Units.py

# Define unit conversion factors and physical constants
#
# Written by Konrad Hinsen
#

"""
Units and physical constants

This module defines constants and prefactors that convert from various
units to MMTK's internal unit system. There are also some common
physical constants.

MMTK's unit system is defined by:

* nm for length
* ps for time
* amu (g/mol) for mass
* the charge of a proton for charge
* rad for angles

All formulas that do not contain electrical quantities (charge,
electric/magnetic field, ...) have the same form in this unit system
as in the SI system. The energy unit that results from the choices
given above is kJ/mol.

The constants defined in this module are:

 * SI Prefixes: ato, femto, pico, nano, micro, milli, centi, deci,
                deca, hecto, kilo, mega, giga, tera, peta
 * Length units: m, cm, mm, nm, pm, fm, Ang, Bohr
 * Angle units: rad, deg
 * Volume units: l
 * Time units: s, ns, ps, fs
 * Frequency units: Hz, invcm (wavenumbers)
 * Mass units: amu, g, kg
 * Quantity-of-matter units: mol
 * Energy units: J, kJ, cal (thermochemical), kcal, Hartree, Bohr
 * Temperature units: K
 * Force units: N, dyn
 * Pressure units: Pa, MPa, GPa, bar, kbar, atm
 * Electrostatic units: C, A, V, D, eV, e
 * Physical constants:

   * c (speed of light)
   * Nav (Avogadro number)
   * h (Planck constant)
   * hbar (Planck constant divided by 2*Pi)
   * k_B (Boltzmann constant)
   * eps0 (permittivity of vacuum)
   * me (electron mass)

 * Other:

   * akma_time (the time unit in the DCD trajectory format)
   * electrostatic_energy (the prefactor in Coulomb's law)

"""

from Scientific import N as Numeric

# Prefixes

ato   = 1.0e-18
femto = 1.0e-15
pico  = 1.0e-12
nano  = 1.0e-9
micro = 1.0e-6
milli = 1.0e-3
centi = 1.0e-2
deci  = 1.0e-1
deca  = 1.0e1
hecto = 1.0e2
kilo  = 1.0e3
mega  = 1.0e6
giga  = 1.0e9
tera  = 1.0e12
peta  = 1.0e15

# Angles
# internal unit: radian

rad = 1.
deg = (Numeric.pi/180.)*rad

# Length units
# internal unit: nm

m = 1./nano                 # Meter (SI)
cm = centi*m
mm = milli*m
nm = nano*m
pm = pico*m
fm = femto*m
Ang = 1.e-10*m              # Angstrom

# Volume units

l = (deci*m)**3             # liter

# Time units
# internal unit: ps

s = 1./pico                 # Second (SI)
ns = nano*s
ps = pico*s
fs = femto*s

# Speed of light

c = 299792458.*m/s

# Frequency units
# internal unit: THz (1./ps)

Hz = 1./s
invcm = c/cm

# Avogadro number

Nav = 6.02214129e23

# Mass units
# internal unit: amu (= g/mol)

amu = 1                     # Atomic mass unit
g = Nav*amu
kg = kilo*g                 # Kilogram (SI)

# Quantity of matter
# internal unit: number

mol = Nav

# Energy units
# internal unit: kJ/mol

J = mol/kilo                # Joule (SI)
kJ = kilo*J
cal = 4.184*J               # Thermochemical calorie
kcal = kilo*cal

# Force units
# internal unit: kJ/mol/nm

N = J/m
dyn = 1.e-5*N

# Electrostatic units
# internal unit: charge in e

e = 1.
C = 6.24150934326018e18*e  # Coulomb (SI)
A = C/s                     # Ampere (SI)
D = 1.e-15*C/c              # Debye
V = J/C                     # Volt
eV = e*V                    # electron volt

# Temperature units
# internal unit: K

K = 1                       # Kelvin

# Pressure units
# internal unit: kJ/mol/nm**3

Pa = J/m**3                 # Pascal
MPa = mega*Pa
GPa = giga*Pa
bar = 1.e5*Pa               # bar
kbar = kilo*bar
atm = 101325*Pa             # atmosphere

# Constants

h = 6.62606957e-34*J*s
hbar = h/(2.*Numeric.pi)
k_B = 1.3806488e-23*J/K
eps0 = 1./(4.e-7*Numeric.pi)*A**2*m/J/c**2

me = 0.510998928*mega*eV/c**2

electrostatic_energy = 1/(4.*Numeric.pi*eps0)

# CHARMM time unit
akma_time = Numeric.sqrt(Ang**2/(kcal/mol))

# "Atomic" units
Bohr = 4.*Numeric.pi*eps0*hbar**2/(me*e**2)
Hartree = hbar**2/(me*Bohr**2)

print 0.425*eV
# Remove symbol "Numeric"
#del Numeric