diff --git a/regtest/basic/rt-atomic-units/Makefile b/regtest/basic/rt-atomic-units/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/basic/rt-atomic-units/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt-atomic-units/colvar.data.reference b/regtest/basic/rt-atomic-units/colvar.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..14f234c39b778f82691ae0206267048eef099daa
--- /dev/null
+++ b/regtest/basic/rt-atomic-units/colvar.data.reference
@@ -0,0 +1,6 @@
+#! FIELDS time d1_bohr d2_bohr d1_angs d2_angs uw_d1.bias uw_d1.force2 uw_d2.bias uw_d2.force2
+ 0.000000 2.6212 7.0204 1.3871 3.7150 0.0000 0.0000 0.4154 1661.5891
+ 20.670687 2.7518 6.8551 1.4562 3.6276 0.0000 0.0000 0.0000 0.0000
+ 41.341373 2.8810 6.6913 1.5246 3.5409 0.0000 0.0000 0.0000 0.0000
+ 62.012060 3.0084 6.5295 1.5920 3.4552 0.0000 0.0000 0.0000 0.0000
+ 82.682747 3.1338 6.3694 1.6584 3.3706 0.0000 0.0000 0.0000 0.0000
diff --git a/regtest/basic/rt-atomic-units/config b/regtest/basic/rt-atomic-units/config
new file mode 100644
index 0000000000000000000000000000000000000000..1c4f1da4113ae2d12fed7b5a7582c6b414a90768
--- /dev/null
+++ b/regtest/basic/rt-atomic-units/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --trajectory-stride 1 --timestep 0.0005 --ixyz coord.xyz --length-units A"
diff --git a/regtest/basic/rt-atomic-units/coord.xyz b/regtest/basic/rt-atomic-units/coord.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..4495c06a59c470befd2c951b8708fa96e28482f5
--- /dev/null
+++ b/regtest/basic/rt-atomic-units/coord.xyz
@@ -0,0 +1,40 @@
+6
+-599.95814 frame 0
+ C -1.1153338489 1.1595963725 0.0026633595
+ F 0.2717008097 1.1635701532 -0.0037364057
+ H -1.4766016787 0.5671994739 0.8176316738
+ H -1.4859910559 0.7392102656 -0.9294986560
+ H -1.4639581356 2.1727043518 0.1272290666
+ Cl -4.8295226891 1.2384273800 0.0007732197
+6
+-599.94812 frame 1
+ C -1.1818659490 1.1524095206 0.0051714001
+ F 0.2741763941 1.1670785764 -0.0075315334
+ H -1.4691409094 0.5862287847 0.7989327007
+ H -1.4884499890 0.7229913626 -0.9006674950
+ H -1.4533091057 2.1388166575 0.1328577020
+ Cl -4.8083944813 1.2398436917 0.0015918304
+6
+-599.92929 frame 2
+ C -1.2476793848 1.1452612884 0.0073511127
+ F 0.2765445930 1.1707086122 -0.0113962548
+ H -1.4643209887 0.6002162818 0.7873648326
+ H -1.4932190110 0.7049505165 -0.8770485882
+ H -1.4459321082 2.1116538815 0.1388695760
+ Cl -4.7872579203 1.2413205427 0.0024433571
+6
+-599.91107 frame 3
+ C -1.3124432920 1.1381643086 0.0090391471
+ F 0.2789248578 1.1742131400 -0.0153725474
+ H -1.4632380536 0.6066769390 0.7865741441
+ H -1.5014485157 0.6840822273 -0.8611897623
+ H -1.4424752128 2.0949336010 0.1447615680
+ Cl -4.7661005384 1.2426817556 0.0033284437
+6
+-599.90230 frame 4
+ C -1.3763183333 1.1310957950 0.0101704350
+ F 0.2811203252 1.1777617486 -0.0193599672
+ H -1.4665738669 0.6028655802 0.8001849044
+ H -1.5132096145 0.6600601686 -0.8548781193
+ H -1.4429893590 2.0914195557 0.1511298281
+ Cl -4.7449797329 1.2439224601 0.0042030197
diff --git a/regtest/basic/rt-atomic-units/plumed.dat b/regtest/basic/rt-atomic-units/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..61ccd3680707be80c5543f2253698424970d43a9
--- /dev/null
+++ b/regtest/basic/rt-atomic-units/plumed.dat
@@ -0,0 +1,26 @@
+UNITS LENGTH=Bohr TIME=atomic ENERGY=Ha CHARGE=e MASS=amu
+d1_bohr: DISTANCE ATOMS=1,2 NOPBC
+d2_bohr: DISTANCE ATOMS=1,6 NOPBC
+d1_angs: CUSTOM ARG=d1_bohr FUNC=0.52917721067*x PERIODIC=NO
+d2_angs: CUSTOM ARG=d2_bohr FUNC=0.52917721067*x PERIODIC=NO
+
+UPPER_WALLS ...
