From 702b0ad636ee11a10d175bc57d6d4e86ba151e1d Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Thu, 9 Aug 2012 16:21:36 +0200
Subject: [PATCH] Added parsing for command line tools that works like actions.
This makes command line tools easy to document in the same manner as Actions
are easy to document
---
regtest/rt-mpi0/config | 2 +-
regtest/rt-mpi1/config | 2 +-
regtest/rt0/config | 2 +-
regtest/rt1/config | 2 +-
regtest/rt10/config | 2 +-
regtest/rt11/config | 2 +-
regtest/rt12/config | 2 +-
regtest/rt14/config | 2 +-
regtest/rt15/config | 2 +-
regtest/rt16/config | 2 +-
regtest/rt17/config | 2 +-
regtest/rt18/config | 2 +-
regtest/rt19-mpi/config | 2 +-
regtest/rt19/config | 2 +-
regtest/rt2/config | 2 +-
regtest/rt20-mpi/config | 2 +-
regtest/rt20/config | 2 +-
regtest/rt21/config | 2 +-
regtest/rt22/config | 2 +-
regtest/rt23/config | 2 +-
regtest/rt24/config | 2 +-
regtest/rt25/config | 2 +-
regtest/rt26/config | 2 +-
regtest/rt27/config | 2 +-
regtest/rt28/config | 2 +-
regtest/rt29/config | 2 +-
regtest/rt3/config | 2 +-
regtest/rt30/config | 2 +-
regtest/rt31/config | 2 +-
regtest/rt32/config | 2 +-
regtest/rt33/config | 2 +-
regtest/rt34/config | 2 +-
regtest/rt35/config | 2 +-
regtest/rt36/config | 2 +-
regtest/rt37/config | 2 +-
regtest/rt4/config | 2 +-
regtest/rt5/config | 2 +-
regtest/rt6/config | 2 +-
regtest/rt7/config | 2 +-
regtest/rt8/config | 2 +-
regtest/rt9/config | 2 +-
src/ActionRegister.cpp | 2 +-
src/CLTool.cpp | 193 ++++++++++++++++++++++++++++++++++++++++
src/CLTool.h | 62 +++++++++++--
src/CLToolDriver.cpp | 193 +++++++++++++++++-----------------------
src/CLToolInfo.cpp | 76 +++++++---------
src/CLToolMain.cpp | 8 +-
src/CLToolManual.cpp | 87 ++++++++----------
src/CLToolRegister.cpp | 19 +++-
src/CLToolRegister.h | 13 ++-
src/CLToolSimpleMD.cpp | 176 ++++++++++++++++++------------------
src/Keywords.cpp | 76 +++++++++++++++-
src/Keywords.h | 10 ++-
src/Tools.cpp | 6 ++
src/Tools.h | 2 +
55 files changed, 651 insertions(+), 354 deletions(-)
create mode 100644 src/CLTool.cpp
diff --git a/regtest/rt-mpi0/config b/regtest/rt-mpi0/config
index 28f95533b..714d1d6dd 100644
--- a/regtest/rt-mpi0/config
+++ b/regtest/rt-mpi0/config
@@ -1,5 +1,5 @@
mpiprocs=4
type=driver
# this is to test a different name
-arg="--plumed=plumed.dat --timestep=0.05 trajectory.xyz --dump-forces ff"
+arg="--plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt-mpi1/config b/regtest/rt-mpi1/config
index 30fb3be36..fd743c293 100644
--- a/regtest/rt-mpi1/config
+++ b/regtest/rt-mpi1/config
@@ -1,5 +1,5 @@
mpiprocs=4
type=driver
# this is to test a different name
-arg="--plumed=plumed.dat --timestep=0.05 trajectory.xyz --dump-forces ff --debug-pd"
+arg="--plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --debug-pd"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt0/config b/regtest/rt0/config
index 20af628e0..fce7937b0 100644
--- a/regtest/rt0/config
+++ b/regtest/rt0/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt1/config b/regtest/rt1/config
index f2791e103..d343ccfdc 100644
--- a/regtest/rt1/config
+++ b/regtest/rt1/config
@@ -3,4 +3,4 @@
# to avoid problems with the numerical derivatives (it is exactly at the border between
# two images)
type=driver
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
diff --git a/regtest/rt10/config b/regtest/rt10/config
index 623ad3cc5..a87726a91 100644
--- a/regtest/rt10/config
+++ b/regtest/rt10/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt11/config b/regtest/rt11/config
index 623ad3cc5..a87726a91 100644
--- a/regtest/rt11/config
+++ b/regtest/rt11/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt12/config b/regtest/rt12/config
index 623ad3cc5..a87726a91 100644
--- a/regtest/rt12/config
+++ b/regtest/rt12/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt14/config b/regtest/rt14/config
index 623ad3cc5..a87726a91 100644
--- a/regtest/rt14/config
+++ b/regtest/rt14/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt15/config b/regtest/rt15/config
index 20af628e0..fce7937b0 100644
--- a/regtest/rt15/config
+++ b/regtest/rt15/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt16/config b/regtest/rt16/config
index 623ad3cc5..a87726a91 100644
--- a/regtest/rt16/config
+++ b/regtest/rt16/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt17/config b/regtest/rt17/config
index 20af628e0..fce7937b0 100644
--- a/regtest/rt17/config
+++ b/regtest/rt17/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt18/config b/regtest/rt18/config
index 20af628e0..fce7937b0 100644
--- a/regtest/rt18/config
+++ b/regtest/rt18/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt19-mpi/config b/regtest/rt19-mpi/config
index ecb920ffc..36dba8dbc 100644
--- a/regtest/rt19-mpi/config
+++ b/regtest/rt19-mpi/config
@@ -1,5 +1,5 @@
mpiprocs=4
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt19/config b/regtest/rt19/config
index 20af628e0..fce7937b0 100644
--- a/regtest/rt19/config
+++ b/regtest/rt19/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt2/config b/regtest/rt2/config
index 20af628e0..fce7937b0 100644
--- a/regtest/rt2/config
+++ b/regtest/rt2/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt20-mpi/config b/regtest/rt20-mpi/config
index ecb920ffc..36dba8dbc 100644
--- a/regtest/rt20-mpi/config
+++ b/regtest/rt20-mpi/config
@@ -1,5 +1,5 @@
mpiprocs=4
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt20/config b/regtest/rt20/config
index 20af628e0..fce7937b0 100644
--- a/regtest/rt20/config
+++ b/regtest/rt20/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt21/config b/regtest/rt21/config
index 20af628e0..fce7937b0 100644
--- a/regtest/rt21/config
+++ b/regtest/rt21/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt22/config b/regtest/rt22/config
index 20af628e0..fce7937b0 100644
--- a/regtest/rt22/config
+++ b/regtest/rt22/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt23/config b/regtest/rt23/config
index 20af628e0..fce7937b0 100644
--- a/regtest/rt23/config
+++ b/regtest/rt23/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt24/config b/regtest/rt24/config
index 47df6596d..192611df2 100644
--- a/regtest/rt24/config
+++ b/regtest/rt24/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt25/config b/regtest/rt25/config
index 47df6596d..192611df2 100644
--- a/regtest/rt25/config
+++ b/regtest/rt25/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt26/config b/regtest/rt26/config
index e592546b3..0a8ccbb18 100644
--- a/regtest/rt26/config
+++ b/regtest/rt26/config
@@ -1,3 +1,3 @@
type=driver
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt27/config b/regtest/rt27/config
index e592546b3..0a8ccbb18 100644
--- a/regtest/rt27/config
+++ b/regtest/rt27/config
@@ -1,3 +1,3 @@
type=driver
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt28/config b/regtest/rt28/config
index e441f5aec..ae36d62c2 100644
--- a/regtest/rt28/config
