Difference between revisions of "Dynlib"

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''Highenough'' is typically the output of ''highenough'' funtion, which returns 1 where the surface is sufficiently above ground level and 0 elsewhere.
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''Highenough'' is typically the output of the ''highenough'' function, which returns 1 where the surface is sufficiently above ground level and 0 elsewhere.
  
 
''ddythres'' is the cutoff y-gradient for pv. The magnitude of (negative) d(pv)/dy must be above ddythres for reversal to be detected; this applies to revc, reva, revci,revai. Typical value 4E-12.
 
''ddythres'' is the cutoff y-gradient for pv. The magnitude of (negative) d(pv)/dy must be above ddythres for reversal to be detected; this applies to revc, reva, revci,revai. Typical value 4E-12.

Revision as of 17:39, 21 January 2013

Documentation

The steps necessary to obtain dynlib are described below. A more thorough documentation is compiled in the main documentation page.

Obtaining dynlib

  1. Copying the source code repository
    git clone /Data/gfi/users/tsp065/lib/dynlib.git
  2. Change into the dynlib folder
    cd dynlib
  3. Compile the library
    ./compile

Quick start to developing with dynlib

Editing the Fortran code

The fortran code lives in the main source code directory. At the moment there are six source code files

$ ls *.f95
dynlib_config.f95 dynlib_const.f95 dynlib_conv.f95 dynlib_diag.f95 dynlib_kind.f95 dynlib_stat.f95

The most important are dynlib_diag.f95 which contains subroutines that calculate various diagnostics, and dynlib_stat.f95 which contains statistical functions. Changed Fortran sources need to be recompiled, again using

./compile

Version control

The changes you made to the source code files can be listed by

git status

or viewed in detailed diff-comparisons by

git diff

or for one file only

git diff [filename]

Commit your changes from time to time and give a sensible and brief description of your changes in the editor that is opened (automatically)

git commit -a

The commit is then stored in your copy of the source code repository, but not yet available for others, which allows you to also commit work-in-progress.

A more thorough introduction to the version control system is given here or on the official documentation.

Using the Fortran functions

An example python script which calculates deformation using the Fortran function is provided with deformation.py.

Dynlib functions

The functions generally operate on real arrays with dimension (nz,ny,nx) where nz is number of times or levels, and ny and nx are the number of latitudes and longitudes, respectively. The function descriptions below contain detailed descriptions of arguments and returns where there is any deviation from this pattern; otherwise they may be assumed to be of the form:

Arguments:
Type Dim Description
u real (nz,ny,nx) Zonal velocity
v real (nz,ny,nx) Meridional velocity
pv real (nz,ny,nx) Potential vorticity
Returns:
Type Dim Description
res real (nz,ny,nx) output data

The ubiquitous inputs dx and dy are all of the form

Type Dim Description
dx real (ny,nx) dx(j,i) = x(j, i+1) - x(j, i-1) (in metres)
dy real (ny,nx) dy(j,i) = y(j+1, i) - y(j-1, i) (in metres)

Typically, the results for each level or time are computed individually in 2-D fashion, though they are returned as a 3-D array of the same size as the input.

ddx : partial x derivative

res=ddx(dat,dx,dy)

Calculates the partial x derivative of dat, using centred differences. For a non-EW-cyclic grid, 0 is returned on the edges of the x domain.

ddy : partial y derivative

res=ddy(dat,dx,dy)

Calculates the partial y derivative of dat, using centred differences. For a non-EW-cyclic grid, 0 is returned on all edges of the x,y domain. For an EW-cyclic grid, 0 is returned on the first and last latitudes.

grad : 2-D gradient of a scalar

(resx,resy)=grad(dat,dx,dy)

Calculates the 2-D gradient of dat, using centred differences in x and y. For a non-EW-cyclic grid, 0 is returned on all edges of the x,y domain. For an EW-cyclic grid, 0 is returned on the first and last latitudes.