+ ARG=d1_bohr
+ AT=7.0
+ KAPPA=1000.0
+ LABEL=uw_d1
+... UPPER_WALLS
+
+UPPER_WALLS ...
+ ARG=d2_bohr
+ AT=7.0
+ KAPPA=1000.0
+ LABEL=uw_d2
+... UPPER_WALLS
+
+PRINT ...
+ STRIDE=1
+ ARG=d1_bohr,d2_bohr,d1_angs,d2_angs,uw_d1.*,uw_d2.*
+ FILE=colvar.data
+ FMT=%8.4f
+... PRINT
diff --git a/src/setup/Units.cpp b/src/setup/Units.cpp
index b47dda7049b613a1f45226a84532b3215b332ab4..804002c242e094a46d6030bc64b4556c1db02928 100644
--- a/src/setup/Units.cpp
+++ b/src/setup/Units.cpp
@@ -33,9 +33,10 @@ namespace setup {
//+PLUMEDOC GENERIC UNITS
/*
This command sets the internal units for the code. A new unit can be set by either
-specifying how to convert from the plumed default unit into that new unit or by using
-the shortcuts described below. This directive MUST appear at the BEGINNING of the
-plumed.dat file. The same units must be used througout the plumed.dat file.
+specifying a conversion factor from the plumed default unit or by using a string
+corresponding to one of the defined units given below. This directive MUST
+appear at the BEGINNING of the plumed.dat file. The same units must be used
+througout the plumed.dat file.
Notice that all input/output will then be made using the specified units.
That is: all the input parameters, all the output files, etc. The only
@@ -43,10 +44,19 @@ exceptions are file formats for which there is a specific convention concerning
the units. For example, trajectories written in .gro format (with \ref DUMPATOMS)
are going to be always in nm.
+The following strings can be used to specify units. Note that the strings are
+case senstive.
+- LENGTH: nm (default), A (for Angstrom), um (for micrometer), Bohr (0.052917721067 nm)
+- ENERGY: kj/mol (default), j/mol, kcal/mol (4.184 kj/mol), eV (96.48530749925792 kj/mol), Ha (for Hartree, 2625.499638 kj/mol)
+- TIME: ps (default), fs, ns, atomic (2.418884326509e-5 ps)
+- MASS: amu (default)
+- CHARGE: e (default)
+
+
\par Examples
\plumedfile
-# this is using nm - kj/mol - fs
+# this is using Angstrom - kj/mol - fs
UNITS LENGTH=A TIME=fs
# compute distance between atoms 1 and 4
@@ -89,9 +99,9 @@ PLUMED_REGISTER_ACTION(Units,"UNITS")
void Units::registerKeywords( Keywords& keys ) {
ActionSetup::registerKeywords(keys);
- keys.add("optional","LENGTH","the units of lengths. Either specify a conversion factor from the default, nm, or A (for angstroms) or um");
- keys.add("optional","ENERGY","the units of energy. Either specify a conversion factor from the default, kj/mol, or use j/mol or kcal/mol");
- keys.add("optional","TIME","the units of time. Either specify a conversion factor from the default, ps, or use ns or fs");
+ keys.add("optional","LENGTH","the units of lengths. Either specify a conversion factor from the default, nm, or use one of the defined units, A (for angstroms), um (for micrometer), and Bohr.");
+ keys.add("optional","ENERGY","the units of energy. Either specify a conversion factor from the default, kj/mol, or use one of the defined units, j/mol, kcal/mol and Ha (for Hartree)");
+ keys.add("optional","TIME","the units of time. Either specify a conversion factor from the default, ps, or use one of the defined units, ns, fs, and atomic");
keys.add("optional","MASS","the units of masses. Specify a conversion factor from the default, amu");
keys.add("optional","CHARGE","the units of charges. Specify a conversion factor from the default, e");
