Warning: This is no longer the latest available version of this module. Please see the releases page for the most recent version. The Webnucleo group strongly recommends the use of the latest version of any of its online modules.
This tutorial demonstrates how to use example codes in the libnucnet distribution src/examples directory. The sample input files used in the tutorial are included in the distribution release and may be located in the data_pub directory.
Example 24: Create a nuclear reaction network from an input xml file and print the valid reactions (those between nuclei in the network) and the invalid reactions (those between nuclei not in the network).
libnucnet routines demonstrated in example24.c are:
- Line 78: Libnucnet__Net__is_valid_input_xml()
- Line 92: Libnucnet__Net__new_from_xml()
- Line 140: Libnucnet__Nuc__getNumberOfSpecies()
- Line 141: Libnucnet__Net__getNuc()
- Line 149: Libnucnet__Net__getReac()
- Line 158: Libnucnet__Net__getNumberOfValidReactions()
- Line 166: Libnucnet__Reac__setReactionCompareFunction()
- Line 175: Libnucnet__Reac__iterateReactions()
- Line 188: Libnucnet__Reac__getNumberOfReactions()
- Line 204: Libnucnet__Net__free()
- Line 221: Libnucnet__Net__isValidReaction()
- Line 222: Libnucnet__Reaction__getString()
The first thing you need to do is to merge the nuclear data xml file and the reaction data xml file into a single network data xml file. Use xsltproc (which you should have installed as described in the compile tutorial):
xsltproc --stringparam reac_doc ../data_pub/example_reac.xml ../../xsl_pub/merge_net.xsl ../../data_pub/example_nuc.xml > ../../data_pub/example_net.xml
To run example24, type the following on the command line:
./example24 ../../data_pub/example_net.xml > ex24_output.txt
The result is ex24_output.txt
Example 25: Create a nuclear reaction network from input xml files and print the reaction Q values for the valid reactions.
libnucnet routines demonstrated in example25.c are:
- Line 77: Libnucnet__Net__new()
- Line 80: Libnucnet__Nuc__updateFromXml()
- Line 81: Libnucnet__Net__getNuc()
- Line 90: Libnucnet__Reac__updateFromXml()
- Line 91: Libnucnet__Net__getReac()
- Line 103: Libnucnet__Reac__setReactionCompareFunction()
- Line 108: Libnucnet__Reac__iterateReactions()
- Line 120: Libnucnet__Net__free()
- Line 136: Libnucnet__Net__isValidReaction()
- Line 141: Libnucnet__Reaction__getString()
- Line 147: Libnucnet__Net__computeReactionQValue()
To run example25, type the following on the command line:
./example25 ../../data_pub/example_nuc.xml ../../data_pub/example_reac.xml > ex25_output.txt
The result is ex25_output.txt
Example 26: Create a nuclear reaction network from an input xml file and print the forward and reverse rates for all valid reactions at the input temperature.
libnucnet routines demonstrated in example26.c are:
- Line 88: Libnucnet__Net__new_from_xml()
- Line 145: Libnucnet__Reac__setReactionCompareFunction()
- Line 146: Libnucnet__Net__getReac()
- Line 150: Libnucnet__Reac__iterateReactions()
- Line 162: Libnucnet__Net__free()
- Line 180: Libnucnet__Net__isValidReaction()
- Line 182: Libnucnet__Net__computeRatesForReaction()
- Line 194: Libnucnet__Reaction__getString()
To print out the forward and reverse rates at t9 = 1, type:
./example26 ../../data_pub/example_net.xml 1. > ex26_output.txt
The result is ex26_output.txt
Example 27: Create a nuclear reaction network from an input xml file and print the forward and reverse rates for a particular reaction (chosen by its string) at a variety of temperatures.
