Dimensional Analysis (working with :mod:`parmed.unit`) ========================================================= The :mod:`unit` package was originally developed by Christopher M. Bruns at SimTK (Stanford University) for the ``simtk`` Python package in OpenMM_. .. _OpenMM: http://simtk.org/home/openmm Different programs use different systems of units internally while performing calculations on quantities with specific dimensions. For instance, the *Amber* and *CHARMM* programs deal with energies in *kcal/mol* and lengths in *Angstroms*, while *GROMACS* and *OpenMM* deal with energies in *kJ/mol* and distances in *nanometers*. Electronic structure packages, on the other hand, tend to use so-called *atomic* units, with energies in Hartrees and lengths in Bohrs. Comparing the results between these programs requires that the results be converted to a common set of units beforehand. More importantly---interconverting these packages, or preparing common input for both, requires that the input for each program conform to its expected system of units. Not doing so can result in `a very costly mistake `_ In all of the examples below, I will assume that the :mod:`unit` package has been imported as follows:: from parmed import unit as u What does :mod:`parmed.unit` do? ----------------------------------- The main classes in the :mod:`unit` module are shown below: .. currentmodule:: parmed.unit .. autosummary:: :toctree: unitobj/ Quantity is_quantity Unit BaseUnit UnitSystem The :mod:`unit` package allows you to turn *numbers* into a :class:`Quantity`, that has both a value and a unit. It allows you to do basic math with units and it automatically performs the requisite dimensional analysis, raising an exception if you try to illegally combine incompatible units. For example:: >>> x = 1.0 * u.nanometers >>> x + 1.0 * u.angstroms Quantity(value=1.1, unit=nanometer) >>> # Find the volume of a cube with side 1 cm >>> x = 1 * u.centimeters >>> v = x ** 3 >>> v Quantity(value=1, unit=centimeter**3) >>> v + 1.0 * u.milliliters Quantity(value=1.9999999999999998, unit=centimeter**3) >>> # Now try to combine incompatible units >>> 1*u.millimeters + 1*u.kelvin TypeError: Cannot add two quantities with incompatible units "millimeter" and "kelvin". Two units can be multiplied together to form a composite unit with the corresponding dimensionality---in the example above, cubing 1 centimeter resulted in a volume, which is a cubic length dimension. This works for much more complex units as well:: >>> x = 1 * u.kilograms * u.meters**2 / u.seconds**2 >>> x Quantity(value=1, unit=kilogram*meter**2/(second**2)) >>> x + 1 * u.joule Quantity(value=2, unit=kilogram*meter**2/(second**2)) How do I use ``units``? ----------------------- There are a variety of tasks you may want to do with units -- the more popular of which is shown in the sections below. Checking to see if an object is a :class:`Quantity` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ There may be times when you want to see if a Python object is a :class:`Quantity` instance, or if it is just a raw number. Many functions in ParmEd do this when taking user input, converting to its internal AKMA unit system (see below). Checking that an object is a :class:`Quantity` is done using the :func:`is_quantity` function in the ``parmed.unit`` namespace:: >>> x = 1 >>> y = 1 * u.nanometers >>> u.is_quantity(x) False >>> u.is_quantity(y) True Creating units ~~~~~~~~~~~~~~ You can create a unit in one of two ways: 1. Use the :class:`Quantity` constructor, as shown below:: >>> u.Quantity(1, u.nanometers) Quantity(1, nanometer) >>> u.Quantity(1, u.meters**-3) # You can raise units to exponents Quantity(value=1, unit=/(meter**3)) 2. Multiply (or divide!) by a specific unit, as shown below:: >>> 1 * u.nanometers Quantity(1, nanometer) >>> 1 / u.meters**3 # You can raise units to exponents Quantity(value=1, unit=/(meter**3)) Seems easy enough, and I usually use method 2 when turning a ``float``, ``int``, ``list``, or ``tuple`` into a :class:`Quantity`. Converting to another unit ~~~~~~~~~~~~~~~~~~~~~~~~~~ Aside from using units as a type-checker to make sure you are not making an arithmetic mistake with your transformations, the most common reason to use the :mod:`unit` package is to handle unit conversions for you. The :class:`Quantity` class defines two functions for this: 1. ``in_units_of(unit)``: This method returns a new :class:`Quantity` instance with the specified ``unit`` (a ``TypeError`` is raised). 2. ``value_in_unit(unit)``: This method returns a copy of the underlying data *without* an attached ``unit`` (i.e., it is *not* a :class:`Quantity` instance). This should be used when a scalar is needed from a quantity for use in a particular API, or if the performance hit from the dimensional analysis is unacceptable. The following example shows both of the above in action, demonstrating their differences:: >>> x = 1 * u.kilocalorie >>> x.in_units_of(u.kilojoule) Quantity(value=4.184, unit=kilojoule) >>> x.value_in_unit(u.kilojoule) 4.184 Converting units in batch -- the :class:`UnitSystem` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The previous section described how to convert a :class:`Quantity` into another :class:`Quantity` in a different, but *compatible* unit. The argument to ``in_units_of`` and ``value_in_unit`` methods *must* be a compatible unit, which can be limiting if you want to write a function that changes the units of an argument with unknown dimensionality into a particular system of units. This is where :class:`UnitSystem` comes in. Each :class:`Quantity` instance also has a corresponding methods for conversion to units compatible within a particular :class:`UnitSystem`: 1. ``in_unit_system(UnitSystem)``: This method returns a new :class:`Quantity` instance composed of the base units defined in that unit system. 