keys.addFlag("NATURAL",false,"use natural units");
@@ -108,32 +118,67 @@ Units::Units(const ActionOptions&ao):
s="";
parse("LENGTH",s);
if(s.length()>0) u.setLength(s);
- if(u.getLengthString().length()>0) log.printf(" length: %s\n",u.getLengthString().c_str());
- else log.printf(" length: %f nm\n",u.getLength());
+ if(u.getLengthString().length()>0 && u.getLengthString()=="nm") {
+ log.printf(" length: %s\n",u.getLengthString().c_str());
+ }
+ else if(u.getLengthString().length()>0 && u.getLengthString()!="nm") {
+ log.printf(" length: %s = %g nm\n",u.getLengthString().c_str(),u.getLength());
+ }
+ else {
+ log.printf(" length: %g nm\n",u.getLength());
+ }
s="";
parse("ENERGY",s);
if(s.length()>0) u.setEnergy(s);
- if(u.getEnergyString().length()>0) log.printf(" energy: %s\n",u.getEnergyString().c_str());
- else log.printf(" energy: %f kj/mol\n",u.getEnergy());
+ if(u.getEnergyString().length()>0 && u.getEnergyString()=="kj/mol") {
+ log.printf(" energy: %s\n",u.getEnergyString().c_str());
+ }
+ else if(u.getEnergyString().length()>0 && u.getEnergyString()!="kj/mol") {
+ log.printf(" energy: %s = %g kj/mol\n",u.getEnergyString().c_str(),u.getEnergy());
+ }
+ else {
+ log.printf(" energy: %g kj/mol\n",u.getEnergy());
+ }
s="";
parse("TIME",s);
if(s.length()>0) u.setTime(s);
- if(u.getTimeString().length()>0) log.printf(" time: %s\n",u.getTimeString().c_str());
- else log.printf(" time: %f ps\n",u.getTime());
+ if(u.getTimeString().length()>0 && u.getTimeString()=="ps") {
+ log.printf(" time: %s\n",u.getTimeString().c_str());
+ }
+ else if(u.getTimeString().length()>0 && u.getTimeString()!="ps") {
+ log.printf(" time: %s = %g ps\n",u.getTimeString().c_str(),u.getTime());
+ }
+ else {
+ log.printf(" time: %g ps\n",u.getTime());
+ }
s="";
parse("CHARGE",s);
if(s.length()>0) u.setCharge(s);
- if(u.getChargeString().length()>0) log.printf(" charge: %s\n",u.getChargeString().c_str());
- else log.printf(" charge: %f e\n",u.getCharge());
+ if(u.getChargeString().length()>0 && u.getChargeString()=="e") {
+ log.printf(" charge: %s\n",u.getChargeString().c_str());
+ }
+ else if(u.getChargeString().length()>0 && u.getChargeString()!="e") {
+ log.printf(" charge: %s = %g e\n",u.getChargeString().c_str(),u.getCharge());
+ }
+ else {
+ log.printf(" charge: %g e\n",u.getCharge());
+ }
s="";
parse("MASS",s);
if(s.length()>0) u.setMass(s);
- if(u.getMassString().length()>0) log.printf(" mass: %s\n",u.getMassString().c_str());
- else log.printf(" mass: %f amu\n",u.getMass());
+ if(u.getMassString().length()>0 && u.getMassString()=="amu") {
+ log.printf(" mass: %s\n",u.getMassString().c_str());
+ }
+ else if(u.getMassString().length()>0 && u.getMassString()!="amu") {
+ log.printf(" mass: %s = %g amu\n",u.getMassString().c_str(),u.getMass());
+ }
+ else {
+ log.printf(" mass: %g amu\n",u.getMass());
+ }
bool natural=false;
parseFlag("NATURAL",natural);
@@ -147,9 +192,8 @@ Units::Units(const ActionOptions&ao):
} else {
log.printf(" using physical units\n");
}
- log.printf(" inside PLUMED, Boltzmann constant is %f\n",plumed.getAtoms().getKBoltzmann());
+ log.printf(" inside PLUMED, Boltzmann constant is %g\n",plumed.getAtoms().getKBoltzmann());
}
}
}
-
diff --git a/src/tools/Units.cpp b/src/tools/Units.cpp
index 1389b7dfb9a658fdfe1e50f87edc958209596801..68340ee30f25e1ed5d37dc55c0e08c1a70ce94d0 100644
--- a/src/tools/Units.cpp
+++ b/src/tools/Units.cpp