libnucnet routines demonstrated in example27.c are:
- Line 75: Libnucnet__Net__new_from_xml()
- Line 82: Libnucnet__Reac__getReactionByString()
- Line 83: Libnucnet__Net__getReac()
- Line 92: Libnucnet__Net__isValidReaction()
- Line 95: Libnucnet__Reaction__getString()
- Line 103: Libnucnet__Net__computeRatesForReaction()
- Line 124: Libnucnet__Net__free()
Choose a particular reaction with a string. For example, try:
./example27 ../../data_pub/example_net.xml "c12 + he4 -> o16 + gamma" > ex27_output.txt
The result is ex27_output.txt
Example 28: Create a nuclear reaction network from an input xml file and print the forward and reverse rates for a particular reaction or set of reactions (chosen by an xpath expression) at a variety of temperatures.
libnucnet routines demonstrated in example28.c are:
- Line 70: Libnucnet__Net__new_from_xml()
- Line 77: Libnucnet__Reac__setReactionCompareFunction()
- Line 78: Libnucnet__Net__getReac()
- Line 82: Libnucnet__Reac__iterateReactions()
- Line 92: Libnucnet__Net__free()
- Line 114: Libnucnet__Net__isValidReaction()
- Line 119: Libnucnet__Reaction__getString()
- Line 127: Libnucnet__Net__computeRatesForReaction()
Choose a reaction or set of reactions with an xpath expression. For example, try:
./example28 ../../data_pub/example_net.xml "[reactant = 'ne21']" > ex28_output.txt
The result is ex28_output.txt
Example 29: Create a nuclear reaction network from an input xml file and check that the forward and reverse rates lie within lower and upper bounds for a given temperature range.
libnucnet routines demonstrated in example29.c are:
- Line 139: Libnucnet__Net__new_from_xml()
- Line 147: Libnucnet__Reac__iterateReactions()
- Line 148: Libnucnet__Net__getReac()
- Line 157: Libnucnet__Net__free()
- Line 175: Libnucnet__Net__isValidReaction()
- Line 187: Libnucnet__Net__computeRatesForReaction()
- Line 200: Libnucnet__Reaction__getString()
To find the forward and reverse rates (for the network in the input file) that are less than 0 or greater than 1.e14 in the temperature range 1.e-3 to 10 billion Kelvins, type:
./example29 ../../data_pub/example_net.xml 1.e-3 10. 0. 1.e14 > ex29_output.txt
The result is ex29_output.txt
Example 30: Create a nuclear reaction network from an input xml file and print the forward and reverse rates at the input temperature and then double the rates and print them out again.
libnucnet routines demonstrated in example30.c are:
- Line 79: Libnucnet__Net__new()
- Line 81: Libnucnet__Nuc__updateFromXml()
- Line 82: Libnucnet__Net__getNuc()
- Line 88: Libnucnet__Reac__updateFromXml()
- Line 89: Libnucnet__Net__getReac()
- Line 105: Libnucnet__Zone__new()
- Line 116: Libnucnet__Zone__computeRates()
- Line 123: Libnucnet__Reac__setReactionCompareFunction()
- Line 138: Libnucnet__Reac__iterateReactions()
- Line 140: Libnucnet__Zone__getNet()
- Line 154: Libnucnet__Reac__clearReactionCompareFunction()
- Line 200: Libnucnet__Zone__free()
- Line 201: Libnucnet__Net__free()
- Line 220: Libnucnet__Net__isValidReaction()
- Line 226: Libnucnet__Zone__getRatesForReaction()
- Line 231: Libnucnet__Reaction__getString()
- Line 267: Libnucnet__Zone__updateRatesForReaction()
To print and double the forward and reverse rates at t9 = 3, type:
./example30 ../../data_pub/example_net.xml 3. > ex30_output.txt
The result is ex30_output.txt
You can also select out certain reactions with an xpath expression. For example, try:
./example30 ../../data_pub/example_net.xml 3. "[product = 'mg25']" > ex30_xpath_output.txt
The result is ex30_xpath_output.txt
Example 31: Create a nuclear reaction network from an input xml file and for rates selected by an XPath expression, print out the forward and reverse rates, the forward screening factor, the reverse ratio correction, and the screened rates.
