MohidWiki - User contributions [en]

Libfproj4

2013-12-10T02:49:09Z

Anatrancoso: /* External Links */

libfproj4 is a Fortran wrapper for [[PROJ4]] library. It was developed as of the [http://www.cbcb.umd.edu/software/glimmer/ GLIMMER] project and can be found in [http://forge.nesc.ac.uk/download.php/10/libfproj4-1.0.tar.gz libfproj4-1.0.tar.gz].
This wrapper is necessary if we want to call PROJ4 conversion subroutines (in C) from a Fortran program.
It is used in MOHID by the ConvertToHDF5 tool to be able to deal with different projections from other models.

=Compilation (Static Library)=

libfproj4 it's a library build on top of [[PROJ4]]. It can se used dynamically or statically. Here, only the static compilation is explained, as the instructions for dynamic compilation are included in the library source code. The first steps in compiling are:

*Download libfproj4 source code from [http://forge.nesc.ac.uk/download.php/10/libfproj4-1.0.tar.gz] or \\kepler\Software\PROJ4\libfproj4-1.0.tar.
*Download proj4 source code from [http://download.osgeo.org/proj/proj-4.7.0.tar.gz] or \\kepler\Software\PROJ4\proj-4.7.0.tar.
*Extract all contents to a place in your computer, from now referred to as ROOT_DIR.

==Windows==

===Compaq Visual Studio===

(Already compiled in \\kepler\Software\PROJ4\libfproj4.lib)

#New project W32 static lib
#Add fort-proj.c (from libfproj4-1.0.tar.gz) and all *.c files (from proj4 source), except all that have main function : css2css, geod, nad2bin, nad2nad, proj.c.
#Project Settings / C/C++ / General / Preprocessor definitions : VISUAL_CPLUSPLUS ou IFORT
#Project Settings / C/C++ / Preprocessor / include : whatever\proj-4.6.0\src (the folder that has projects.h, because of directives #include <projects.h>)

===Visual Studio 2008 with Intel Fortran===

(Already compiled in [http://mohid.codeplex.com] ExternalLibs/Proj4)

#Open Visual Studio and select File/New/Project/Visual C++/W32/Win32 Console Application. Name it libfproj4, and select location as $ROOT_DIR\libfproj4-1.0. Click ok.
#In the wizard, click Next and then choose "Console application" and "Empty project" in the following window. Then click Finish.
#Go to Project / Properties / Configuration Properties / Configuration Type and select "Static Library (.lib)". Click ok. (we don't choose this type in the project creation because if so VS2008 automatic header files that we don't want).
#Go to Project / Add Existing Item. Add $ROOT_DIR\libfproj4-1.0\fort-proj.c.
#Go to Project / Add Existing Item. Add all *.c files in $ROOT_DIR\proj-4.7.0\src except the ones that have the main function: cs2cs.c, geod.c, nad2bin.c, nad2nad.c, proj.c.
#Rename proj_config.h.in to proj_config.h in ROOT_DIR\proj-4.7.0\src
#Go to Project / libfproj4 Properties:
#*C/C++ / General / Additional Include Directories: ..\..\..\proj-4.7.0\src (where the *.h files are)
#*C/C++ / Preprocessor / Preprocessor Definitions: IFORT
#*C/C++ / Code Generation / Runtime Library : Multi-threaded Debug (/MTd) (para versao Debug)
#*C/C++ / Code Generation / Runtime Library : Multi-threaded (/MT) (para versao Release)
#Build Solution

==Linux==

Prepare files and folders:
cd $ROOT_DIR
tar -zxvf proj-4.7.0.tar.gz
tar -zxvf libfproj4-1.0.tar.gz
mkdir src
cp libfproj4-1.0/fort-proj.c src/
cp libfproj4-1.0/cfortran.h src/
cp -r proj-4.7.0/src/*.c src/
cp -r proj-4.7.0/src/*.h src/
cp proj-4.7.0/src/proj_config.h.in src/proj_config.h