+++ b/regtest/rt28/config
@@ -1,3 +1,3 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
diff --git a/regtest/rt29/config b/regtest/rt29/config
index e441f5aec..ae36d62c2 100644
--- a/regtest/rt29/config
+++ b/regtest/rt29/config
@@ -1,3 +1,3 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
diff --git a/regtest/rt3/config b/regtest/rt3/config
index 20af628e0..fce7937b0 100644
--- a/regtest/rt3/config
+++ b/regtest/rt3/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt30/config b/regtest/rt30/config
index ee245fbbb..980c469ec 100644
--- a/regtest/rt30/config
+++ b/regtest/rt30/config
@@ -1,2 +1,2 @@
type=driver
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 ala12_trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
diff --git a/regtest/rt31/config b/regtest/rt31/config
index ee245fbbb..980c469ec 100644
--- a/regtest/rt31/config
+++ b/regtest/rt31/config
@@ -1,2 +1,2 @@
type=driver
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 ala12_trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
diff --git a/regtest/rt32/config b/regtest/rt32/config
index ee245fbbb..980c469ec 100644
--- a/regtest/rt32/config
+++ b/regtest/rt32/config
@@ -1,2 +1,2 @@
type=driver
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 ala12_trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
diff --git a/regtest/rt33/config b/regtest/rt33/config
index 7d0e9d21d..b3efe6c3c 100644
--- a/regtest/rt33/config
+++ b/regtest/rt33/config
@@ -1,2 +1,2 @@
type=driver
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 amyloid.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz amyloid.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
diff --git a/regtest/rt34/config b/regtest/rt34/config
index 20af628e0..fce7937b0 100644
--- a/regtest/rt34/config
+++ b/regtest/rt34/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt35/config b/regtest/rt35/config
index cbf38b9c3..45386cb93 100644
--- a/regtest/rt35/config
+++ b/regtest/rt35/config
@@ -1,2 +1,2 @@
type=driver
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 ../../trajectories/diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz ../../trajectories/diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
diff --git a/regtest/rt36/config b/regtest/rt36/config
index 20af628e0..fce7937b0 100644
--- a/regtest/rt36/config
+++ b/regtest/rt36/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt37/config b/regtest/rt37/config
index cbf38b9c3..45386cb93 100644
--- a/regtest/rt37/config
+++ b/regtest/rt37/config
@@ -1,2 +1,2 @@
type=driver
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 ../../trajectories/diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz ../../trajectories/diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
diff --git a/regtest/rt4/config b/regtest/rt4/config
index 623ad3cc5..a87726a91 100644
--- a/regtest/rt4/config
+++ b/regtest/rt4/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt5/config b/regtest/rt5/config
index 623ad3cc5..a87726a91 100644
--- a/regtest/rt5/config
+++ b/regtest/rt5/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt6/config b/regtest/rt6/config
index 623ad3cc5..a87726a91 100644
--- a/regtest/rt6/config
+++ b/regtest/rt6/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt7/config b/regtest/rt7/config
index 623ad3cc5..a87726a91 100644
--- a/regtest/rt7/config
+++ b/regtest/rt7/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt8/config b/regtest/rt8/config
index 623ad3cc5..a87726a91 100644
--- a/regtest/rt8/config
+++ b/regtest/rt8/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/regtest/rt9/config b/regtest/rt9/config
index 623ad3cc5..a87726a91 100644
--- a/regtest/rt9/config
+++ b/regtest/rt9/config
@@ -1,4 +1,4 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
extra_files="../trajectories/trajectory.xyz"
diff --git a/src/ActionRegister.cpp b/src/ActionRegister.cpp
index fd976193c..87d0081c6 100644
--- a/src/ActionRegister.cpp
+++ b/src/ActionRegister.cpp
@@ -89,7 +89,7 @@ Action* ActionRegister::create(const ActionOptions&ao){
bool ActionRegister::printManual( const std::string& action ){
if ( check(action) ){
Keywords keys; mk[action](keys);
- keys.print_html(); keys.destroyData();
+ keys.print_html(true); keys.destroyData();
return true;
} else {
return false;
diff --git a/src/CLTool.cpp b/src/CLTool.cpp
new file mode 100644
index 000000000..6a4b749d1
--- /dev/null
+++ b/src/CLTool.cpp
@@ -0,0 +1,193 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.0.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "CLTool.h"
+
+using namespace PLMD;
+
+Keywords CLToolOptions::emptyKeys;
+
+CLToolOptions::CLToolOptions(const std::string &name):
+line(1,name),
+keys(emptyKeys)
+{
+}
+
+CLToolOptions::CLToolOptions(const CLToolOptions& co, const Keywords& k):
+line(co.line),
+keys(k)
+{
+}
+
+void CLTool::registerKeywords( Keywords& keys ){
+ keys.addFlag("--help",false,"print this help");
+}
+
+CLTool::CLTool(const CLToolOptions& co ):
+name(co.line[0]),
+keywords(co.keys),
+inputdata(unset)
+{
+}
+
+void CLTool::parseFlag( const std::string&key, bool&t ){
+ plumed_massert(keywords.exists(key),"keyword " + key + " has not been registered");
+ plumed_massert(keywords.style(key,"flag"),"keyword " + key + " has not been registered as a flag");
+ plumed_assert(inputData.count(key)>0);
+ if( inputData[key]=="true") t=true;
+ else if( inputData[key]=="false") t=false;
+ else plumed_assert(0);
+}
+
+bool CLTool::readInput( int argc, char**argv, FILE* in, FILE*out ){
+ plumed_massert( inputdata!=unset,"You have not specified where your tool reads its input. "
+ "If it is from the command line (like driver) add inputdata=commandline to the "
+ "tools constructor. If it reads everything from an input file (like simplemd) "
+ "add inputdata=ifile to the tools constructor");
+ if(inputdata==commandline) return readCommandLineArgs( argc, argv, out );
+ if(inputdata==ifile) return readInputFile( argc, argv, in, out );
+ readInput( argc, argv, in, out ); // This allows the user to specify the particular form for input
+ return true;
+}
+
+bool CLTool::readCommandLineArgs( int argc, char**argv, FILE*out ){
+ plumed_assert(inputdata==commandline);
+ std::string prefix(""), a(""), thiskey;
+
+ // Set all flags to default false
+ for(int k=0;k<keywords.size();++k){
+ thiskey=keywords.get(k);
+ if( keywords.style(thiskey,"flag") ) inputData.insert(std::pair<std::string,std::string>(thiskey,"false"));
+ }
+
+ // Read command line arguments
+ bool printhelp=false;
+ for(int i=1;i<argc;i++){
+ a=prefix+argv[i];
+ if(a.length()==0) continue;
+ if(a=="-h" || a=="--help"){
+ printhelp=true;
+ } else {
+ bool found=false;
+ for(int k=0;k<keywords.size();++k){
+ thiskey=keywords.get(k);
+ if( keywords.style(thiskey,"flag") ){
+ if( a==thiskey ){ found=true; inputData[thiskey]="true"; }
+ } else {
+ if( a==thiskey ){
+ prefix=thiskey+"="; found=true;