libnucnet routines demonstrated in example31.c are:
- Line 114: Libnucnet__Net__new_from_xml()
- Line 157: Libnucnet__Reac__iterateReactions()
- Line 158: Libnucnet__Net__getReac()
- Line 167: Libnucnet__Net__free()
- Line 182: Libnucnet__Net__isValidReaction()
- Line 184: Libnucnet__Net__computeRatesForReaction()
- Line 194: Libnucnet__Net__computeScreeningFactorForReaction()
- Line 205: Libnucnet__Net__computeReverseRatioCorrectionFactorForReaction()
- Line 216: Libnucnet__Reaction__getString()
To print the correction factor and screened rates for reactions involving n15 as a reactant at t9 = 3, a mass density of 1.e8 g/cc, an electron-to-baryon ratio of 0.5, and a second moment of the abundances with respect to atomic number of 0.15, type:
./example31 ../../data_pub/example_net.xml 3. 1.e8 0.5 0.15 "[reactant = 'n15']" > ex31_output.txt
The result is ex31_output.txt
Example 32: Create a full libnucnet nuclear reaction network structure (nuclei plus reactions among them) from an input xml file print out data about the input zones, remove the zones, and add a zone.
libnucnet routines demonstrated in example32.c are:
- Line 74: Libnucnet__is_valid_input_xml()
- Line 83: Libnucnet__new_from_xml()
- Line 93: Libnucnet__getNumberOfZones()
- Line 103: Libnucnet__setZoneCompareFunction()
- Line 108: Libnucnet__iterateZones()
- Line 120: Libnucnet__freeAllZones()
- Line 134: Libnucnet__Zone__new()
- Line 135: Libnucnet__getNet()
- Line 141: Libnucnet__addZone()
- Line 148: Libnucnet__Nuc__getSpeciesByName()
- Line 149: Libnucnet__Net__getNuc()
- Line 155: Libnucnet__Zone__updateSpeciesAbundance()
- Line 156: Libnucnet__Species__getA()
- Line 190: Libnucnet__relabelZone()
- Line 228: Libnucnet__free()
- Line 251: Libnucnet__Zone__getLabel()
- Line 259: Libnucnet__Nuc__iterateSpecies()
- Line 261: Libnucnet__Zone__getNet()
- Line 270: Libnucnet__Zone__computeAMoment()
- Line 293: Libnucnet__Zone__getSpeciesAbundance()
- Line 299: Libnucnet__Species__getName()
The first thing you need to do is to merge the nuclear network xml file and an input mass fractions data xml file into a single xml file appropriate as a libnucnet input file. Use xsltproc (which you should have installed during the compilation tutorial):
xsltproc --stringparam initial_mass_frac_doc ../data_pub/initial_mass_fractions_3d.xml ../../xsl_pub/merge_full.xsl ../../data_pub/example_net.xml > ../../data_pub/example_3d.xml
To run example32, type the following on the command line:
./example32 ../../data_pub/example_3d.xml > ex32_output.txt
The result is ex32_output.txt
Example 33: Create a full libnucnet structure (network plus zones) and print out data about the zones.
libnucnet routines demonstrated in example33.c are:
- Line 77: Libnucnet__new_from_xml()
- Line 85: Libnucnet__getNumberOfZones()
- Line 92: Libnucnet__setZoneCompareFunction()
- Line 97: Libnucnet__iterateZones()
- Line 107: Libnucnet__free()
- Line 123: Libnucnet__Zone__getLabel()
- Line 131: Libnucnet__Nuc__iterateSpecies()
- Line 132: Libnucnet__Net__getNuc()
- Line 133: Libnucnet__Zone__getNet()
- Line 160: Libnucnet__Zone__getSpeciesAbundance()
- Line 165: Libnucnet__Species__getName()
To run example33, type the following on the command line:
./example33 ../../data_pub/example_3d.xml > ex33_output.txt
The result is ex33_output.txt
Example 34: Create a full libnucnet structure (network plus zones) and print out mass fractions for a zone chosen by its labels.