lap2 : 2-D laplacian of a scalar

res=lap2(dat,dx,dy)

Calculates the 2-D laplacian of dat, using centred differences. For a non-EW-cyclic grid, 0 is returned on all edges of the x,y domain. For an EW-cyclic grid, 0 is returned on the first and last latitudes.

vor : 2-D vorticity

res=vor(u,v,dx,dy)

Calculates the z component of vorticity of (u,v), using centred differences.

div : 2-D divergence

res=div(u,v,dx,dy)

Calculates the 2-D divergence of (u,v), using centred differences.

def_shear : shear deformation

res=def_shear(u,v,dx,dy)

Calculates the shear (antisymmetric) deformation of (u,v), using centred differences.

def_stretch : stretch deformation

res=def_stretch(u,v,dx,dy)

Calculates the stretch (symmetric) deformation of (u,v), using centred differences.

def_total : total deformation

res=def_total(u,v,dx,dy)

Calculates the total (rotation-independent) deformation of (u,v), using centred differences.

def_angle : deformation angle

res=def_angle(u,v,dx,dy)

Calculates the angle between the x-axis and the dilatation axis of the deformation of (u,v).

isopv_angle : iso-PV contour angle

res=isopv_angle(pv,dx,dy)

Calculates the angle between the x-axis and the iso-lines of PV.

beta : angle between dilatation axis and iso-PV contours

res=beta(u,v,pv,dx,dy)

Calculates the angle between the dilatation axis and the iso-lines of PV.

stretch_stir : fractional stretching rate and angular rotation rate of grad(PV)

(stretch,stir)=stretch_stir(u,v,pv,dx,dy)

Returns real arrays, dim (nz,ny,nx):

stretch 
= fractional PV gradient stretching rate 
= 1/|gradPV| * d/dt(|gradPV|)
= gamma, 'stretching rate' (Lapeyre Klein Hua)LapKleHua1999 
= -1/|gradPV| * Fn (Keyser Reeder Reed)KeyReeRee1988 
Fn = 0.5*|gradPV|(D-E*cos(2*beta))
   =  1/|gradPV| * F (Markowski Richardson)Mar2010 
stir 
= angular rotation rate of grad(PV) (aka stirring rate)
= d(theta)/dt (Lapeyre Klein Hua)LapKleHua1999 
= 1/|gradPV| * Fs  (Keyser Reeder Reed)KeyReeRee1988 
 Fs = 0.5*|gradPV|(vort+E*sin(2*beta))

geop_from_montgp : geopotential

res = geop_from_montgp(m,theta,p,dx,dy)

Calculates geopotential (res) from montgomery potential (m), potential temperature (theta) and pressure (p)

rev : PV gradient reversal

(resa,resc,resai,resci,resaiy,resciy,tested) = rev(pv,highenough,latitudes,ddythres,dx,dy)

Finds the reversals of PV y-gradient (where the negative y-gradient exceeds some threshold) and classifies them as c (cyclonic) or a (anticyclonic). Three measures of c and a reversals are returned (6 in total). Only points flagged in highenough are tested.

Arguments:
Type Dim Description
pv real (nz,ny,nx) potential vorticity
highenough int*1 (nz,ny,nx) array of flags denoting whether to test the point for reversal
latitudes real (ny) vector of latitudes
ddythres real 0 Cutoff y-gradient for pv

Highenough is typically the output of the highenough function, which returns 1 where the surface is sufficiently above ground level and 0 elsewhere.

ddythres is the cutoff y-gradient for pv. The magnitude of (negative) d(pv)/dy must be above ddythres for reversal to be detected; this applies to revc, reva, revci,revai. Typical value 4E-12.