+ inputData.insert(std::pair<std::string,std::string>(thiskey,""));
+ } else if( a.find(thiskey+"=")==0){
+ a.erase(0,a.find("=")+1); prefix=""; found=true;
+ if(inputData.count(thiskey)==0){
+ inputData.insert(std::pair<std::string,std::string>(thiskey,a));
+ } else {
+ inputData[thiskey]=a;
+ }
+ }
+ }
+ }
+ if(!found){
+ fprintf(out,"ERROR : unknown option %s\n\n", a.c_str() );
+ printhelp=true;
+ }
+ }
+ if(printhelp) break;
+ }
+
+ if(!printhelp) setRemainingToDefault(out);
+
+ if(printhelp){
+ fprintf(out,"Usage: %s [options] \n\n", name.c_str() );
+ keywords.print( out );
+ }
+
+ return !printhelp;
+}
+
+void CLTool::setRemainingToDefault(FILE* out){
+ std::string def, thiskey;
+ for(int k=0;k<keywords.size();++k){
+ thiskey=keywords.get(k);
+ if( keywords.style(thiskey,"compulsory") ){
+ if( inputData.count(thiskey)==0 ){
+ if( keywords.getDefaultValue(thiskey,def) ){
+ plumed_assert( def.length()>0 );
+ inputData.insert(std::pair<std::string,std::string>(thiskey,def));
+ } else {
+ fprintf(out,"ERROR : argument %s is compulsory. Use --help option for help\n",thiskey.c_str() );
+ }
+ }
+ }
+ }
+}
+
+bool CLTool::readInputFile( int argc, char**argv, FILE* in, FILE*out ){
+ plumed_assert(inputdata==ifile);
+
+ // Check if use is just asking for help
+ std::string a;
+ for(int i=1;i<argc;i++){
+ a=argv[i];
+ if(a.length()==0) continue;
+ if(a=="-h" || a=="--help"){
+ fprintf(out,"Usage: %s < inputFile \n", name.c_str() );
+ fprintf(out,"inputFile should contain one directive per line. The directives should come from amongst the following\n\n");
+ keywords.print( out );
+ return false;
+ }
+ }
+
+ FILE* mystdin=in;
+ if(argc==2) mystdin=fopen(argv[1],"r");
+
+ char buffer[256]; std::string line; line.resize(256);
+ while(fgets(buffer,256,mystdin)){
+ line=buffer;
+ for(int i=0;i<line.length();++i) if(line[i]=='#' || line[i]=='\n') line.erase(i);
+ Tools::stripLeadingAndTrailingBlanks( line );
+ if(line.length()==0) continue;
+ sscanf(line.c_str(),"%s",buffer);
+ std::string keyword=buffer; bool found=false;
+ for(unsigned i=0;i<keywords.size();++i){
+ std::string thiskey=keywords.get(i);
+ if(thiskey==keyword){
+ found=true;
+ std::size_t keypos=line.find_first_of(keyword)+keyword.length();
+ inputData.insert(std::pair<std::string,std::string>(thiskey,line.substr(keypos)));
+ Tools::stripLeadingAndTrailingBlanks( inputData[thiskey] );
+ }
+ }
+ if(!found){
+ fprintf(stderr,"Unknown keyword found in input file :%s\n",keyword.c_str());
+ return false;
+ }
+ }
+
+ if(argc==2) fclose(mystdin);
+ setRemainingToDefault(out);
+ return true;
+}
+
+void CLTool::readInputData( int argc, char**argv, FILE* in, FILE*out ){
+ plumed_assert( inputdata!=commandline && inputdata!=ifile );
+ if( inputdata==userspec ) plumed_massert(0, "You have to actually write the routine in the base class!");
+}
diff --git a/src/CLTool.h b/src/CLTool.h
index 1dc435baa..354e608d3 100644
--- a/src/CLTool.h
+++ b/src/CLTool.h
@@ -25,17 +25,25 @@
#include <cstdio>
#include <vector>
#include <string>
+#include <cstdio>
+#include "Tools.h"
+#include "Keywords.h"
namespace PLMD{
class PlumedCommunicator;
class CLToolOptions{
+ friend class CLTool;
friend class CLToolRegister;
+private:
std::vector<std::string> line;
+/// The documentation for this command line tool
+ const Keywords& keys;
+ static Keywords emptyKeys;
public:
- CLToolOptions(const std::string &name):
- line(1,name) { }
+ CLToolOptions(const std::string &name);
+ CLToolOptions(const CLToolOptions& co, const Keywords& k);
};
/**
@@ -44,18 +52,62 @@ Interface to all the command-line tools.
This class just define an interface, and does not implement anything.
Inherits from this class to create a new command-line tool.
*/
-class CLTool
-{
+class CLTool {
+// This is a fried so we can create input data quickly
+// when you do debug-float.
+template <typename real>
+friend class CLToolDriver;
+private:
+/// The name of this command line tool
+ const std::string name;
+/// The list of keywords for this CLTool
+ const Keywords& keywords;
+/// The data read in from the command line stored in a map with the keywords
+ std::map<std::string,std::string> inputData;
+/// Read the arguments from the command line
+ bool readCommandLineArgs( int argc, char**argv, FILE*out );
+/// Read the arguments from an input file specified on the command line
+ bool readInputFile( int argc, char**argv, FILE* in, FILE*out );
+/// Set arguments from the default options provided to Keywords
+ void setRemainingToDefault(FILE* out);
+protected:
+/// Get the value of one of the command line arguments
+ template<class T>
+ bool parse(const std::string&key,T&t);
+/// Find out whether one of the command line flags is present or not
+ void parseFlag(const std::string&key,bool&t);
public:
+/// How is the input specified on the command line or in an input file
+ enum {unset,commandline,ifile,userspec} inputdata;
+/// Create the help keywords
+ static void registerKeywords( Keywords& keys );
+ CLTool(const CLToolOptions& co );
+/// Read the arguments from the command line
+ bool readInput( int argc, char**argv, FILE* in, FILE*out );
+/// Read the input in the derived class (overwrite this if you are not using
+/// command line arguments or an input file in the style of simplemd's)
+ virtual void readInputData( int argc, char**argv, FILE* in, FILE*out );
/// virtual function mapping to the specific main for each tool
- virtual int main(int argc, char **argv,FILE*in,FILE*out,PlumedCommunicator&pc)=0;
+ virtual int main( FILE*out, PlumedCommunicator&pc )=0;
/// virtual function returning a one-line descriptor for the tool
virtual std::string description()const{return "(no description available)";};
/// virtual destructor to allow inheritance
virtual ~CLTool(){};
};
+template<class T>
+bool CLTool::parse(const std::string&key,T&t){
+ plumed_massert(keywords.exists(key),"keyword " + key + " has not been registered");
+ if(keywords.style(key,"compulsory") ){
+ plumed_assert(inputData.count(key)>0);
+ plumed_assert( Tools::convert(inputData[key],t) );
+ return true;
+ }
+ if( inputData.count(key)==0 ) return false;
+ Tools::convert(inputData[key],t);
+ return true;
}
+}
#endif
diff --git a/src/CLToolDriver.cpp b/src/CLToolDriver.cpp
index 73b155e44..b1c9e6721 100644
--- a/src/CLToolDriver.cpp
+++ b/src/CLToolDriver.cpp
@@ -34,21 +34,53 @@ using namespace std;
namespace PLMD {
//+PLUMEDOC TOOLS driver
-/**
-driver is a tool that allows one to to use plumed to post-process
-an existing trajectory.
+/*
+driver is a tool that allows one to to use plumed to post-process an existing trajectory.
+
+The input to driver is specified using the command line arguments described below.
+
+\par Examples
+
+The following command tells plumed to postprocess the trajectory contained in trajectory.xyz
+ by calcualting the actions described in the input file plumed.dat.
