From 962515ad8fdc8c2c18990e25543dd9488ff1ebbd Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Sun, 30 Jun 2019 17:01:24 +0100
Subject: [PATCH] Changes to documentation for EDS
---
src/eds/EDS.cpp | 25 ++++++++++++++++++++-----
1 file changed, 20 insertions(+), 5 deletions(-)
diff --git a/src/eds/EDS.cpp b/src/eds/EDS.cpp
index d17321cd3..5e38af4cf 100644
--- a/src/eds/EDS.cpp
+++ b/src/eds/EDS.cpp
@@ -105,35 +105,50 @@ dist: DISTANCE ATOMS=1,2
dist2: COMBINE ARG=dist POWERS=2 PERIODIC=NO
#add the option to write to a restart file
-eds: EDS ARG=dist,dist2 CENTER=2.0,1.0 PERIOD=50000 TEMP=1.0 OUT_RESTART=restart.dat
+eds: EDS ARG=dist,dist2 CENTER=2.0,1.0 PERIOD=50000 TEMP=1.0 OUT_RESTART=checkpoint.eds
\endplumedfile
+The first few lines of the restart file that is output if we run a calculation with one CV will look something like this:
+
+\auxfile{restart.eds}
+#! FIELDS time d1_center d1_set d1_target d1_coupling d1_maxrange d1_maxgrad d1_accum d1_mean d1_std
+#! SET adaptive 1
+#! SET update_period 1
+#! SET seed 0
+#! SET kbt 2.4943
+ 0.0000 1.0000 0.0000 0.0000 0.0000 7.4830 0.1497 0.0000 0.0000 0.0000
+ 1.0000 1.0000 0.0000 0.0000 0.0000 7.4830 0.1497 0.0000 0.0000 0.0000
+ 2.0000 1.0000 -7.4830 0.0000 0.0000 7.4830 0.1497 0.0224 0.0000 0.0000
+ 3.0000 1.0000 -7.4830 0.0000 -7.4830 7.4830 0.1497 0.0224 0.0000 0.0000
+ 4.0000 1.0000 -7.4830 0.0000 -7.4830 7.4830 0.1497 0.0224 0.0000 0.0000
+\endauxfile
+
Read in a previous restart file. Adding RESTART flag makes output append
\plumedfile
d1: DISTANCE ATOMS=1,2
-eds: EDS ARG=d1 CENTER=2.0 PERIOD=50000 TEMP=1.0 IN_RESTART=restart.dat RESTART=YES
+eds: EDS ARG=d1 CENTER=2.0 PERIOD=50000 TEMP=1.0 IN_RESTART=restart.eds RESTART=YES
\endplumedfile
Read in a previous restart file and freeze the bias at the final level from the previous simulation
\plumedfile
d1: DISTANCE ATOMS=1,2
-eds: EDS ARG=d1 CENTER=2.0 TEMP=1.0 IN_RESTART=restart.dat FREEZE
+eds: EDS ARG=d1 CENTER=2.0 TEMP=1.0 IN_RESTART=restart.eds FREEZE
\endplumedfile
Read in a previous restart file and freeze the bias at the mean from the previous simulation
\plumedfile
d1: DISTANCE ATOMS=1,2
-eds: EDS ARG=d1 CENTER=2.0 TEMP=1.0 IN_RESTART=restart.dat FREEZE MEAN
+eds: EDS ARG=d1 CENTER=2.0 TEMP=1.0 IN_RESTART=restart.eds FREEZE MEAN
\endplumedfile
Read in a previous restart file and continue the bias, but use the mean from the previous run as the starting point
\plumedfile
d1: DISTANCE ATOMS=1,2
-eds: EDS ARG=d1 CENTER=2.0 PERIOD=50000 TEMP=1.0 IN_RESTART=restart.dat FREEZE MEAN
+eds: EDS ARG=d1 CENTER=2.0 PERIOD=50000 TEMP=1.0 IN_RESTART=restart.eds FREEZE MEAN
\endplumedfile
--
GitLab