libnucnet routines demonstrated in example34.c are:
- Line 74: Libnucnet__new()
- Line 76: Libnucnet__Nuc__updateFromXml()
- Line 77: Libnucnet__Net__getNuc()
- Line 78: Libnucnet__getNet()
- Line 84: Libnucnet__assignZoneDataFromXml()
- Line 92: Libnucnet__getZoneByLabels()
- Line 104: Libnucnet__Zone__getLabel()
- Line 113: Libnucnet__free()
- Line 127: Libnucnet__Nuc__iterateSpecies()
- Line 129: Libnucnet__Zone__getNet()
- Line 137: Libnucnet__Zone__computeAMoment()
- Line 152: Libnucnet__Zone__getSpeciesAbundance()
- Line 157: Libnucnet__Species__getName()
- Line 159: Libnucnet__Species__getA()
To run example34, type the following on the command line:
./example34 ../../data_pub/example_net.xml ../../data_pub/initial_mass_fractions_3d.xml x1 y1 z1 > ex34_output.txt
The result is ex34_output.txt
Example 35: Create a full libnucnet structure (network plus zones) and print out mass fractions for a given species in all zones.
libnucnet routines demonstrated in example35.c are:
- Line 73: Libnucnet__new_from_xml()
- Line 78: Libnucnet__new()
- Line 80: Libnucnet__Nuc__updateFromXml()
- Line 81: Libnucnet__Net__getNuc()
- Line 82: Libnucnet__getNet()
- Line 88: Libnucnet__assignZoneDataFromXml()
- Line 95: Libnucnet__Nuc__getSpeciesByName()
- Line 129: Libnucnet__setZoneCompareFunction()
- Line 134: Libnucnet__iterateZones()
- Line 144: Libnucnet__free()
- Line 164: Libnucnet__Zone__getSpeciesAbundance()
- Line 169: Libnucnet__Zone__getLabel()
- Line 172: Libnucnet__Species__getA()
To run example35, type the following on the command line:
./example35 ../../data_pub/example_nuc.xml ../../data_pub/initial_mass_fractions_stooges.xml he4 > ex35_output.txt
The result is ex35_output.txt
Example 36: Create a zone mass fractions file from a Rauscher et al. (2002) stellar model data file.
libnucnet routines demonstrated in example36.c are:
- Line 83: Libnucnet__new()
- Line 85: Libnucnet__Nuc__updateFromXml()
- Line 86: Libnucnet__Net__getNuc()
- Line 87: Libnucnet__getNet()
- Line 178: Libnucnet__Zone__new()
- Line 185: Libnucnet__Zone__updateProperty()
- Line 207: Libnucnet__Nuc__getSpeciesByName()
- Line 210: Libnucnet__Zone__updateSpeciesAbundance()
- Line 211: Libnucnet__Species__getA()
- Line 216: Libnucnet__addZone()
- Line 230: Libnucnet__writeZoneDataToXmlFile()
- Line 241: Libnucnet__free()
To run example36, type the following on the command line:
./example36 ../../data_pub/star_read_nuc.xml ../../data_pub/star_data.txt ex36_output.xml
The result is ex36_output.xml
Example 37: Extract a subset of zones containing a subset of nuclei from the original zone xml file and dump to a new xml.
libnucnet routines demonstrated in example37.c are:
- Line 88: Libnucnet__new()
- Line 94: Libnucnet__Nuc__updateFromXml()
- Line 95: Libnucnet__Net__getNuc()
- Line 96: Libnucnet__getNet()
- Line 106: Libnucnet__assignZoneDataFromXml()
- Line 114: Libnucnet__Net__updateFromXml()
- Line 125: Libnucnet__iterateZones()
- Line 135: Libnucnet__writeZoneDataToXmlFile()
- Line 141: Libnucnet__free()
- Line 169: Libnucnet__Zone__getLabel()
- Line 174: Libnucnet__Zone__new()
- Line 190: Libnucnet__Zone__iterateOptionalProperties()
- Line 200: Libnucnet__Nuc__iterateSpecies()
- Line 206: Libnucnet__addZone()
- Line 233: Libnucnet__Nuc__getSpeciesByName()
- Line 235: Libnucnet__Zone__getNet()
- Line 237: Libnucnet__Species__getName()
- Line 240: Libnucnet__Zone__updateSpeciesAbundance()
- Line 243: Libnucnet__Zone__getSpeciesAbundance()
- Line 266: Libnucnet__Zone__updateProperty()
To run example37, type the following on the command line:
./example37 ../../data_pub/star_read_nuc.xml ../../data_pub/s25a28d_expl.xml "[(@label1 >= '214' and @label1 <= '216') or @label1 = 'wind']" "[ z <= 30 ]" ex37_output.xml
The result is ex37_output.xml
More complicated xpath expressions are possible. For example to extract zones for which the the mass fraction of iron-60 is greater than 1.e-10 and include them in a file that includes only species with z < 30, type:
./example37 ../../data_pub/star_read_nuc.xml ../../data_pub/s25a28d_expl.xml "[mass_fractions/nuclide[@name='fe60' and x > 1.e-10]]" "[ z <= 30 ]" ex37_output_xpath2.xml
The result is ex37_output_xpath2.xml
Example 38: Average the abundances in the zones.