+\verbatim
+plumed driver --plumed plumed.dat --ixyz trajectory.xyz
+\endverbatim
+
*/
//+ENDPLUMEDOC
template<typename real>
-class CLToolDriver:
-public CLTool
-{
+class CLToolDriver : public CLTool {
public:
- int main(int argc,char**argv,FILE*in,FILE*out,PlumedCommunicator& pc);
+ static void registerKeywords( Keywords& keys );
+ CLToolDriver(const CLToolOptions& co );
+ int main(FILE*out,PlumedCommunicator& pc);
string description()const;
};
+template<typename real>
+void CLToolDriver<real>::registerKeywords( Keywords& keys ){
+ CLTool::registerKeywords( keys );
+ keys.addFlag("--help-debug",false,"print special options that can be used to create regtests");
+ keys.add("compulsory","--plumed","plumed.dat","specify the name of the plumed input file");
+ keys.add("compulsory","--timestep","0.001","the timestep for the trajectory in picoseconds");
+ keys.add("compulsory","--stride","1","stride between frames on which to do the calculation");
+ keys.add("atoms","--ixyz","the trajectory in xyz format");
+ keys.add("optional","--dump-forces","dump the forces on a file");
+ keys.add("optional","--dump-forces-fmt","( default=%%f ) the format to use to dump the forces");
+ keys.add("hidden","--debug-float","turns on the single precision version (to check float interface)");
+ keys.add("hidden","--debug-dd","use a fake domain decomposition");
+ keys.add("hidden","--debug-pd","use a fake particle decomposition");
+}
+
+template<typename real>
+CLToolDriver<real>::CLToolDriver(const CLToolOptions& co ):
+CLTool(co)
+{
+ inputdata=commandline;
+}
+
template<typename real>
string CLToolDriver<real>::description()const{ return "analyze trajectories with plumed"; }
@@ -57,110 +89,49 @@ string CLToolDriver<float>::description()const{ return "analyze trajectories wit
template<typename real>
-int CLToolDriver<real>::main(int argc,char**argv,FILE*in,FILE*out,PlumedCommunicator& pc){
-
-// to avoid warnings:
- (void) in;
-
- string plumedFile("plumed.dat");
- string dumpforces("");
- string dumpforcesFmt("%f");
- string trajectoryFile("");
- real timestep(real(0.001));
- unsigned stride(1);
- bool printhelp=false;
- bool printhelpdebug=false;
- bool debug_dd=false;
- bool debug_pd=false;
-
-// Start parsing options
- string prefix("");
- string a("");
- for(int i=1;i<argc;i++){
- a=prefix+argv[i];
- if(a.length()==0) continue;
- if(a=="-h" || a=="--help"){
- printhelp=true;
- break;
- } else if(a=="--help-debug"){
- printhelp=true;
- printhelpdebug=true;
- break;
- } else if(a=="--debug-float"){
- if(sizeof(real)!=sizeof(float)){
- CLTool* cl=new CLToolDriver<float>;
- int ret=cl->main(argc,argv,in,out,pc);
- delete cl;
- return ret;
- }
- } else if(a=="--debug-pd"){
- debug_pd=true;
- } else if(a=="--debug-dd"){
- debug_dd=true;
- } else if(a.find("--plumed=")==0){
- a.erase(0,a.find("=")+1);
- plumedFile=a;
- prefix="";
- } else if(a=="--plumed"){
- prefix="--plumed=";
- } else if(a.find("--timestep=")==0){
- a.erase(0,a.find("=")+1);
- double t;
- Tools::convert(a,t);
- timestep=real(t);
- prefix="";
- } else if(a=="--timestep"){
- prefix="--timestep=";
- } else if(a.find("--stride=")==0){
- a.erase(0,a.find("=")+1);
- Tools::convert(a,stride);
- prefix="";
- } else if(a=="--stride"){
- prefix="--stride=";
- } else if(a.find("--dump-forces=")==0){
- a.erase(0,a.find("=")+1);
- dumpforces=a;
- prefix="";
- } else if(a=="--dump-forces"){
- prefix="--dump-forces=";
- } else if(a.find("--dump-forces-fmt=")==0){
- a.erase(0,a.find("=")+1);
- dumpforcesFmt=a;
- prefix="";
- } else if(a=="--dump-forces-fmt"){
- prefix="--dump-forces-fmt=";
- } else if(a[0]=='-') {
- string msg="ERROR: Unknown option " +a;
- fprintf(stderr,"%s\n",msg.c_str());
- return 1;
- } else if(trajectoryFile.length()==0){
- trajectoryFile=a;
- } else {
- string msg="ERROR: maximum one file at a time";
- fprintf(stderr,"%s\n",msg.c_str());
- return 1;
- }
+int CLToolDriver<real>::main(FILE*out,PlumedCommunicator& pc){
+
+// Parse everything
+ bool printhelpdebug; parseFlag("--help-debug",printhelpdebug);
+ if( printhelpdebug ){
+ fprintf(out,"%s",
+ "Additional options for debug (only to be used in regtest):\n"
+ " [--debug-float] : turns on the single precision version (to check float interface)\n"
+ " [--debug-dd] : use a fake domain decomposition\n"
+ " [--debug-pd] : use a fake particle decomposition\n"
+ );
+ return 0;
+ }
+ std::string fakein;
+ bool debugfloat=parse("--debug-float",fakein);
+ if(debugfloat && sizeof(real)!=sizeof(float)){
+ CLTool* cl=cltoolRegister().create(CLToolOptions("driver-float")); //new CLToolDriver<float>(*this);
+ cl->inputData=this->inputData;
+ int ret=cl->main(out,pc);
+ delete cl;
+ return ret;
}
- if(printhelp){
- fprintf(out,"%s",
- "Usage: driver [options] trajectory.xyz\n"
- "Options:\n"
- " [--help|-h] : prints this help\n"
- " [--help-debug] : prints this help plus special options for debug\n"
- " [--plumed FILE] : plumed script file (default: plumed.dat)\n"
- " [--timestep TS] : timestep (default: 0.001) in picoseconds\n"
- " [--stride ST] : stride between frames (default: 1)\n"
- " [--dump-forces FILE] : dump forces on file FILE (default: do not dump)\n"
- " [--dump-forces-fmt FMT] : dump forces on file FILE (default: %f)\n"
-);
- if(printhelpdebug)
- fprintf(out,"%s",
- "Additional options for debug (only to be used in regtest):\n"
- " [--debug-float] : turns on the single precision version (to check float interface)\n"
- " [--debug-dd] : use a fake domain decomposition\n"
- " [--debug-pd] : use a fake particle decomposition\n"
-);
+ bool debug_pd=parse("--debug-pd",fakein);
+ bool debug_dd=parse("--debug-dd",fakein);
+// Read the plumed input file name
+ string plumedFile; parse("--plumed",plumedFile);
+// the timestep
+ double t; parse("--timestep",t);
+ real timestep=real(t);
+// the stride
+ unsigned stride; parse("--stride",stride);
+// are we writing forces
+ string dumpforces(""), dumpforcesFmt("%f");;
+ parse("--dump-forces",dumpforces);
+ if(dumpforces!="") parse("--dump-forces-fmt",dumpforcesFmt);
+
+// Read in an xyz file
+ string trajectoryFile("");
+ std::string traj_xyz; parse("--ixyz",traj_xyz);
+ if(traj_xyz.length()>0 && trajectoryFile.length()==0) trajectoryFile=traj_xyz;
+ if(trajectoryFile.length()==0){
+ fprintf(out,"ERROR: missing trajectory data\n");
return 0;
}
@@ -179,7 +150,6 @@ int CLToolDriver<real>::main(int argc,char**argv,FILE*in,FILE*out,PlumedCommunic
p.cmd("setRealPrecision",&rr);
int checknatoms=0;
int step=0;
-
FILE* fp=fopen(trajectoryFile.c_str(),"r");
@@ -316,8 +286,9 @@ int CLToolDriver<real>::main(int argc,char**argv,FILE*in,FILE*out,PlumedCommunic
}
typedef CLToolDriver<double> CLToolDriverDouble;
-
+typedef CLToolDriver<float> CLToolDriverFloat;
PLUMED_REGISTER_CLTOOL(CLToolDriverDouble,"driver")
+PLUMED_REGISTER_CLTOOL(CLToolDriverFloat,"driver-float")
diff --git a/src/CLToolInfo.cpp b/src/CLToolInfo.cpp
index 44c407979..393649e44 100644
--- a/src/CLToolInfo.cpp
+++ b/src/CLToolInfo.cpp
@@ -32,8 +32,19 @@ using namespace std;
namespace PLMD {
//+PLUMEDOC TOOLS info
-/**
-This is a tool that allows you to obtain information about your plumed version
+/*
+This tool allows you to obtain information about your plumed version
+
+You can specify the information you require using the following command line
+arguments
+
+\par Examples
+
+The following command returns the root directory for your plumed distribution.
