From 6cbdfb5b17103f7542f62edba8b2087898e96c5f Mon Sep 17 00:00:00 2001
From: carlocamilloni <carlo.camilloni@gmail.com>
Date: Fri, 29 Sep 2017 23:04:54 +0200
Subject: [PATCH] regtest: fret
---
regtest/isdb/rt-fret/Makefile | 1 +
regtest/isdb/rt-fret/config | 6 ++++++
regtest/isdb/rt-fret/der2.reference | 31 +++++++++++++++++++++++++++
regtest/isdb/rt-fret/der3.reference | 31 +++++++++++++++++++++++++++
regtest/isdb/rt-fret/der4.reference | 31 +++++++++++++++++++++++++++
regtest/isdb/rt-fret/der5.reference | 31 +++++++++++++++++++++++++++
regtest/isdb/rt-fret/der6.reference | 31 +++++++++++++++++++++++++++
regtest/isdb/rt-fret/der7.reference | 31 +++++++++++++++++++++++++++
regtest/isdb/rt-fret/der8.reference | 31 +++++++++++++++++++++++++++
regtest/isdb/rt-fret/forces.reference | 20 +++++++++++++++++
regtest/isdb/rt-fret/plumed.dat | 27 +++++++++++++++++++++++
regtest/isdb/rt-fret/trajectory.xyz | 20 +++++++++++++++++
12 files changed, 291 insertions(+)
create mode 100644 regtest/isdb/rt-fret/Makefile
create mode 100644 regtest/isdb/rt-fret/config
create mode 100644 regtest/isdb/rt-fret/der2.reference
create mode 100644 regtest/isdb/rt-fret/der3.reference
create mode 100644 regtest/isdb/rt-fret/der4.reference
create mode 100644 regtest/isdb/rt-fret/der5.reference
create mode 100644 regtest/isdb/rt-fret/der6.reference
create mode 100644 regtest/isdb/rt-fret/der7.reference
create mode 100644 regtest/isdb/rt-fret/der8.reference
create mode 100644 regtest/isdb/rt-fret/forces.reference
create mode 100644 regtest/isdb/rt-fret/plumed.dat
create mode 100644 regtest/isdb/rt-fret/trajectory.xyz
diff --git a/regtest/isdb/rt-fret/Makefile b/regtest/isdb/rt-fret/Makefile
new file mode 100644
index 000000000..3703b27ce
--- /dev/null
+++ b/regtest/isdb/rt-fret/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/isdb/rt-fret/config b/regtest/isdb/rt-fret/config
new file mode 100644
index 000000000..5d23ac270
--- /dev/null
+++ b/regtest/isdb/rt-fret/config
@@ -0,0 +1,6 @@
+# this is a stupid test to verify that virial is computed properly
+# notice that in the second conformation (fcc) one atom is slightly shifted
+# to avoid problems with the numerical derivatives (it is exactly at the border between
+# two images)
+type=driver
+arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
diff --git a/regtest/isdb/rt-fret/der2.reference b/regtest/isdb/rt-fret/der2.reference
new file mode 100644
index 000000000..3a6339a5b
--- /dev/null
+++ b/regtest/isdb/rt-fret/der2.reference
@@ -0,0 +1,31 @@
+#! FIELDS time parameter d2 d2_n
+ 0.000000 0 0.00 0.00
+ 0.000000 1 0.00 0.00
+ 0.000000 2 -0.09 -0.09
+ 0.000000 3 0.00 0.00
+ 0.000000 4 0.00 0.00
+ 0.000000 5 0.09 0.09
+ 0.000000 6 0.00 0.00
+ 0.000000 7 0.00 0.00
+ 0.000000 8 0.00 0.00
+ 0.000000 9 0.00 0.00
+ 0.000000 10 0.00 0.00
+ 0.000000 11 0.00 0.00
+ 0.000000 12 0.00 0.00
+ 0.000000 13 0.00 0.00
+ 0.000000 14 0.09 0.09
+ 0.050000 0 0.00 0.00
+ 0.050000 1 0.00 0.00
+ 0.050000 2 0.00 0.00
+ 0.050000 3 0.00 0.00
+ 0.050000 4 0.00 0.00
+ 0.050000 5 -0.00 -0.00
+ 0.050000 6 0.00 0.00
+ 0.050000 7 0.00 0.00
+ 0.050000 8 0.00 0.00
+ 0.050000 9 0.00 0.00
+ 0.050000 10 0.00 0.00
+ 0.050000 11 0.00 0.00
+ 0.050000 12 0.00 0.00
+ 0.050000 13 0.00 0.00
+ 0.050000 14 0.00 0.00
diff --git a/regtest/isdb/rt-fret/der3.reference b/regtest/isdb/rt-fret/der3.reference
new file mode 100644
index 000000000..b5e951a25
--- /dev/null
+++ b/regtest/isdb/rt-fret/der3.reference
@@ -0,0 +1,31 @@
+#! FIELDS time parameter d3 d3_n
+ 0.000000 0 0.00 0.00
+ 0.000000 1 -0.09 -0.09
+ 0.000000 2 0.00 0.00
+ 0.000000 3 0.00 0.00
+ 0.000000 4 0.09 0.09
+ 0.000000 5 0.00 0.00
+ 0.000000 6 0.00 0.00
+ 0.000000 7 0.00 0.00
+ 0.000000 8 0.00 0.00
+ 0.000000 9 0.00 0.00
+ 0.000000 10 0.09 0.09
+ 0.000000 11 0.00 0.00
+ 0.000000 12 0.00 0.00
+ 0.000000 13 0.00 0.00
+ 0.000000 14 0.00 0.00
+ 0.050000 0 0.00 0.00
+ 0.050000 1 0.00 0.00
+ 0.050000 2 0.00 0.00
+ 0.050000 3 0.00 0.00
+ 0.050000 4 -0.00 -0.00
+ 0.050000 5 0.00 0.00
+ 0.050000 6 0.00 0.00
+ 0.050000 7 0.00 0.00
+ 0.050000 8 0.00 0.00
+ 0.050000 9 0.00 0.00
+ 0.050000 10 0.00 0.00
+ 0.050000 11 0.00 0.00
+ 0.050000 12 0.00 0.00
+ 0.050000 13 0.00 0.00
+ 0.050000 14 0.00 0.00
diff --git a/regtest/isdb/rt-fret/der4.reference b/regtest/isdb/rt-fret/der4.reference
new file mode 100644
index 000000000..786487e33
--- /dev/null
+++ b/regtest/isdb/rt-fret/der4.reference
@@ -0,0 +1,31 @@
+#! FIELDS time parameter d4 d4_n
+ 0.000000 0 0.00 0.00
+ 0.000000 1 -0.30 -0.30