libnucnet routines demonstrated in example38.c are:
- Line 71: Libnucnet__new()
- Line 77: Libnucnet__Nuc__updateFromXml()
- Line 78: Libnucnet__Net__getNuc()
- Line 79: Libnucnet__getNet()
- Line 89: Libnucnet__assignZoneDataFromXml()
- Line 97: Libnucnet__Nuc__getNumberOfSpecies()
- Line 128: Libnucnet__getZoneByLabels()
- Line 135: Libnucnet__Zone__getAbundances()
- Line 168: Libnucnet__Zone__new()
- Line 175: Libnucnet__addZone()
- Line 177: Libnucnet__Zone__updateAbundances()
- Line 183: Libnucnet__writeZoneDataToXmlFile()
- Line 191: Libnucnet__free()
To run example38, type the following on the command line:
./example38 ../../data_pub/star_read_nuc.xml ../../data_pub/s25a28d_expl.xml ../../data_pub/average.txt ex38_output.xml
The result is ex38_output.xml
Example 39: Create a full libnucnet structure (network plus zones) and print out the screening and correction factors for the reactions in a zone.
libnucnet routines demonstrated in example39.c are:
- Line 104: Libnucnet__new_from_xml()
- Line 114: Libnucnet__getZoneByLabels()
- Line 130: Libnucnet__Zone__computeZMoment()
- Line 132: Libnucnet__Zone__setScreeningFunction()
- Line 145: Libnucnet__Zone__setNseCorrectionFactorFunction()
- Line 155: Libnucnet__Zone__computeRates()
- Line 162: Libnucnet__Zone__clearScreeningFunction()
- Line 163: Libnucnet__Zone__clearNseCorrectionFactorFunction()
- Line 174: Libnucnet__Reac__setReactionCompareFunction()
- Line 175: Libnucnet__Net__getReac()
- Line 176: Libnucnet__Zone__getNet()
- Line 181: Libnucnet__Reac__iterateReactions()
- Line 196: Libnucnet__free()
- Line 211: Libnucnet__Net__isValidReaction()
- Line 220: Libnucnet__Reaction__getString()
- Line 221: Libnucnet__Zone__getScreeningFactorForReaction()
- Line 222: Libnucnet__Zone__getReverseRatioCorrectionFactorForReaction()
The first thing you need to do is to merge the nuclear network xml file and an input mass fractions data xml file appropriate for a single zone calculation into a single xml file appropriate as a libnucnet input file. Use xsltproc (which you should have installed during the compilation tutorial):
xsltproc --stringparam initial_mass_frac_doc ../data_pub/initial_mass_fractions_single_zone.xml ../../xsl_pub/merge_full.xsl ../../data_pub/example_net.xml > ../../data_pub/example_single_zone.xml
To print out the screening and reverse ratio correction factors for the zone with labels 0, 0, 0 at t9 = 1 and mass density = 1.e8 g/cc, type:
./example39 ../../data_pub/example_single_zone.xml 1. 1.e8 0 0 0 > ex39_output.txt
The result is ex39_output.txt
Example 40: Create a full libnucnet structure (network plus zones) and generate the Jacobian matrix.