+\verbatim
+plumed info --root
+\endverbatim
+
*/
//+ENDPLUMEDOC
@@ -41,56 +52,35 @@ class CLToolInfo:
public CLTool
{
public:
- int main(int argc,char**argv,FILE*in,FILE*out,PlumedCommunicator& pc);
+ static void registerKeywords( Keywords& keys );
+ CLToolInfo(const CLToolOptions& co );
+ int main(FILE*out,PlumedCommunicator& pc);
string description()const{
return "provide informations about plumed";
}
};
-
PLUMED_REGISTER_CLTOOL(CLToolInfo,"info")
-int CLToolInfo::main(int argc,char**argv,FILE*in,FILE*out,PlumedCommunicator& pc){
-
-// to avoid warnings:
- (void) in;
-
- bool printconfiguration(false);
- bool printhelp(false);
-
-// Start parsing options
- string prefix("");
- string a("");
- for(int i=1;i<argc;i++){
- a=prefix+argv[i];
- if(a.length()==0) continue;
- if(a=="-h" || a=="--help"){
- printhelp=true;
- break;
- }
- if(a=="--configuration"){
- printconfiguration=true;
- break;
- } else if(a=="--root"){
- fprintf(out,"%s\n",plumedRoot.c_str());
- } else {
- string msg="ERROR: maximum one file at a time";
- fprintf(stderr,"%s\n",msg.c_str());
- return 1;
- }
- }
+void CLToolInfo::registerKeywords( Keywords& keys ){
+ CLTool::registerKeywords( keys );
+ keys.addFlag("--configuration",false,"prints the configuration file");
+ keys.addFlag("--root",false,"print the location of the root directory for the plumed source");
+}
- if(printhelp){
- fprintf(out,"%s",
- "Usage: info [options]\n"
- "Options:\n"
- " [--help|-h] : prints this help\n"
- " [--configuration] : prints the configuration file\n"
-);
- return 0;
- }
+CLToolInfo::CLToolInfo(const CLToolOptions& co ):
+CLTool(co)
+{
+ inputdata=commandline;
+}
+
+int CLToolInfo::main(FILE*out,PlumedCommunicator& pc){
+
+ bool printconfiguration; parseFlag("--configuration",printconfiguration);
+ bool printroot; parseFlag("--root",printroot);
+ if(printroot) fprintf(out,"%s\n",plumedRoot.c_str());
- if(printconfiguration){
+ if(printconfiguration){
static const unsigned char conf [] ={
#include "Makefile.conf.xxd"
, 0x00 };
diff --git a/src/CLToolMain.cpp b/src/CLToolMain.cpp
index ce4dd6aed..1dd927a5f 100644
--- a/src/CLToolMain.cpp
+++ b/src/CLToolMain.cpp
@@ -203,8 +203,10 @@ int CLToolMain::run(int argc, char **argv,FILE*in,FILE*out,PlumedCommunicator& p
if(find(availableCxx.begin(),availableCxx.end(),command)!=availableCxx.end()){
CLTool *cl=cltoolRegister().create(command);
- plumed_assert(cl);
- int ret=cl->main(argc-i,&argv[i],in,out,pc);
+ plumed_assert(cl);
+ // Read the command line options (returns false if we are just printing help)
+ if( !cl->readInput( argc-i,&argv[i],in,out ) ){ delete cl; return 0; }
+ int ret=cl->main(out,pc);
delete cl;
return ret;
}
@@ -218,7 +220,7 @@ int CLToolMain::run(int argc, char **argv,FILE*in,FILE*out,PlumedCommunicator& p
return 0;
}
- string msg="ERROR: unknown command " + command;
+ string msg="ERROR: unknown command " + command + ". Use 'plumed help' for help";
fprintf(stderr,"%s\n",msg.c_str());
return 1;
diff --git a/src/CLToolManual.cpp b/src/CLToolManual.cpp
index 0754891bc..3f35621ee 100644
--- a/src/CLToolManual.cpp
+++ b/src/CLToolManual.cpp
@@ -34,9 +34,22 @@ using namespace std;
namespace PLMD {
//+PLUMEDOC TOOLS manual
-/**
+/*
manual is a tool that you can use to construct the manual page for
a particular action
+
+The manual constructed by this action is in html. In all probability you will never need to use this
+tool. However, it is used within the scripts that generate plumed's html manual. If you need to use this
+tool outside those scripts the input is specified using the following command line arguments.
+
+\par Examples
+
+The following generates the html manual for the action DISTANCE.