+ 0.000000 2 -0.30 -0.30
+ 0.000000 3 0.00 0.00
+ 0.000000 4 0.30 0.30
+ 0.000000 5 0.30 0.30
+ 0.000000 6 0.00 0.00
+ 0.000000 7 0.00 0.00
+ 0.000000 8 0.00 0.00
+ 0.000000 9 0.00 0.00
+ 0.000000 10 0.30 0.30
+ 0.000000 11 0.30 0.30
+ 0.000000 12 0.00 0.00
+ 0.000000 13 0.30 0.30
+ 0.000000 14 0.30 0.30
+ 0.050000 0 0.00 0.00
+ 0.050000 1 -0.30 -0.30
+ 0.050000 2 -0.30 -0.30
+ 0.050000 3 0.00 0.00
+ 0.050000 4 0.30 0.30
+ 0.050000 5 0.30 0.30
+ 0.050000 6 0.00 0.00
+ 0.050000 7 0.00 0.00
+ 0.050000 8 0.00 0.00
+ 0.050000 9 0.00 0.00
+ 0.050000 10 0.30 0.30
+ 0.050000 11 0.30 0.30
+ 0.050000 12 0.00 0.00
+ 0.050000 13 0.30 0.30
+ 0.050000 14 0.30 0.30
diff --git a/regtest/isdb/rt-fret/der5.reference b/regtest/isdb/rt-fret/der5.reference
new file mode 100644
index 000000000..51dbc735c
--- /dev/null
+++ b/regtest/isdb/rt-fret/der5.reference
@@ -0,0 +1,31 @@
+#! FIELDS time parameter d5 d5_n
+ 0.000000 0 -0.09 -0.09
+ 0.000000 1 0.00 0.00
+ 0.000000 2 0.00 0.00
+ 0.000000 3 0.09 0.09
+ 0.000000 4 0.00 0.00
+ 0.000000 5 0.00 0.00
+ 0.000000 6 0.09 0.09
+ 0.000000 7 0.00 0.00
+ 0.000000 8 0.00 0.00
+ 0.000000 9 0.00 0.00
+ 0.000000 10 0.00 0.00
+ 0.000000 11 0.00 0.00
+ 0.000000 12 0.00 0.00
+ 0.000000 13 0.00 0.00
+ 0.000000 14 0.00 0.00
+ 0.050000 0 0.00 0.00
+ 0.050000 1 0.00 0.00
+ 0.050000 2 0.00 0.00
+ 0.050000 3 -0.00 -0.00
+ 0.050000 4 0.00 0.00
+ 0.050000 5 0.00 0.00
+ 0.050000 6 0.00 0.00
+ 0.050000 7 0.00 0.00
+ 0.050000 8 0.00 0.00
+ 0.050000 9 0.00 0.00
+ 0.050000 10 0.00 0.00
+ 0.050000 11 0.00 0.00
+ 0.050000 12 0.00 0.00
+ 0.050000 13 0.00 0.00
+ 0.050000 14 0.00 0.00
diff --git a/regtest/isdb/rt-fret/der6.reference b/regtest/isdb/rt-fret/der6.reference
new file mode 100644
index 000000000..1dceab54e
--- /dev/null
+++ b/regtest/isdb/rt-fret/der6.reference
@@ -0,0 +1,31 @@
+#! FIELDS time parameter d6 d6_n
+ 0.000000 0 -0.30 -0.30
+ 0.000000 1 0.00 0.00
+ 0.000000 2 -0.30 -0.30
+ 0.000000 3 0.30 0.30
+ 0.000000 4 0.00 0.00
+ 0.000000 5 0.30 0.30
+ 0.000000 6 0.30 0.30
+ 0.000000 7 0.00 0.00
+ 0.000000 8 0.30 0.30
+ 0.000000 9 0.00 0.00
+ 0.000000 10 0.00 0.00
+ 0.000000 11 0.00 0.00
+ 0.000000 12 0.30 0.30
+ 0.000000 13 0.00 0.00
+ 0.000000 14 0.30 0.30
+ 0.050000 0 -0.30 -0.30
+ 0.050000 1 0.00 0.00