2. ``value_in_unit_system(UnitSystem)``: This method returns a scalar of the value in that particular unit system. For example:: >>> x = 1 * u.kilocalorie >>> x.in_unit_system(u.md_unit_system) Quantity(value=4.184, unit=nanometer**2*mole*dalton/(picosecond**2)) >>> x.value_in_unit_system(u.md_unit_system) 4.184 This can be useful when designing a function that needs to handle arbitrary units, but it comes with some drawbacks (see below), so you should avoid unit system conversions when you can. A warning about :class:`UnitSystem` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Note that this method does not provide the added security of checking that the *dimensions* are correct -- it simply converts all base dimensions to the ones defining the unit system. For instance, consider the two functions below:: def area(x, y): """ Computes the area of a rectangle Parameters ---------- x : distance Quantity The length of the first side y : distance Quantity The length of the second side Returns ------- area : float Area in nanometers^2 """ return (x.value_in_unit_system(u.md_unit_system) * y.value_in_unit_system(u.md_unit_system)) def area2(x, y): return (x.value_in_unit(u.nanometers) * y.value_in_unit(u.nanometers)) As long as you provide the correct dimensions in the arguments, both functions yield the same result:: >>> area(1*u.angstroms, 1*u.millimeters) 100000.0 >>> area2(1*u.angstroms, 1*u.millimeters) 100000.0 Consider what happens if you make a small mistake, though:: >>> area(1/u.angstroms, 1*u.millimeters) 9999999.999999998 >>> area2(1/u.angstroms, 1*u.millimeters) TypeError: Unit "/angstrom" is not compatible with Unit "nanometer". Converting ``1/angstrom`` to the ``md_unit_system`` converts the value to ``10/nanometer`` (rather than ``1 angstrom`` to ``0.1 nanometer``), leading to a result that is 2 orders of magnitude larger than expected! The ``area2`` function catches the error and raises an exception, though, thereby making the mistake easier to find. Available :class:`UnitSystem` options ------------------------------------- The :mod:`unit` module contains a number of :class:`UnitSystem` instances available in the ``parmed.unit`` namespace. They are summarized in the table below, along with the units defining them (the energy unit is a composite of the mass unit times the square of the ratio of the length-to-time units): +------------------------+-------------+-----------+---------------+-----------------+------------------+-------------+-------------+ | :class:`UnitSystem` | Length unit | Mass unit | Time unit | Charge unit [1] | Temperature unit | Amount unit | Energy unit | +========================+=============+===========+===============+=================+==================+=============+=============+ | ``si_unit_system`` | meters | kilograms | second | Ampere | kelvin | mole | joule | +------------------------+-------------+-----------+---------------+-----------------+------------------+-------------+-------------+ | ``cgs_unit_system`` | centimeters | gram | second | Ampere | kelvin | mole | 1e-7 joule | +------------------------+-------------+-----------+---------------+-----------------+------------------+-------------+-------------+ | ``md_unit_system`` | nanometers | daltons | picosecond | q electron | kelvin | mole | kilojoule | +------------------------+-------------+-----------+---------------+-----------------+------------------+-------------+-------------+ | ``planck_unit_system`` | pl. length | pl. mass | pl. time | pl. charge | pl. temperature | item | pl. energy | +------------------------+-------------+-----------+---------------+-----------------+------------------+-------------+-------------+ | ``akma_unit_system`` | angstroms | daltons | akma time [2] | q electron | kelvin | mole | kilocalorie | +------------------------+-------------+-----------+---------------+-----------------+------------------+-------------+-------------+ [1] Some unit systems use current instead of charge as a base unit, while others use the charge. [2] The time in the AKMA unit system (Angstroms, Kilocalories per Mole, Atomic mass units) does not have an official name, and is roughly equal to 20.455 picoseconds. Different programs tend to use different unit systems. As a general reference, the table below summarizes a subset of programs and the unit systems they use: +---------+----------------------+ | Program | Unit System | +=========+======================+ | AMBER | ``akma_unit_system`` | +---------+----------------------+ | CHARMM | ``akma_unit_system`` | +---------+----------------------+ | Tinker | ``akma_unit_system`` | +---------+----------------------+ | Desmond | ``akma_unit_system`` | +---------+----------------------+ | LAMMPS | ``akma_unit_system`` | +---------+----------------------+ | NAMD | ``akma_unit_system`` | +---------+----------------------+ | AceMD | ``akma_unit_system`` | +---------+----------------------+ | OpenMM | ``md_unit_system`` | +---------+----------------------+ | Gromacs | ``md_unit_system`` | +---------+----------------------+ | Gromos | ``md_unit_system`` | +---------+----------------------+