libnucnet routines demonstrated in example40.c are:
- Line 111: Libnucnet__new_from_xml()
- Line 118: Libnucnet__getZoneByLabels()
- Line 130: Libnucnet__Reac__getDuplicateReactions()
- Line 131: Libnucnet__Net__getReac()
- Line 132: Libnucnet__Zone__getNet()
- Line 136: Libnucnet__Reac__iterateReactions()
- Line 142: Libnucnet__Reac__free()
- Line 155: Libnucnet__Zone__computeZMoment()
- Line 157: Libnucnet__Zone__setScreeningFunction()
- Line 170: Libnucnet__Zone__setNseCorrectionFactorFunction()
- Line 182: Libnucnet__Zone__computeRates()
- Line 189: Libnucnet__Zone__computeJacobianMatrix()
- Line 206: Libnucnet__free()
To print out the Jacobian matrix for the abundances in the zone with labels 0, 0, 0 at t9 = 1 and mass density = 1000 g/cc, type:
./example40 ../../data_pub/example_single_zone.xml 0 0 0 1. 1.e3 ex40_output.txt
The result is ex40_output.txt
Example 41: Create a full libnucnet structure (network plus zones) and run a single-zone network calculation for the input temperature, density, and duration.
libnucnet routines demonstrated in example41.c are:
- Line 155: Libnucnet__is_valid_input_xml()
- Line 165: Libnucnet__new_from_xml()
- Line 187: Libnucnet__getZoneByLabels()
- Line 194: Libnucnet__Reac__getDuplicateReactions()
- Line 195: Libnucnet__Net__getReac()
- Line 196: Libnucnet__Zone__getNet()
- Line 200: Libnucnet__Reac__iterateReactions()
- Line 206: Libnucnet__Reac__free()
- Line 219: Libnucnet__Zone__computeZMoment()
- Line 221: Libnucnet__Zone__setScreeningFunction()
- Line 234: Libnucnet__Zone__setNseCorrectionFactorFunction()
- Line 249: Libnucnet__Nuc__setSpeciesCompareFunction()
- Line 250: Libnucnet__Net__getNuc()
- Line 254: Libnucnet__Nuc__sortSpecies()
- Line 264: Libnucnet__Zone__updateProperty()
- Line 319: Libnucnet__Zone__updateTimeStep()
- Line 335: Libnucnet__free()
- Line 356: Libnucnet__Nuc__getNumberOfSpecies()
- Line 366: Libnucnet__Zone__getAbundances()
- Line 372: Libnucnet__Zone__computeRates()
- Line 375: Libnucnet__Zone__getProperty()
- Line 392: Libnucnet__Zone__computeFlowVector()
- Line 405: Libnucnet__Zone__computeJacobianMatrix()
- Line 439: Libnucnet__Zone__updateAbundances()
- Line 470: Libnucnet__Zone__updateAbundanceChanges()
- Line 505: Libnucnet__Nuc__iterateSpecies()
- Line 516: Libnucnet__Zone__computeAMoment()
- Line 533: Libnucnet__Zone__getSpeciesAbundance()
- Line 538: Libnucnet__Species__getZ()
- Line 539: Libnucnet__Species__getA()
- Line 541: Libnucnet__Zone__getSpeciesAbundanceChange()
- Line 563: Libnucnet__Species__getName()
Use a network of nuclei with Z <= 10 to compute the evolution of the abundances of species with initial abundances in the input file at an initial T9 = 10 and density of 1.e8 g/cc expanding with a density e-folding timescale of 0.1 seconds for 10 seconds, printing out the abundances every 20 time steps:
./example41 ../../data_pub/example_single_zone.xml 0 0 0 10. 1.e8 0.1 10. 20 "[z <= 10]" > ex41_output.txt
The result is ex41_output.txt
Example 42: Create a full libnucnet structure (network plus zones) and run a single-zone network calculation but with the forward and reverse rates for a particular reaction at all temperatures multipled by a constant factor.