+ 0.050000 2 -0.30 -0.30
+ 0.050000 3 0.30 0.30
+ 0.050000 4 0.00 0.00
+ 0.050000 5 0.30 0.30
+ 0.050000 6 0.30 0.30
+ 0.050000 7 0.00 0.00
+ 0.050000 8 0.30 0.30
+ 0.050000 9 0.00 0.00
+ 0.050000 10 0.00 0.00
+ 0.050000 11 0.00 0.00
+ 0.050000 12 0.30 0.30
+ 0.050000 13 0.00 0.00
+ 0.050000 14 0.30 0.30
diff --git a/regtest/isdb/rt-fret/der7.reference b/regtest/isdb/rt-fret/der7.reference
new file mode 100644
index 000000000..85a9f2a96
--- /dev/null
+++ b/regtest/isdb/rt-fret/der7.reference
@@ -0,0 +1,31 @@
+#! FIELDS time parameter d7 d7_n
+ 0.000000 0 -0.30 -0.30
+ 0.000000 1 -0.30 -0.30
+ 0.000000 2 0.00 0.00
+ 0.000000 3 0.30 0.30
+ 0.000000 4 0.30 0.30
+ 0.000000 5 0.00 0.00
+ 0.000000 6 0.30 0.30
+ 0.000000 7 0.30 0.30
+ 0.000000 8 0.00 0.00
+ 0.000000 9 0.30 0.30
+ 0.000000 10 0.30 0.30
+ 0.000000 11 0.00 0.00
+ 0.000000 12 0.00 0.00
+ 0.000000 13 0.00 0.00
+ 0.000000 14 0.00 0.00
+ 0.050000 0 -0.30 -0.30
+ 0.050000 1 -0.30 -0.30
+ 0.050000 2 0.00 0.00
+ 0.050000 3 0.30 0.30
+ 0.050000 4 0.30 0.30
+ 0.050000 5 0.00 0.00
+ 0.050000 6 0.30 0.30
+ 0.050000 7 0.30 0.30
+ 0.050000 8 0.00 0.00
+ 0.050000 9 0.30 0.30
+ 0.050000 10 0.30 0.30
+ 0.050000 11 0.00 0.00
+ 0.050000 12 0.00 0.00
+ 0.050000 13 0.00 0.00
+ 0.050000 14 0.00 0.00
diff --git a/regtest/isdb/rt-fret/der8.reference b/regtest/isdb/rt-fret/der8.reference
new file mode 100644
index 000000000..fd8fad971
--- /dev/null
+++ b/regtest/isdb/rt-fret/der8.reference
@@ -0,0 +1,31 @@
+#! FIELDS time parameter d8 d8_n
+ 0.000000 0 -0.42 -0.42
+ 0.000000 1 -0.42 -0.42
+ 0.000000 2 -0.42 -0.42
+ 0.000000 3 0.42 0.42
+ 0.000000 4 0.42 0.42
+ 0.000000 5 0.42 0.42
+ 0.000000 6 0.42 0.42
+ 0.000000 7 0.42 0.42
+ 0.000000 8 0.42 0.42
+ 0.000000 9 0.42 0.42
+ 0.000000 10 0.42 0.42
+ 0.000000 11 0.42 0.42
+ 0.000000 12 0.42 0.42
+ 0.000000 13 0.42 0.42
+ 0.000000 14 0.42 0.42
+ 0.050000 0 -0.00 -0.00
+ 0.050000 1 0.00 0.00
+ 0.050000 2 -0.00 -0.00
+ 0.050000 3 0.00 0.00
+ 0.050000 4 -0.00 -0.00
+ 0.050000 5 0.00 0.00
+ 0.050000 6 0.00 0.00
+ 0.050000 7 -0.00 -0.00
+ 0.050000 8 0.00 0.00
+ 0.050000 9 -0.00 -0.00
+ 0.050000 10 0.00 0.00
+ 0.050000 11 -0.00 -0.00
+ 0.050000 12 0.00 0.00
+ 0.050000 13 -0.00 -0.00
+ 0.050000 14 0.00 0.00
