eds/rt-eds-covar/eds_restart.reference
@@ -6,6 +6,6 @@
0 1 0 0 0 7.483015889999999 0.1496603178 1 0 0 0 7.483015889999999 0.1496603178 1 0 0 0 7.483015889999999 0.1496603178
0 1 0 0 0 7.483015889999999 0.1496603178 1 0 0 0 7.483015889999999 0.1496603178 1 0 0 0 7.483015889999999 0.1496603178
1 1 0 0 0 7.483015889999999 0.1496603178 1 0 0 0 7.483015889999999 0.1496603178 1 0 0 0 7.483015889999999 0.1496603178
- 2 1 0 0 0 7.483015889999999 0.1496603178 1 -1.107575371820062 0 0 7.483015889999999 0.1496603178 1 0 0 0 7.483015889999999 0.1496603178
- 3 1 0 0 0 7.483015889999999 0.1496603178 1 -1.107575371820062 0 -1.107575371820062 7.483015889999999 0.1496603178 1 0 0 0 7.483015889999999 0.1496603178
- 4 1 0 0 0 7.483015889999999 0.1496603178 1 -1.107575371820062 0 -1.107575371820062 7.483015889999999 0.1496603178 1 0 0 0 7.483015889999999 0.1496603178
+ 2 1 -1.107575371820062 0 0 7.483015889999999 0.1496603178 1 -1.107575371820062 0 0 7.483015889999999 0.1496603178 1 -1.107575371820062 0 0 7.483015889999999 0.1496603178
+ 3 1 -1.107575371820062 0 -1.107575371820062 7.483015889999999 0.1496603178 1 -1.107575371820062 0 -1.107575371820062 7.483015889999999 0.1496603178 1 -1.107575371820062 0 -1.107575371820062 7.483015889999999 0.1496603178
+ 4 1 -1.107575371820062 0 -1.107575371820062 7.483015889999999 0.1496603178 1 -1.107575371820062 0 -1.107575371820062 7.483015889999999 0.1496603178 1 -1.107575371820062 0 -1.107575371820062 7.483015889999999 0.1496603178
diff --git a/regtest/eds/rt-eds-covar/plumed.dat b/regtest/eds/rt-eds-covar/plumed.dat
index e76a0a05e..2b9798d23 100644
--- a/regtest/eds/rt-eds-covar/plumed.dat
+++ b/regtest/eds/rt-eds-covar/plumed.dat
@@ -1,4 +1,4 @@
d1: DISTANCE ATOMS=1,2
d2: DISTANCE ATOMS=2,3
d3: DISTANCE ATOMS=3,4
-EDS ARG=d1,d2,d3 CENTER=1.0,1.0,1.0 BIAS_SCALE=0.5,0.25,0.75 PERIOD=2 LABEL=eds OUT_RESTART=eds_restart TEMP=300.0 COVAR SEED=574
+EDS ARG=d1,d2,d3 CENTER=1.0,1.0,1.0 BIAS_SCALE=0.5,0.25,0.75 PERIOD=2 LABEL=eds OUT_RESTART=eds_restart TEMP=300.0 COVAR SEED=574 MULTI_PROP=0.9
diff --git a/src/eds/EDS.cpp b/src/eds/EDS.cpp
index 07e0a05aa..57d9755e9 100644
--- a/src/eds/EDS.cpp
+++ b/src/eds/EDS.cpp
@@ -145,6 +145,7 @@ private:
int update_calls_;
double kbt_;
double c_range_increase_f_;
+ double multi_prop_;
Random rand_;
Value* value_force2_;
@@ -182,8 +183,12 @@ public:
keys.add("compulsory","SEED","0","Seed for random order of changing bias");
keys.add("compulsory","INIT","0","Starting value for coupling coefficients");
keys.add("compulsory","FIXED","0","Fixed target values for bias factors (not adaptive)");
- keys.add("optional","BIAS_SCALE","A divisor to set the units of the bias. If not set, this will be the experimental value by default (as is done in White and Voth 2014).");
+ keys.add("optional","BIAS_SCALE","A divisor to set the units of the bias. "
+ "If not set, this will be the experimental value by default (as is done in White and Voth 2014).");
keys.add("optional","TEMP","The system temperature. If not provided will be taken from MD code (if available)");
+ keys.add("optional","MULTI_PROP","What proportion of dimensions to update at each step. "