libnucnet routines demonstrated in example42.c are:
- Line 153: Libnucnet__is_valid_input_xml()
- Line 163: Libnucnet__new_from_xml()
- Line 182: Libnucnet__getZoneByLabels()
- Line 194: Libnucnet__Reac__getDuplicateReactions()
- Line 195: Libnucnet__Net__getReac()
- Line 196: Libnucnet__Zone__getNet()
- Line 200: Libnucnet__Reac__iterateReactions()
- Line 206: Libnucnet__Reac__free()
- Line 219: Libnucnet__Zone__computeZMoment()
- Line 221: Libnucnet__Zone__setScreeningFunction()
- Line 234: Libnucnet__Zone__setNseCorrectionFactorFunction()
- Line 249: Libnucnet__Nuc__setSpeciesCompareFunction()
- Line 250: Libnucnet__Net__getNuc()
- Line 254: Libnucnet__Nuc__sortSpecies()
- Line 264: Libnucnet__Zone__updateProperty()
- Line 324: Libnucnet__Zone__updateTimeStep()
- Line 340: Libnucnet__free()
- Line 365: Libnucnet__Nuc__getNumberOfSpecies()
- Line 375: Libnucnet__Zone__getAbundances()
- Line 381: Libnucnet__Zone__computeRates()
- Line 384: Libnucnet__Zone__getProperty()
- Line 397: Libnucnet__Reac__getReactionByString()
- Line 409: Libnucnet__Zone__getRatesForReaction()
- Line 416: Libnucnet__Zone__updateRatesForReaction()
- Line 430: Libnucnet__Zone__computeFlowVector()
- Line 443: Libnucnet__Zone__computeJacobianMatrix()
- Line 477: Libnucnet__Zone__updateAbundances()
- Line 508: Libnucnet__Zone__updateAbundanceChanges()
- Line 543: Libnucnet__Nuc__iterateSpecies()
- Line 554: Libnucnet__Zone__computeAMoment()
- Line 571: Libnucnet__Zone__getSpeciesAbundance()
- Line 576: Libnucnet__Species__getZ()
- Line 577: Libnucnet__Species__getA()
- Line 579: Libnucnet__Zone__getSpeciesAbundanceChange()
- Line 602: Libnucnet__Species__getName()
Use a network of nuclei with Z <= 10 to compute the evolution of the abundances of species with initial abundances in the input file at an initial T9 = 10 and density of 1.e8 g/cc expanding with a density e-folding timescale of 0.1 seconds for 10 seconds but with the forward and reverse rates for the reaction he4 + he4 + he4 -> c12 + gamma increased by a factor of 10 at all temperatures, printing out the abundances every 20 time steps:
./example42 ../../data_pub/example_single_zone.xml 10. 1.e8 0.1 10. 20 "he4 + he4 + he4 -> c12 + gamma" 10 "[z <= 10]" > ex42_output.txt
The result is ex42_output.txt
Example 43: Create a full libnucnet structure (network plus zones) and run a single-zone network calculation for the input temperature, density, and initial mass fractions from text files.