+\verbatim
+plumed manual --action DISTANCE
+\endverbatim
+
+
*/
//+ENDPLUMEDOC
@@ -44,7 +57,9 @@ class CLToolManual:
public CLTool
{
public:
- int main(int argc,char**argv,FILE*in,FILE*out,PlumedCommunicator& pc);
+ static void registerKeywords( Keywords& keys );
+ CLToolManual(const CLToolOptions& co );
+ int main(FILE*out,PlumedCommunicator& pc);
string description()const{
return "print out a description of the keywords for an action in html";
}
@@ -52,56 +67,28 @@ public:
PLUMED_REGISTER_CLTOOL(CLToolManual,"manual")
-int CLToolManual::main(int argc,char**argv,FILE*in,FILE*out,PlumedCommunicator& pc){
-
-// to avoid warnings:
- (void) in;
-
- std::string action="none";
- bool printhelp(false);
-
-// Start parsing options
- string prefix("");
- std::string a("");
- for(int i=1;i<argc;i++){
- a=prefix+argv[i];
- if(a.length()==0) continue;
- if(a=="-h" || a=="--help"){
- printhelp=true;
- break;
- }
- if(a.find("--action=")==0){
- a.erase(0,a.find("=")+1);
- action=a;
- prefix="";
- } else if(a=="--action"){
- prefix="--action=";
- } else {
- string msg="ERROR: unknown option"+a;
- fprintf(stderr,"%s\n",msg.c_str());
- return 1;
- }
- }
-
- if(printhelp){
- fprintf(out,"%s",
- "Usage: info [options]\n"
- "Options:\n"
- " [--help|-h] : prints this help\n"
- " [--action] : print the manual for this action\n"
-);
- return 0;
- }
+void CLToolManual::registerKeywords( Keywords& keys ){
+ CLTool::registerKeywords( keys );
+ keys.add("compulsory","--action","print the manual for this particular action");
+}
- if(action=="none"){
- fprintf(stderr,"missing --action flag\n");
- return 1;
- }
+CLToolManual::CLToolManual(const CLToolOptions& co ):
+CLTool(co)
+{
+ inputdata=commandline;
+}
- std::cerr<<actionRegister();
- if( !actionRegister().printManual(action) ){
- fprintf(stderr,"specified action is not registered\n");
- return 1;
+int CLToolManual::main(FILE*out,PlumedCommunicator& pc){
+
+ std::string action;
+ if( !parse("--action",action) ) return 1;
+ std::cerr<<"LIST OF DOCUMENTED ACTIONS:\n";
+ std::cerr<<actionRegister()<<"\n";
+ std::cerr<<"LIST OF DOCUMENTED COMMAND LINE TOOLS:\n";
+ std::cerr<<cltoolRegister()<<"\n\n";
+ if( !actionRegister().printManual(action) && !cltoolRegister().printManual(action) ){
+ fprintf(stderr,"specified action is not registered\n");
+ return 1;
}
return 0;
diff --git a/src/CLToolRegister.cpp b/src/CLToolRegister.cpp
index 4d9292b99..b382de20d 100644
--- a/src/CLToolRegister.cpp
+++ b/src/CLToolRegister.cpp
@@ -50,12 +50,14 @@ void CLToolRegister::remove(creator_pointer f){
}
}
-void CLToolRegister::add(string key,creator_pointer f){
+void CLToolRegister::add(string key,creator_pointer f,keywords_pointer kf){
if(m.count(key)){
m.erase(key);
disabled.insert(key);
}else{
m.insert(pair<string,creator_pointer>(key,f));
+ Keywords keys; kf(keys);
+ mk.insert(pair<string,Keywords>(key,keys));
};
}
@@ -67,8 +69,10 @@ bool CLToolRegister::check(string key){
CLTool* CLToolRegister::create(const CLToolOptions&ao){
if(ao.line.size()<1)return NULL;
CLTool* cltool;
- if(check(ao.line[0])) cltool=m[ao.line[0]](ao);
- else cltool=NULL;
+ if(check(ao.line[0])){
+ CLToolOptions nao( ao,mk[ao.line[0]] );
+ cltool=m[ao.line[0]](nao);
+ } else cltool=NULL;
return cltool;
}
@@ -88,6 +92,15 @@ std::ostream & PLMD::operator<<(std::ostream &log,const CLToolRegister&ar){
return log;
}
+bool CLToolRegister::printManual( const std::string& cltool ){
+ if ( check(cltool) ){
+ mk[cltool].print_html(false);
+ return true;
+ } else {
+ return false;
+ }
+}
+
vector<string> CLToolRegister::list()const{
vector<string> s;
for(const_mIterator it=m.begin();it!=m.end();++it)
diff --git a/src/CLToolRegister.h b/src/CLToolRegister.h
index 251a1be8c..7c1331461 100644
--- a/src/CLToolRegister.h
+++ b/src/CLToolRegister.h
@@ -27,6 +27,7 @@
#include <set>
#include <vector>
#include <iosfwd>
+#include "Keywords.h"
namespace PLMD{
@@ -39,8 +40,12 @@ class CLToolRegister{
friend std::ostream &operator<<(std::ostream &,const CLToolRegister&);
/// Pointer to a function which, given the options, create an CLTool
typedef CLTool*(*creator_pointer)(const CLToolOptions&);
+/// Pointer to a function which, returns the keywords allowed
+ typedef void(*keywords_pointer)(Keywords&);
/// Map cltool to a function which creates the related object
std::map<std::string,creator_pointer> m;
+/// Map cltool name to the keywords for this function
+ std::map<std::string,Keywords> mk;
/// Iterator over the map
typedef std::map<std::string,creator_pointer>::iterator mIterator;
/// Iterator over the map
@@ -51,7 +56,7 @@ public:
/// Register a new class.
/// \param key The name of the directive to be used in the input file
/// \param key A pointer to a function which creates an object of that class
- void add(std::string key,creator_pointer);
+ void add(std::string key,creator_pointer,keywords_pointer);
/// Verify if a directive is present in the register
bool check(std::string cltool);
/// Create an CLTool of the type indicated in the options
@@ -61,6 +66,8 @@ public:
~CLToolRegister();
/// Returns a list of the allowed CLTools
std::vector<std::string> list()const;
+/// Print out the instructions for using the tool in html ready for input into the manual
+ bool printManual(const std::string& cltool);
};
/// Function returning a reference to the CLToolRegister.
@@ -83,9 +90,9 @@ std::ostream & operator<<(std::ostream &log,const CLToolRegister&ar);
/// This macro should be used in the .cpp file of the corresponding class
#define PLUMED_REGISTER_CLTOOL(classname,directive) \
static class classname##RegisterMe{ \
- static PLMD::CLTool* create(const PLMD::CLToolOptions&ao){(void)ao;return new classname;} \
+ static PLMD::CLTool* create(const PLMD::CLToolOptions&ao){return new classname(ao);} \
public: \
- classname##RegisterMe(){PLMD::cltoolRegister().add(directive,create);}; \
+ classname##RegisterMe(){PLMD::cltoolRegister().add(directive,create,classname::registerKeywords);}; \
~classname##RegisterMe(){PLMD::cltoolRegister().remove(create);}; \
} classname##RegisterMeObject;
diff --git a/src/CLToolSimpleMD.cpp b/src/CLToolSimpleMD.cpp
index 0a7d9ca49..925b0d095 100644
--- a/src/CLToolSimpleMD.cpp
+++ b/src/CLToolSimpleMD.cpp
@@ -34,6 +34,45 @@ using namespace PLMD;
namespace PLMD{
+//+PLUMEDOC TOOLS simplemd
+/*
+simplemd allows one to do molecular dynamics on systems of Lennard-Jones atoms.
+
+The input to simplemd is spcified in an input file. Configurations are input and
+output in xyz format. The input file should contain one directive per line.
+The directives available are as follows:
+
+\par Examples
+
+You run an MD simulation using simplemd with the following command:
+\verbatim
+plumed simplemd < in
+\endverbatim
+
+The following is an example of an input file for a simplemd calculation. This file
+instructs simplemd to do 50 steps of MD at a temperature of 0.722
+\verbatim
+nputfile input.xyz
+outputfile output.xyz
+temperature 0.722
+tstep 0.005
+friction 1
+forcecutoff 2.5
+listcutoff 3.0
+nstep 50
+nconfig 10 trajectory.xyz
+nstat 10 energies.dat
+\endverbatim
+
+If you run the following a description of all the directives that can be used in the
+input file will be output.
