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Unverified Commit 5cac51e2 authored by Giovanni's avatar Giovanni Committed by GitHub
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Merge pull request #387 from valsson/atomic_units 

Atomic units
parents 9086b711 50e24e2c
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with 168 additions and 33 deletions
regtest/basic/rt-atomic-units/Makefile 0 → 100644
+ 1
− 0
View file @ 5cac51e2
include ../../scripts/test.make
regtest/basic/rt-atomic-units/colvar.data.reference 0 → 100644
+ 6
− 0
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#! 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
regtest/basic/rt-atomic-units/config 0 → 100644
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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"
regtest/basic/rt-atomic-units/coord.xyz 0 → 100644
+ 40
− 0
View file @ 5cac51e2
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
regtest/basic/rt-atomic-units/plumed.dat 0 → 100644
+ 26
− 0
View file @ 5cac51e2
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
src/setup/Units.cpp
+ 63
− 19
View file @ 5cac51e2
......@@ -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());
}
}
}
src/tools/Units.cpp
+ 26
− 11
View file @ 5cac51e2
......@@ -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) {
}
src/tools/Units.h
+ 3
− 3
View file @ 5cac51e2
......@@ -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 &);
......
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