Compile:

cd $ROOT_DIR/src
rm -rf cs2cs.c geod.c nad2nad.c nad2bin.c proj.c # with main functions
icc -DIFORT -c *.c
ar rc libfproj4.a *.o

Install:

cd $ROOT_DIR
mkdir lib
mkdir include
cp src/libfproj4.a lib/
cp libfproj4-1.0/proj4.inc include

=Usage=

==Windows==

#Create $ROOT_DIR\teste
#Copy test-proj.f90, proj4.f90 and proj4.inc from $ROOT_DIR\libfproj4-1.0 to $ROOT_DIR\teste.
#Copy libfproj4.lib from $ROOT_DIR\libfproj4-1.0\libfproj4\Debug to $ROOT_DIR\teste.
#Open Visual Studio and select File/New/Project/Intel(R) Visual Fortran / Console Application / Empty Project. Name it teste and select location as $ROOT_DIR\teste. Click ok.
#Project / Add Existing Item: Add test-proj.f90 and proj4.f90
#Project / Properties:
#*Linker / General / Additional Library Directories: ..\..\..\teste (or where libfproj4.lib file is).
#*Linker / Input / Additional Dependencies: libfproj4.lib

==Linux==

cd $ROOT_DIR/
mkdir teste
cd teste
cp ../libfproj4-1.0/test-proj.f90 .
cp ../libfproj4-1.0/proj4.f90 .
cp ../libfproj4-1.0/proj4.inc .
cp ../src/libfproj4.a .
ifort -c proj4.f90 #-I../libfproj4-1.0 # needs proj4.inc
ifort -c test-proj.f90
ifort proj4.o test-proj.o libfproj4.a -o test-proj.exe
./test-proj.exe

=InternalLinks=

*[[PROJ4]]
*[[ConvertToHDF5]]

=External Links=
*[http://forge.nesc.ac.uk/download.php/10/libfproj4-1.0.tar.gz libfproj4-1.0.tar.gz] (deprecated)
*[https://github.com/mhagdorn/proj4-fortran proj4-fortran] (new link)
[[Category:Tools]]

2010-02-15T17:25:42Z

Anatrancoso: /* EcoToxicity Model */

=Overview=

This module can be used by two models: [[Mohid_Land|MOHID Land]], and [[Mohid_River_Network|MOHID River Network]]. Like other modules, it has a specific input file, called '''DrainageNetwork_X.dat''', where X is the simulation number. The following tables describe the keywords that can be used, their data type, and the default values (in case of omission).

==DrainageNetwork_X.dat Keywords==

===General===

Keyword : Data Type Default !Comment
NETWORK_FILE : char - !Path to drainage network file
CHECK_NODES : 0/1 [1] !Ckeck nodes consistency
CHECK_REACHES : 0/1 [1] !Check reaches consistency
GLOBAL_MANNING : real - !Rugosity in Channels
GEO_CONVERSATION_FACTOR : real [1.] !Lat to Meters rough estimation

===Stabilization===

Keyword : Data Type Default !Comment
STABILIZE : 0/1 [0] !Restart time iteration if high volume gradients
STABILIZE_FACTOR : real [0.1] !max gradient in time steps as fraction of old volume
MAX_ITERATIONS : int [100] !Max iterations for stabilized check
DT_FACTOR : real [0.8] !Factor for DT Prediction
MAX_DT_FLOOD : real [10.0] !Max DT if channel water level exceeds full bank

===Hydrodynamic===

Keyword : Data Type Default !Comment
HYDRODYNAMIC_APROX : int [1] !1 - KinematicWave, 2 - DiffusionWave, 3 - DynamicWave
NUMERICAL_SCHEME : int [0] !0 - ExplicitScheme, 1 - ImplicitScheme
MASS_ERR : real(8) [0.001] !Max error in mass conservation
MIN_WATER_DEPTH : real [0.001] !Min water depth in nodes (For h < MIN_WATER_DEPTH water stops flowing)
INITIAL_WATER_DEPTH : real [0.0] !Initial water depth
MINIMUM_SLOPE : real [0.0] !Minimum Slope for Kinematic Wave