+ "Must be in interval [1,0), where 1 indicates all and any other indicates a stochastic update. "
+ "If not set, default is 1 / N, where N is the number of CVs. ");
keys.add("optional","OUT_RESTART","Output file for all information needed to continue EDS simulation. "
"If you have the RESTART directive set (global or for EDS), this file will be appended to. "
@@ -200,7 +205,7 @@ public:
keys.use("RESTART");
keys.addOutputComponent("force2","default","squared value of force from the bias");
- keys.addOutputComponent("_coupling","default","For each named CV biased, there will be a corresponding output CV_coupling storing the current linear bias prefactor.");
+ keys.addOutputComponent("_coupling","default", "For each named CV biased, there will be a corresponding output CV_coupling storing the current linear bias prefactor.");
}
EDS::EDS(const ActionOptions&ao):
@@ -234,6 +239,7 @@ public:
update_calls_(0),
kbt_(0.0),
c_range_increase_f_(1.25),
+ multi_prop_(-1.0),
value_force2_(NULL)
{
double temp=-1.0;
@@ -241,10 +247,10 @@ public:
addComponent("force2");
componentIsNotPeriodic("force2");
- value_force2_=getPntrToComponent("force2");
+ value_force2_ = getPntrToComponent("force2");
for(unsigned int i = 0;i<ncvs_;i++){
- std::string comp=getPntrToArgument(i)->getName()+"_coupling";
+ std::string comp = getPntrToArgument(i)->getName() + "_coupling";
addComponent(comp);
componentIsNotPeriodic(comp);
out_coupling_[i]=getPntrToComponent(comp);
@@ -258,6 +264,7 @@ public:
parse("PERIOD",update_period_);
parse("TEMP",temp);
parse("SEED",seed_);
+ parse("MULTI_PROP",multi_prop_);
parse("OUT_RESTART",out_restart_name_);
parseFlag("RAMP",b_ramp_);
parseFlag("FREEZE",b_freeze_);
@@ -309,11 +316,13 @@ public:
//in driver, this results in kbt of 0
if(kbt_ == 0){
- error(" Unable to determine valid kBT. Probably because you are runnning from driver.\n Consider setting temperature manually.");
+ error(" Unable to determine valid kBT. "
+ "Could be because you are runnning from driver or MD didn't give temperature.\n"
+ "Consider setting temperature manually with the TEMP keyword.");
kbt_ = 1;
}
- log.printf(" with kBT = %f\n",kbt_);
+ log.printf(" kBT = %f\n",kbt_);
log.printf(" Updating every %i steps\n",update_period_);
log.printf(" with centers:");
@@ -377,6 +386,15 @@ public:
}
}
+ if(multi_prop_ == -1.0) {
+ log.printf(" Will update each dimension stochastically with probability 1 / number of CVs\n");
+ multi_prop_ = 1.0 / ncvs_;
+ } else if(multi_prop_ > 0 && multi_prop_ <= 1.0) {
+ log.printf(" Will update each dimension stochastically with probability %f\n", multi_prop_);
+ } else{
+ error(" MULTI_PROP must be between 0 and 1\n");
+ }
+
if(out_restart_name_.length()>0) {
log.printf(" writing restart information every %i steps to file: %s\n",abs(update_period_),out_restart_name_.c_str());
b_write_restart_ = true;
@@ -686,7 +704,7 @@ public:
reset_statistics();
//multidimesional stochastic step
- if(ncvs_ == 1 || (rand_.RandU01() < (1. / ncvs_) ) ) {
+ if(ncvs_ == 1 || (rand_.RandU01() < (multi_prop_) ) ) {
coupling_accum_[i] += step_size_[i] * step_size_[i];
//equation 5 in White and Voth, JCTC 2014
--
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