+\verbatim
+plumed simplemd --help
+\endverbatim
+
+*/
+//+ENDPLUMEDOC
+
class CLToolSimpleMD:
public PLMD::CLTool
{
@@ -52,7 +91,26 @@ FILE* write_statistics_fp;
public:
-CLToolSimpleMD(){
+static void registerKeywords( Keywords& keys ){
+ keys.add("compulsory","nstep","The number of steps of dynamics you want to run");
+ keys.add("compulsory","temperature","NVE","the temperature at which you wish to run the simulation in LJ units");
+ keys.add("compulsory","friction","off","The friction (in LJ units) for the langevin thermostat that is used to keep the temperature constant");
+ keys.add("compulsory","tstep","0.005","the integration timestep in LJ units");
+ keys.add("compulsory","inputfile","An xyz file containing the initial configuration of the system");
+ keys.add("compulsory","forcecutoff","2.5","");
+ keys.add("compulsory","listcutoff","3.0","");
+ keys.add("compulsory","outputfile","An output xyz file containing the final configuration of the system");
+ keys.add("compulsory","nconfig","10","The frequency with which to write configurations to the trajectory file followed by the name of the trajectory file");
+ keys.add("compulsory","nstat","1","The frequency with which to write the statistics to the statistics file followed by the name of the statistics file");
+ keys.add("compulsory","maxneighbours","10000","The maximum number of neighbours an atom can have");
+ keys.add("compulsory","idum","0","The random number seed");
+ keys.add("compulsory","ndim","3","The dimensionality of the system (some interesting LJ clusters are two dimensional)");
+}
+
+CLToolSimpleMD( const CLToolOptions& co ) :
+CLTool(co)
+{
+ inputdata=ifile;
for(int i=0;i<32;i++) iv[i]=0.0;
iy=0;
iset=0;
@@ -66,8 +124,7 @@ CLToolSimpleMD(){
private:
void
-read_input(FILE* fp,
- double& temperature,
+read_input(double& temperature,
double& tstep,
double& friction,
double& forcecutoff,
@@ -84,99 +141,49 @@ read_input(FILE* fp,
int& ndim,
int& idum)
{
- temperature=1.0;
- tstep=0.005;
- friction=0.0;
- forcecutoff=2.5;
- listcutoff=3.0;
- nstep=1;
- nconfig=10;
- nstat=1;
- maxneighbours=1000;
- idum=0;
- ndim=3;
- wrapatoms=false;
- statfile="";
- trajfile="";
- outputfile="";
- inputfile="";
-
- string line;
-
- line.resize(256);
- char buffer[256];
- char buffer1[256];
-
- while(fgets(buffer,256,fp)){
- line=buffer;
- for(int i=0;i<line.length();++i) if(line[i]=='#' || line[i]=='\n') line.erase(i);
- for(int i=line.length()-1;i>=0;--i){
- if(line[i]!=' ')break;
- line.erase(i);
- }
- if(line.length()==0) continue;
- sscanf(line.c_str(),"%s",buffer);
- string keyword=buffer;
- if(keyword=="temperature")
- sscanf(line.c_str(),"%s %lf",buffer,&temperature);
- else if(keyword=="tstep")
- sscanf(line.c_str(),"%s %lf",buffer,&tstep);
- else if(keyword=="friction")
- sscanf(line.c_str(),"%s %lf",buffer,&friction);
- else if(keyword=="forcecutoff")
- sscanf(line.c_str(),"%s %lf",buffer,&forcecutoff);
- else if(keyword=="listcutoff")
- sscanf(line.c_str(),"%s %lf",buffer,&listcutoff);
- else if(keyword=="nstep")
- sscanf(line.c_str(),"%s %d",buffer,&nstep);
- else if(keyword=="nconfig")
- {
- sscanf(line.c_str(),"%s %d %s",buffer,&nconfig,buffer1);
- trajfile=buffer1;
- }
- else if(keyword=="nstat")
- {
- sscanf(line.c_str(),"%s %d %s",buffer,&nstat,buffer1);
- statfile=buffer1;
- }
- else if(keyword=="maxneighbours")
- sscanf(line.c_str(),"%s %d",buffer,&maxneighbours);
- else if(keyword=="inputfile")
- {
- sscanf(line.c_str(),"%s %s",buffer,buffer1);
- inputfile=buffer1;
- }
- else if(keyword=="outputfile")
- {
- sscanf(line.c_str(),"%s %s",buffer,buffer1);
- outputfile=buffer1;
- }
- else if(keyword=="idum")
- sscanf(line.c_str(),"%s %d",buffer,&idum);
- else if(keyword=="ndim")
- sscanf(line.c_str(),"%s %d",buffer,&ndim);
- else{
- fprintf(stderr,"Unknown keywords :%s\n",keyword.c_str());
- exit(1);
- }
- }
+ // Read everything from input file
+ char buffer1[256];
+ std::string tempstr; parse("temperature",tempstr);
+ if( tempstr!="NVE" ) Tools::convert(tempstr,temperature);
+ parse("tstep",tstep);
+ std::string frictionstr; parse("friction",frictionstr);
+ if( tempstr!="NVE" ){
+ if(frictionstr=="off"){ fprintf(stderr,"Specify friction for thermostat\n"); exit(1); }
+ Tools::convert(frictionstr,friction);
+ }
+ parse("forcecutoff",forcecutoff);
+ parse("listcutoff",listcutoff);
+ parse("nstep",nstep);
+ parse("maxneighbours",maxneighbours);
+ parse("idum",idum);
+
+ // Read in stuff with sanity checks
+ parse("inputfile",inputfile);
if(inputfile.length()==0){
fprintf(stderr,"Specify input file\n");
exit(1);
}
+ parse("outputfile",outputfile);
if(outputfile.length()==0){
fprintf(stderr,"Specify output file\n");
exit(1);
}
+ std::string nconfstr; parse("nconfig",nconfstr);
+ sscanf(nconfstr.c_str(),"%d %s",&nconfig,buffer1);
+ trajfile=buffer1;
if(trajfile.length()==0){
fprintf(stderr,"Specify traj file\n");
exit(1);
}
+ std::string nstatstr; parse("nstat",nstatstr);
+ sscanf(nstatstr.c_str(),"%d %s",&nconfig,buffer1);
+ statfile=buffer1;
if(statfile.length()==0){
fprintf(stderr,"Specify stat file\n");
exit(1);
}
+ parse("ndim",ndim);
if(ndim<1 || ndim>3){
fprintf(stderr,"ndim should be 1,2 or 3\n");
exit(1);
@@ -369,7 +376,7 @@ void write_statistics(const string & statfile,const int istep,const double tstep
-int main(int argc,char**argv,FILE*in,FILE*out,PLMD::PlumedCommunicator& pc){
+int main(FILE*out,PLMD::PlumedCommunicator& pc){
int natoms; // number of atoms
vector<Vector> positions; // atomic positions
vector<Vector> velocities; // velocities
@@ -423,18 +430,11 @@ int main(int argc,char**argv,FILE*in,FILE*out,PLMD::PlumedCommunicator& pc){
plumed->cmd("setRealPrecision",&s);
}
- FILE* mystdin=in;
-
- if(argc==2) mystdin=fopen(argv[1],"r");
-
- read_input(mystdin,temperature,tstep,friction,forcecutoff,
+ read_input(temperature,tstep,friction,forcecutoff,
listcutoff,nstep,nconfig,nstat,
wrapatoms,inputfile,outputfile,trajfile,statfile,
maxneighbour,ndim,idum);
- if(argc==2) fclose(mystdin);
-
-
// number of atoms is read from file inputfile
read_natoms(inputfile,natoms);
diff --git a/src/Keywords.cpp b/src/Keywords.cpp
index d1d302508..de9a5e083 100644
--- a/src/Keywords.cpp
+++ b/src/Keywords.cpp
@@ -218,13 +218,14 @@ bool Keywords::reserved( const std::string & k ) const {
return false;
}
-void Keywords::print_html() const {
+void Keywords::print_html( const bool isaction ) const {
unsigned nkeys=0;
for(unsigned i=0;i<keys.size();++i){
if ( (types.find(keys[i])->second).isAtomList() ) nkeys++;
}
if( nkeys>0 ){
- std::cout<<"\\par Specifying the atoms involved\n\n";
+ if(isaction) std::cout<<"\\par Specifying the atoms involved\n\n";
+ else std::cout<<"\\par The input trajectory is specified using one of the following\n\n";
std::cout<<" <table align=center frame=void width=95%% cellpadding=5%%> \n";