===Downstream Boundary===

Keyword : Data Type Default !Comment
DOWNSTREAM_BOUNDARY : int [1] !0 - Dam, 1 - ZDG, 2 - CD, 3 - ImposedWaterDepth, 3 - ImposedVelocity
DEFAULTVALUE : real - !Default value at downstream boundary
FILE_IN_TIME : char [NONE] !If DOWNSTREAM_BOUNDARY = ImposedWaterDepth, this can be NONE or TIMESERIE
FILENAME : char - !If FILE_IN_TIME = TIMESERIE, this is the name of timeserie file for the downstream boundary
DATA_COLUMN : int - !Number of column with data in FILE_IN_TIME

===Output===

Output is given for all nodes in HDF5 format, and also as time series for the specified nodes in TIME_SERIE_LOCATION file. These nodes are identified by their IDS (see Network file) and have to be inside the block '''<BeginNodeTimeSerie> / <EndNodeTimeSerie>'''.

Keyword : Data Type Default !Comment
OUTPUT_TIME : int int... [-] !time interval between outputs for all nodes, in HDF5 format.
TIME_SERIE_LOCATION : char - !Path to time serie file with the specified nodes (can be this file)
MAX_BUFFER_SIZE : 1000
COMPUTE_RESIDUAL : 1
DT_OUTPUT_TIME : 1200
TIME_SERIE_BY_NODES : 0/1 [0] !Keyword to see if the user wants the time series to be written by nodes, i.e.,
!One file per node, with all variables in the headers list
!if FALSE, its one file per variable with nodes in the headers.

===Processes===

Keyword : Data Type Default !Comment
MIN_WATER_DEPTH_PROCESS : real [0.01] !Water Quality Process / Surface Fluxes shutdown
DISCHARGES : 0/1 [0] !Use module discharges (WWTP, etc)
TRANSMISSION_LOSSES : 0/1 [0] !If user wants to use transmission losses
HYDRAULIC_CONDUCTIVITY : real - !Hydraulic Conductivity to calculate transmission losses
REMOVE_OVERTOP : 0/1 [0] !Removes Water if channels are overtoped
AERATION_METHOD : int [-] !1 - PoolAndRifle, 2 - ChannelControled_
T90_DECAY_MODEL : 0 [1] !0 - Constant, 1 - Canteras, 2 - Chapra
T90 : real [7200.] !if T90_DECAY_MODEL = Constant
SHADING_FACTOR : real [1.] !0-1 fraction of riparian shading
FRACTION_SEDIMENT : 0/1 [0]
GLOBAL_TOXICITY : char ['SUM'] !Global Toxicity Computation Method : SUM,MAX,RISKRATIO

===Properties===

Each property keywords must be inside a block '''<beginproperty>/<endproperty>'''.