@@ -50,11 +50,15 @@ void Units::setEnergy(const std::string &s) {
energy=0.001;
} else if(s=="eV") {
energy=96.48530749925792;
+ } else if(s =="Ha") {
+ energy=2625.499638;
} else {
energy=-1.0;
energyString="";
- Tools::convert(s,energy);
- plumed_massert(energy>0.0,"energy units should be positive");
+ if(!Tools::convert(s,energy)) {
+ plumed_merror("problem with setting the energy unit, either use give an numerical value or use one of the defined units: kj/mol, kcal/mol, j/mol, eV, Ha (case senstive)");
+ }
+ plumed_massert(energy>0.0,"energy unit should be positive");
}
}
@@ -66,11 +70,15 @@ void Units::setLength(const std::string &s) {
length=0.1;
} else if(s=="um") {
length=1000.0;
+ } else if(s=="Bohr") {
+ length=0.052917721067;
} else {
length=-1.0;
lengthString="";
- Tools::convert(s,length);
- plumed_massert(length>0.0,"length units should be positive");
+ if(!Tools::convert(s,length)) {
+ plumed_merror("problem with setting the length unit, either use give an numerical value or use one of the defined units: nm, A, um, Bohr (case senstive)");
+ }
+ plumed_massert(length>0.0,"length unit should be positive");
}
}
@@ -82,11 +90,15 @@ void Units::setTime(const std::string &s) {
time=1000.0;
} else if(s=="fs") {
time=0.001;
+ } else if(s=="atomic") {
+ time=2.418884326509e-5;
} else {
time=-1.0;
timeString="";
- Tools::convert(s,time);
- plumed_massert(time>0.0,"time units should be positive");
+ if(!Tools::convert(s,time)) {
+ plumed_merror("problem with setting the time unit, either use give an numerical value or use one of the defined units: ps, fs, atomic (case senstive)");
+ }
+ plumed_massert(time>0.0,"time unit should be positive");
}
}
@@ -97,8 +109,10 @@ void Units::setCharge(const std::string &s) {
} else {
charge=-1.0;
chargeString="";
- Tools::convert(s,charge);
- plumed_massert(charge>0.0,"charge units should be positive");
+ if(!Tools::convert(s,charge)) {
+ plumed_merror("problem with setting the charge unit, either use give an numerical value or use one of the defined units: e (case senstive)");
+ }
+ plumed_massert(charge>0.0,"charge unit should be positive");
}
}
@@ -109,8 +123,10 @@ void Units::setMass(const std::string &s) {
} else {
mass=-1.0;
massString="";
- Tools::convert(s,mass);
- plumed_massert(mass>0.0,"mass units should be positive");
+ if(!Tools::convert(s,mass)) {
+ plumed_merror("problem with setting the mass unit, either use give an numerical value or use one of the defined units: amu (case senstive)");
+ }
+ plumed_massert(mass>0.0,"mass unit should be positive");
}
}
@@ -142,4 +158,3 @@ void Units::setMass(const double s) {
}
-
diff --git a/src/tools/Units.h b/src/tools/Units.h
index dd35cddbcfd18a7a436446f5cd58a094adf466da..79417eca1f5e836ba0f0e9cf9a5368560fde8816 100644
--- a/src/tools/Units.h
+++ b/src/tools/Units.h
@@ -59,15 +59,15 @@ public:
Units();
/// Set energy units from string.
/// Also understands the following strings:
-/// kj/mol, kcal/mol, j/mol, and eV.
+/// kj/mol, kcal/mol, j/mol, eV, and Ha.
void setEnergy(const std::string &);
/// Set time units from string.
/// Also understands the following strings:
-/// ps, ns, fs.
+/// ps, ns, fs, and atomic.
void setTime(const std::string &);
/// Set lengh units from string.
/// Also understands the following strings:
-/// nm, A, um.
+/// nm, A, um, and Bohr.
void setLength(const std::string &);
/// Set charge units from string.
void setCharge(const std::string &);