for(unsigned i=0;i<keys.size();++i){
if ( (types.find(keys[i])->second).isAtomList() ) print_html_item( keys[i] );
@@ -236,7 +237,8 @@ void Keywords::print_html() const {
if ( (types.find(keys[i])->second).isCompulsory() ) nkeys++;
}
if( nkeys>0 ){
- std::cout<< "\\par Compulsory keywords\n\n";
+ if(isaction) std::cout<< "\\par Compulsory keywords\n\n";
+ else std::cout<<"\\par The following must be present\n\n";
std::cout<<" <table align=center frame=void width=95%% cellpadding=5%%> \n";
for(unsigned i=0;i<keys.size();++i){
if ( (types.find(keys[i])->second).isCompulsory() ) print_html_item( keys[i] );
@@ -248,7 +250,8 @@ void Keywords::print_html() const {
if ( (types.find(keys[i])->second).isFlag() ) nkeys++;
}
if( nkeys>0 ){
- std::cout<<"\\par Options\n\n";
+ if(isaction) std::cout<<"\\par Options\n\n";
+ else std::cout<<"\\par The following options are available\n\n";
std::cout<<" <table align=center frame=void width=95%% cellpadding=5%%> \n";
for(unsigned i=0;i<keys.size();++i){
if ( (types.find(keys[i])->second).isFlag() ) print_html_item( keys[i] );
@@ -270,6 +273,66 @@ void Keywords::print_html() const {
std::cout<<"</table>\n\n";
}
+void Keywords::print( FILE* out ) const {
+ unsigned nkeys=0;
+ for(unsigned i=0;i<keys.size();++i){
+ if ( (types.find(keys[i])->second).isAtomList() ) nkeys++;
+ }
+ if( nkeys>0 ){
+ fprintf(out,"The input trajectory can be in any of the following formats: \n\n");
+ for(unsigned i=0;i<keys.size();++i){
+ if ( (types.find(keys[i])->second).isAtomList() ) printKeyword( keys[i], out );
+ }
+ }
+ nkeys=0;
+ for(unsigned i=0;i<keys.size();++i){
+ if ( (types.find(keys[i])->second).isCompulsory() ) nkeys++;
+ }
+ if( nkeys>0 ){
+ fprintf(out,"\nThe following arguments are compulsory: \n\n");
+ for(unsigned i=0;i<keys.size();++i){
+ if ( (types.find(keys[i])->second).isCompulsory() ) printKeyword( keys[i], out ); //log.printKeyword( keys[i], documentation[i] );
+ }
+ }
+ nkeys=0;
+ for(unsigned i=0;i<keys.size();++i){
+ if ( (types.find(keys[i])->second).isFlag() ) nkeys++;
+ }
+ if( nkeys>0 ){
+ fprintf( out,"\nIn addition you may use the following options: \n\n");
+ for(unsigned i=0;i<keys.size();++i){
+ if ( (types.find(keys[i])->second).isFlag() ) printKeyword( keys[i], out ); //log.printKeyword( keys[i], documentation[i] );
+ }
+ }
+ nkeys=0;
+ for(unsigned i=0;i<keys.size();++i){
+ if ( (types.find(keys[i])->second).isOptional() ) nkeys++;
+ }
+ if( nkeys>0 ){
+ for(unsigned i=0;i<keys.size();++i){
+ if ( (types.find(keys[i])->second).isOptional() ) printKeyword( keys[i], out ); //log.printKeyword( keys[i], documentation[i] );
+ }
+ fprintf(out,"\n");
+ }
+}
+
+void Keywords::printKeyword( const std::string& key, FILE* out ) const {
+ bool killdot=( (documentation.find(key)->second).find("\\f$")!=std::string::npos ); // Check for latex
+ std::vector<std::string> w=Tools::getWords( documentation.find(key)->second );
+ fprintf(out,"%23s - ", key.c_str() );
+ unsigned nl=0; std::string blank=" ";
+ for(unsigned i=0;i<w.size();++i){
+ nl+=w[i].length() + 1;
+ if( nl>60 ){
+ fprintf(out,"\n%23s %s ", blank.c_str(), w[i].c_str() ); nl=0;
+ } else {
+ fprintf(out,"%s ", w[i].c_str() );
+ }
+ if( killdot && w[i].find(".")!=std::string::npos ) break; // If there is latex only write up to first dot
+ }
+ fprintf(out,"\n");
+}
+
void Keywords::print( Log& log ) const {
unsigned nkeys=0;
for(unsigned i=0;i<keys.size();++i){
@@ -338,6 +401,11 @@ void Keywords::print_html_item( const std::string& key ) const {
printf("</tr>\n");
}
+std::string Keywords::get( const unsigned k ) const {
+ plumed_assert( k<size() );
+ return keys[k];
+}
+
bool Keywords::getLogicalDefault( std::string key, bool& def ) const {
if( booldefs.find(key)!=booldefs.end() ){
def=booldefs.find(key)->second;
diff --git a/src/Keywords.h b/src/Keywords.h
index dfd87ea9f..e1923248e 100644
--- a/src/Keywords.h
+++ b/src/Keywords.h
@@ -76,11 +76,13 @@ private:
void print_html_item( const std::string& ) const;
/// Print a particular keyword
void printKeyword( const std::string& j, Log& log ) const ;
+/// Print a particular keyword (copy of the above that works with files)
+ void printKeyword( const std::string& j, FILE* out ) const ;
/// find out whether flag key is on or off by default.
bool getLogicalDefault( std::string key, bool& def ) const ;
+public:
/// Get the value of the default for the keyword named key
bool getDefaultValue( std::string key, std::string& def ) const ;
-public:
/// Return the number of defined keywords
unsigned size() const;
/// Check if numbered keywords are allowed for this action
@@ -89,12 +91,16 @@ public:
std::string getKeyword( const unsigned i ) const ;
/// Print the documentation to the log file (used by PLMD::Action::error)
void print( Log& log ) const ;
+/// Print the documentation to a file (use by PLUMED::CLTool::readCommandLineArgs)
+ void print( FILE* out ) const ;
/// Reserve a keyword
void reserve( const std::string & t, const std::string & k, const std::string & d );
/// Reserve a flag
void reserveFlag( const std::string & k, const bool def, const std::string & d );
/// Use one of the reserved keywords
void use( const std::string k );
+/// Get the ith keyword
+ std::string get( const unsigned k ) const ;
/// Add a new keyword of type t with name k and description d
void add( const std::string & t, const std::string & k, const std::string & d );
/// Add a new compulsory keyword (t must equal compulsory) with name k, default value def and description d
@@ -110,7 +116,7 @@ public:
/// Check if the keyword with name k has style t
bool style( const std::string & k, const std::string & t ) const ;
/// Print an html version of the documentation
- void print_html() const ;
+ void print_html( const bool isaction ) const ;
/// Change the style of a keyword
void reset_style( const std::string & k, const std::string & style );
/// Add keywords from one keyword object to another
diff --git a/src/Tools.cpp b/src/Tools.cpp
index 987462134..161ec8227 100644
--- a/src/Tools.cpp
+++ b/src/Tools.cpp
@@ -235,3 +235,9 @@ vector<string> Tools::ls(const string&d){
}
return result;
}
+
+void Tools::stripLeadingAndTrailingBlanks( std::string& str ){
+ std::size_t first=str.find_first_not_of(' ');
+ std::size_t last=str.find_last_not_of(' ');
+ if( first<last ) str=str.substr(first,last+1);
+}
diff --git a/src/Tools.h b/src/Tools.h
index 65b7c5c41..1c4f62f8d 100644
--- a/src/Tools.h
+++ b/src/Tools.h
@@ -104,6 +104,8 @@ public:
static void interpretLabel(std::vector<std::string>&s);
/// list files in a directory
static std::vector<std::string> ls(const std::string&);
+/// removes leading and trailing blanks from a string
+ static void stripLeadingAndTrailingBlanks( std::string& str );
};
template <class T>
--
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