Keyword : Data Type Default !Comment
<beginproperty>
NAME : char [-] !Property name, must be on of [[Properties_names]]
UNITS : char [-] !usually mg/L (see IS_COEF)
IS_COEF : real [1.e-3] !Conversion factor to the International System
DESCRIPTION : char [-] !Property description
DEFAULT_VALUE : real [0.0] !Property initial concentration
MIN_VALUE : real [0.0] !Property minimum concentration
OVERLAND_CONCENTRATION : real [0.0] !Concentration discharged from overland
GROUNDWATER_CONCENTRATION : real [0.0] !Concentration discharged from ground water
DIFFUSEWATER_CONCENTRATION : real [0.0]
ADVECTION_DIFUSION : 0/1 [1] !1 - want to transport property; 0 - no transport
ADVECTION_SCHEME : int [1] !1 - UpwindOrder1 (currently no more options)
DIFFUSION_SCHEME : int [5] !5 - CentralDiff (currently no more options)
DIFFUSIVITY : real [1e-8] !Molecular diffusivity of property in m2/s
DISCHARGES : 0/1 [0] !1 - property is discharged; 0 - no discharges
TOXICITY : 0/1 [0] !1 - property has an associated toxicity
TOX_EVOLUTION : int [1] !1 - Saturation, 2 - Linear, 3 - RiskRatio
EC50 : real [0.5] !If TOX_EVOLUTION = Saturation or RiskRatio,
!EC50 is the concentration that causes 50% of effect (Tox = 0.5)
!in fraction of initial concentration units [%]
SLOPE : real [1.0] !If TOX_EVOLUTION = Linear
DECAY : 0/1 [0] !1- want to use bacterial decay model. 0 - no use. Must have DISCHARGES = 1 and [[Mohid_River_Network|atmosphere]].
SURFACE_FLUXES : 0/1 [0] !Property has surface fluxes (e.g. evaporation). Needs [[Mohid_River_Network|atmosphere]].
BOTTOM_FLUXES : 0/1 [0] !Property has bottom fluxes. Must be particulated.
BOTTOM_CONC : real [0.0] !Bottom Initial Concentration
BOTTOM_MIN_CONC : real [0.0] !Bottom Minimum Concentration
EROSION : 0/1 [1] !Compute erosion fluxes
CRIT_SS_EROSION : real [0.2] !Critical Erosion Shear Stress [Pa]
EROSION_COEF : real [5.0E-4] !Erosion Coefficient [kg m-2 s-1]
DEPOSITION : 0/1 [1] !Compute deposition fluxes
CRIT_SS_DEPOSITION : real [0.1] !Critical Deposition Shear Stress [Pa]
CHS : real [4.0] !Hindered settling [kg m-3] - See [[Module_FreeVerticalMovement]].
WS_TYPE : int [1] !Settling type: WSConstant = 1, SPMFunction = 2
WS_VALUE : real [0.0001] !Constant settling velocity [m s-1]
KL : real [0.1] !See [[Module_FreeVerticalMovement]].
KL1 : real [0.1] !See [[Module_FreeVerticalMovement]].
ML : real [4.62] !See [[Module_FreeVerticalMovement]].
M : real [1.0] !See [[Module_FreeVerticalMovement]].
WATER_QUALITY : 0/1 [0] !1 - use [[Module_WaterQuality|Water Quality Model]] for property transformation; 0 - no use
BENTHOS : 0/1 [0] !1 - use [[Module_Benthos|Benthos Model]] for property transformation; 0 - no use
CEQUALW2 : 0/1 [0] !1 - use [[Module_CEQUALW2|CEQUALW2 Model]] for property transformation; 0 - no use
LIFE : 0/1 [0] !1 - use [[Module_Life|Life Model]] for property transformation; 0 - no use
EXTINCTION_PARAMETER : real [1.0] !LIGHT EXTINCTION COEFFICIENT
TIME_SERIE : 0/1 [0] !Output this property in time series files.
OUTPUT_NAME : char [NAME] !Can be NAME or DESCRIPTION.
COMPUTE_LOAD : 0/1 [0] !Output concentration (in UNITS) x Flow [m3 s-1]
SUMTOTALCONC : 0/1 [0] 0 !Checks if user wants to calculate total Concentration (Column + Bottom) must be particulate
<endproperty>

====Toxicity Model====
*The formulation is to associate an eco-toxiciy value to the property (From project ECORIVER 2002).
*Every toxic property must be discharged.
*Its concentration in the river network is set to 0.0.
*Discharge concentration must be equal to 1, because we are measuring the dilution D = 1 - C_new / C_ini
*The variable property%toxicity%concentration represents C/c_ini so it starts by being 1.
*This is not even close to a final version. For more details, or sugestions/corrections, contact MARETEC (Rosa Trancoso).
*EC50 - Concentration that causes 50% of effect (Tox = 0.5)