Returns:
Type Dim Description
revc int*1 (nz,ny,nx) Flag =1 for cyclonic reversal (threshold test applied)
reva int*1 (nz,ny,nx) Flag =1 for anticyclonic reversal (threshold test applied)
revci real (nz,ny,nx) Absolute PV gradient where reversal is cyclonic (threshold test applied)
revai real (nz,ny,nx) Absolute PV gradient where reversal is anticyclonic (threshold test applied)
revciy real (nz,ny,nx) Absolute PV y-gradient where reversal is cyclonic (no threshold test applied)
revaiy real (nz,ny,nx) Absolute PV y-gradient where reversal is anticyclonic (no threshold test applied)
tested int*1 (nz,ny,nx) flag to 1 all tested points: where highenough==1 and point not on grid edge

prepare_fft : make data periodic in y for FFT

res = prepare_fft(thedata,dx,dy)

Returns the data extended along complementary meridians (for fft). For each lon, the reflected (lon+180) is attached below so that data is periodic in x and y. NOTE: Input data must be lats -90 to 90, and nx must be even.

Arguments:
Type Dim Description
thedata real (nz,ny,nx) input data
Returns:
Type Dim Description
res real (nz,2*ny-2,nx) output data

sum_kix : sum along k for flagged k-values

(res,nres) = sum_kix(thedata,kix,dx,dy)

Calculates sum along k dimension for k values which are flagged to 1 in kix vector (length nz).

Arguments:
Type Dim Description
thedata real (nz,ny,nx) input data
kix int (nz) index flag for summation
Returns:
Type Dim Description
res real (ny,nx) (summed) output data
nres int 0 Number of data summed = sum(kix)

Sum_kix is typically used for calculating seasonal means. To do this, kix is set to 1 for times in the relevant season and 0 elsewhere. After (further) summing res and nres over all years, res/nres gives the mean for the season for all years.

high_enough : flags points which are sufficiently above ground

res = high_enough(zdata,ztest,zthres,dx,dy)

Arguments:
Type Dim Description
zdata real (nz,ny,nx) geopotential of gridpoints
ztest real (1,ny,nx) geopotential of topography
zthres real 0 threshold geopotential height difference


Returns:
Type Dim Description
res int*1 (nz,ny,nx)
3-D flag array set to:
1 if zdata(t,y,x) > (ztest(1,y,x) + zthres)
0 otherwise

contour_rwb : detects RWB events, Riviere algorithm

(beta_a_out,beta_c_out) = contour_rwb(pv_in,lonvalues,latvalues,ncon,lev,dx,dy)

Detects the occurrence of anticyclonic and cyclonic wave-breaking events from a PV field on isentropic coordinates.

Reference: Riviere 2009Riv2009 : See the appendix C.

Arguments:
Type Dim Description
pv_in real (nz,ny,nx) isentropic pv. Should be on a regular lat-lon grid and 180W must be the first longitude. (If 180W is not the first longitude, the outputs will have 180W as the first, so must be rearranged)
lonvalues real (nx) vector of longitudes
latvalues real (ny) vector of latitudes
ncon int 0 number of contours to test, normally 41 or 21
lev real 0 potential temperature of the level
Returns:
Type Dim Description
beta_a_out int (nz,ny,nx) flag array, =1 if anticyclonic wave breaking
beta_c_out int (nz,ny,nx) flag array, =1 if cyclonic wave breaking

v_g : geostrophic velocity

(resx,resy) = v_g(mont,lat,dx,dy)

Calculates geostrophic velocity. Returns zero on equator.

okuboweiss : Okubo-Weiss criterion

res = okuboweiss(u,v,dx,dy)

Calculates Okubo-Weiss criterion lambda_0=1/4 * (sigma^2-omega^2)= 1/4 W, where sigma is total deformation and omega is vorticity.

This is the square of the eigenvalues in Okubo's paperOku1969 (assumes divergence is negligible).

laccel : Lagrangian acceleration

(resx,resy) = laccel(u,v,mont,lat,dx,dy)

Calculates Lagrangian acceleration on the isentropic surface, based on Montgomery potential.