diff --git a/regtest/isdb/rt-fret/forces.reference b/regtest/isdb/rt-fret/forces.reference
new file mode 100644
index 000000000..98fd7e05d
--- /dev/null
+++ b/regtest/isdb/rt-fret/forces.reference
@@ -0,0 +1,20 @@
+8
+ 0.0000 0.0000 0.0000
+X 0.0000 0.0000 0.0000
+X 0.0000 0.0000 0.0000
+X 0.0000 0.0000 0.0000
+X 0.0000 0.0000 0.0000
+X 0.0000 0.0000 0.0000
+X 0.0000 0.0000 0.0000
+X 0.0000 0.0000 0.0000
+X 0.0000 0.0000 0.0000
+8
+ 0.0000 0.0000 0.0000
+X 0.0000 0.0000 0.0000
+X 0.0000 0.0000 0.0000
+X 0.0000 0.0000 0.0000
+X 0.0000 0.0000 0.0000
+X 0.0000 0.0000 0.0000
+X 0.0000 0.0000 0.0000
+X 0.0000 0.0000 0.0000
+X 0.0000 0.0000 0.0000
diff --git a/regtest/isdb/rt-fret/plumed.dat b/regtest/isdb/rt-fret/plumed.dat
new file mode 100644
index 000000000..e10e40adc
--- /dev/null
+++ b/regtest/isdb/rt-fret/plumed.dat
@@ -0,0 +1,27 @@
+d2: FRET ATOMS=1,2 R0=2
+d3: FRET ATOMS=1,3 R0=2
+d4: FRET ATOMS=1,4 R0=2
+d5: FRET ATOMS=1,5 R0=2
+d6: FRET ATOMS=1,6 R0=2
+d7: FRET ATOMS=1,7 R0=2
+d8: FRET ATOMS=1,8 R0=2
+
+d2_n: FRET ATOMS=1,2 R0=2 NUMERICAL_DERIVATIVES
+d3_n: FRET ATOMS=1,3 R0=2 NUMERICAL_DERIVATIVES
+d4_n: FRET ATOMS=1,4 R0=2 NUMERICAL_DERIVATIVES
+d5_n: FRET ATOMS=1,5 R0=2 NUMERICAL_DERIVATIVES
+d6_n: FRET ATOMS=1,6 R0=2 NUMERICAL_DERIVATIVES
+d7_n: FRET ATOMS=1,7 R0=2 NUMERICAL_DERIVATIVES
+d8_n: FRET ATOMS=1,8 R0=2 NUMERICAL_DERIVATIVES
+
+DUMPDERIVATIVES ARG={d2 d2_n} FILE=der2 FMT=%6.2f
+DUMPDERIVATIVES ARG={d3 d3_n} FILE=der3 FMT=%6.2f
+DUMPDERIVATIVES ARG={d4 d4_n} FILE=der4 FMT=%6.2f
+DUMPDERIVATIVES ARG={d5 d5_n} FILE=der5 FMT=%6.2f
+DUMPDERIVATIVES ARG={d6 d6_n} FILE=der6 FMT=%6.2f
+DUMPDERIVATIVES ARG={d7 d7_n} FILE=der7 FMT=%6.2f
+DUMPDERIVATIVES ARG={d8 d8_n} FILE=der8 FMT=%6.2f
+
+PRINT FILE=COLVAR ARG=d2,d3,d4,d5,d6,d7,d8
+
+ENDPLUMED
diff --git a/regtest/isdb/rt-fret/trajectory.xyz b/regtest/isdb/rt-fret/trajectory.xyz
new file mode 100644
index 000000000..aa856131c
--- /dev/null
+++ b/regtest/isdb/rt-fret/trajectory.xyz
@@ -0,0 +1,20 @@
+8
+10 0 0 0 10 0 0 0 10
+X 0.5 0.5 0.5
+X 0.5 0.5 9.5
+X 0.5 9.5 0.5
+X 0.5 9.5 9.5
+X 9.5 0.5 0.5
+X 9.5 0.5 9.5
+X 9.5 9.5 0.5
+X 9.5 9.5 9.5
+8
+10 10 0 0 10 10 10 0 10
+X 0.5 0.5 0.5
+X 0.5 0.5 9.5
+X 0.5 9.5 0.5
+X 0.5 9.5 9.5
+X 9.5 0.5 0.5
+X 9.5 0.5 9.5
+X 9.5 9.5 0.5
+X 9.5 9.4 9.5
--
GitLab