===Network file:===

<BeginNode>
ID : int - !Node ID number
COORDINATES : real real - !Node coordinates
GRID_I : int - !I position of node, if grid
GRID_J : int - !J position of node, if grid
TERRAIN_LEVEL : real - !Bottom level of cross section
MANNING_CHANNEL : real GLOBAL_MANNING !Node rugosity
WATER_DEPTH : real INITIAL_WATER_DEPTH !Node initial water depth
CROSS_SECTION_TYPE : int [1] !1 - Trapezoidal, 2 - TrapezoidalFlood, 3 - Tabular
1 - Trapezoidal, 2 - TrapezoidalFlood
BOTTOM_WIDTH : real - !Bottom width of cross section
TOP_WIDTH : real - !Top width of cross section
HEIGHT : real - !Max height of cross section
2 - TrapezoidalFlood
MIDDLE_WIDTH : real - !Middle width of cross section
MIDDLE_HEIGHT : real - !Middle height of cross section
3 - Tabular
N_STATIONS : integer - !number os stations that define the cross section
STATION : real real ... - !station values
ELEVATION/LEVEL : real real ... - !elevation values
<EndNode>
<BeginReach>
ID : int - !Reach ID Number
DOWNSTREAM_NODE : int - !Downstream node ID
UPSTREAM_NODE : int - !Upstream node ID
<EndReach>

===Sample===

NETWORK_FILE : ..\..\GeneralData\DrainageNetwork\DrainageNetworkAlcabrichel_100ha_terrain.dnt
CHECK_NODES : 1
CHECK_REACHES : 1
HYDRODYNAMIC_APROX : 1
MASS_ERR : 0.001
GLOBAL_MANNING : 0.06
MIN_WATER_DEPTH : 0.01
INITIAL_WATER_DEPTH : 0.0
XS_CALC : 1
DOWNSTREAM_BOUNDARY : 1
TIME_SERIE_LOCATION : ..\..\GeneralData\Timeseries\TimeSerieLocation_200_new.dat

OUTPUT_TIME : 0 864000

DISCHARGES : 1 (1-if have a discharge file; 0 if not discharging)
CONTINUOUS : 0

MAX_DT_FLOOD : 100
STABILIZE : 1
DT_FACTOR : 0.75
STABILIZE_FACTOR : 0.05

MINIMUM_SLOPE : 0.0001

====If want to model Properties ====

Than additionaly to the above options need to define properties to be modelled. One block for each property (see a list

<beginproperty>
NAME : salinity
UNITS : psu
DESCRIPTION : salinity
DEFAULT_VALUE : 0.3
MIN_VALUE : 0.0
ADVECTION_DIFUSION : 1 !1-want to transport property; 0 - no transport
DISCHARGES : 0 !1-property is discharged;0 - no discharges
TIME_SERIE : 1
WATER_QUALITY : 0 !1-use water quality model for property transformation;0-no transformation
<endproperty>

==Creatig a drainage network file==

*Obtain a drainage network with MOHID GIS in [[MOHID_GIS#Delineate_Basins|Delineate Basins]]

*Alternatively can also obtain a drainage network with program BasinDelimiter (from SourceSafe) with a basin.dat with the keywords, adapted to the study watershed:

TOPOGRAPHIC_FILE : ..\..\GeneralData\DTM\MDT200mSD.dat
TRESHOLD_AREA : 100000
DELINEATE_BASIN : 1
OUTLET_I : 1
OUTLET_J : 44
WRITE_REACHES : 1
REACHES_FILE : ..\..\GeneralData\DrainageNetwork\DrainageNetwork.dnt

*Define the cross sections for the drainage network file in [[Mohid_GIS#Auto_Cross_Sections|MOHID GIS]].
DO NOT FORGET TO SELECT SAVE ALL IN MOHID GIS TO UPDATE THE FILE!!!

(Currently in this version of the cross sections program keyword TERRAIN_LEVEL is not written, instead is written BOTTOM_LEVEL (old version). TERRAIN LEVEL = BOTTOM_LEVEL + HEIGHT. Change it for example with excel, new program should be written)

*Define the network file just created in the drainage network data file with:

NETWORK_FILE : ..\..\GeneralData\DrainageNetwork\DrainageNetwork.dnt