Arguments:
Type Dim Description
u real (nz,ny,nx) zonal velocity
v real (nz,ny,nx) meridional velocity
mont real (nz,ny,nx) Montgomery potential
lat real (ny) vector of latitudes

accgrad_eigs : Lagrangian acceleration gradient tensor eigenvalues

(respr,respi,resmr,resmi) = accgrad_eigs(u,v,mont,lat,dx,dy)

Calculates eigenvalues of the lagrangian acceleration gradient tensor.

Arguments:
Type Dim Description
u real (nz,ny,nx) zonal velocity
v real (nz,ny,nx) meridional velocity
mont real (nz,ny,nx) Montgomery potential
lat real (ny) vector of latitudes
Returns:
Type Dim Description
respr real (nz,ny,nx) Real part of positive eigenvalue
respi real (nz,ny,nx) Imaginary part of positive eigenvalue
resmr real (nz,ny,nx) Real part of negative eigenvalue
resmi real (nz,ny,nx) Imaginary part of negative eigenvalue
ncon int 0 number of contours to test, normally 41 or 21
lev real 0 potential temperature of the level

dphidt : Lagrangian derivative of compression axis angle

res = dphidt(u,v,mont,lat,dx,dy)

Calculates Lagrangian time derivative of compression axis angle: d(phi)/dt (ref Lapeyre et. al 1999LapKleHua1999 ), from deformation and Lagrangian acceleration tensor.

Arguments:
Type Dim Description
u real (nz,ny,nx) zonal velocity
v real (nz,ny,nx) meridional velocity
mont real (nz,ny,nx) Montgomery potential
lat real (ny) vector of latitudes

References

<biblio>

  1. KeyReeRee1988 bibtex@article{KeyReeRee1988
  author = {Keyser, D. and Reeder, M. J. and Reed, R. J.},
  title = {A Generalization of Petterssen Frontogenesis Function and Its Relation to the Forcing of Vertical Motion},
  journal = {Monthly Weather Review},
  volume = {116},
  number = {3},
  pages = {762-780},
  year = {1988},
  url = {<Go to ISI>://A1988N255100017},

}

  1. LapKleHua1999 bibtex@article{LapKleHua1999
  author = {Lapeyre, G. and Klein, P. and Hua, B. L.},
  title = {Does the tracer gradient vector align with the strain eigenvectors in 2D turbulence?},
  journal = {Physics of Fluids},
  volume = {11},
  number = {12},
  pages = {3729-3737},
  year = {1999},
  url = {<Go to ISI>://000083495900013

http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=PHFLE6000011000012003729000001&idtype=cvips&doi=10.1063/1.870234&prog=normal}, }

  1. Mar2010 bibtex@book{Mar2010
  author = {Markowski, Paul},
  title = {Mesoscale meteorology in midlatitudes},
  publisher = {Chichester, West Sussex, UK ;Hoboken, NJ : Wiley-Blackwell, 2010},
  url = {http://books.scholarsportal.info/viewdoc.html?id=/ebooks/ebooks2/wiley/2011-12-13/2/9780470682104},
  year = {2010},

}

  1. Oku1969 bibtex@article{Oku1969
  author = {Okubo, A.},
  title = {Horizontal Dispersion of Foreign Particles in Vicinity of Velocity Singularities Such as Convergences},
  journal = {Transactions-American Geophysical Union},
  volume = {50},
  number = {4},
  pages = {182-&},
  year = {1969},
  url = {<Go to ISI>://A1969C982700332},

}

  1. Riv2009 bibtex@article{Riv2009
  author = {Riviere, G.},
  title = {Effect of Latitudinal Variations in Low-Level Baroclinicity on Eddy Life Cycles and Upper-Tropospheric Wave-Breaking Processes},
  journal = {Journal of the Atmospheric Sciences},
  volume = {66},
  number = {6},
  pages = {1569-1592},
  year = {2009},
  url = {<Go to ISI>://000267263300006},

} </biblio>