libnucnet routines demonstrated in example43.c are:
- Line 161: Libnucnet__Net__is_valid_input_xml()
- Line 170: Libnucnet__new()
- Line 173: Libnucnet__Net__updateFromXml()
- Line 174: Libnucnet__getNet()
- Line 199: Libnucnet__Zone__new()
- Line 201: Libnucnet__addZone()
- Line 266: Libnucnet__Nuc__getSpeciesByName()
- Line 267: Libnucnet__Net__getNuc()
- Line 273: Libnucnet__Zone__updateSpeciesAbundance()
- Line 276: Libnucnet__Species__getA()
- Line 296: Libnucnet__getZoneByLabels()
- Line 303: Libnucnet__Reac__getDuplicateReactions()
- Line 304: Libnucnet__Net__getReac()
- Line 305: Libnucnet__Zone__getNet()
- Line 309: Libnucnet__Reac__iterateReactions()
- Line 315: Libnucnet__Reac__free()
- Line 328: Libnucnet__Zone__computeZMoment()
- Line 330: Libnucnet__Zone__setScreeningFunction()
- Line 343: Libnucnet__Zone__setNseCorrectionFactorFunction()
- Line 358: Libnucnet__Nuc__setSpeciesCompareFunction()
- Line 363: Libnucnet__Nuc__sortSpecies()
- Line 414: Libnucnet__Zone__updateTimeStep()
- Line 434: Libnucnet__free()
- Line 455: Libnucnet__Nuc__getNumberOfSpecies()
- Line 465: Libnucnet__Zone__getAbundances()
- Line 471: Libnucnet__Zone__computeRates()
- Line 474: Libnucnet__Zone__getProperty()
- Line 491: Libnucnet__Zone__computeFlowVector()
- Line 504: Libnucnet__Zone__computeJacobianMatrix()
- Line 538: Libnucnet__Zone__updateAbundances()
- Line 569: Libnucnet__Zone__updateAbundanceChanges()
- Line 604: Libnucnet__Nuc__iterateSpecies()
- Line 615: Libnucnet__Zone__computeAMoment()
- Line 632: Libnucnet__Zone__getSpeciesAbundance()
- Line 637: Libnucnet__Species__getZ()
- Line 640: Libnucnet__Zone__getSpeciesAbundanceChange()
- Line 662: Libnucnet__Species__getName()
- Line 830: Libnucnet__Zone__updateProperty()
Use a network of nuclei with Z <= 10 to compute the evolution of the abundances of species with initial abundances in an input file text file using a thermodynamics trajectory from an input text file evolving for 30 seconds and printing out the abundances every 20 time steps:
./example43 ../../data_pub/example_net.xml ../../data_pub/zone_ascii.txt ../../data_pub/mass_fractions.txt 30. 20 "[z <= 10]" > ex43_output.txt
The result is ex43_output.txt
Example 44: Create a full libnucnet structure (network plus zones) and run a multi-zone network calculation for the input conditions.
libnucnet routines demonstrated in example44.c are:
- Line 151: Libnucnet__is_valid_input_xml()
- Line 161: Libnucnet__new_from_xml()
- Line 172: Libnucnet__iterateZones()
- Line 247: Libnucnet__setZoneCompareFunction()
- Line 258: Libnucnet__clearZoneCompareFunction()
- Line 298: Libnucnet__free()
- Line 321: Libnucnet__Nuc__getNumberOfSpecies()
- Line 322: Libnucnet__Net__getNuc()
- Line 323: Libnucnet__getNet()
- Line 327: Libnucnet__getNumberOfZones()
- Line 476: Libnucnet__Zone__getLabel()
- Line 494: Libnucnet__Nuc__iterateSpecies()
- Line 496: Libnucnet__Zone__getNet()
- Line 505: Libnucnet__Zone__computeAMoment()
- Line 520: Libnucnet__Zone__getSpeciesAbundance()
- Line 526: Libnucnet__Species__getZ()
- Line 527: Libnucnet__Species__getA()
- Line 529: Libnucnet__Zone__getSpeciesAbundanceChange()
- Line 546: Libnucnet__Zone__updateTimeStep()
- Line 573: Libnucnet__Zone__getAbundances()
- Line 614: Libnucnet__Zone__getProperty()
- Line 622: Libnucnet__Zone__computeRates()
- Line 632: Libnucnet__Zone__computeFlowVector()
- Line 671: Libnucnet__Zone__computeJacobianMatrix()
- Line 734: Libnucnet__getZoneByLabels()
- Line 869: Libnucnet__Zone__updateAbundances()
- Line 914: Libnucnet__Zone__updateAbundanceChanges()
- Line 980: Libnucnet__Zone__updateProperty()
- Line 1010: Libnucnet__Reac__getDuplicateReactions()
- Line 1011: Libnucnet__Net__getReac()
- Line 1016: Libnucnet__Reac__iterateReactions()
- Line 1022: Libnucnet__Reac__free()
- Line 1035: Libnucnet__Zone__computeZMoment()
- Line 1037: Libnucnet__Zone__setScreeningFunction()
- Line 1050: Libnucnet__Zone__setNseCorrectionFactorFunction()
The first thing you need to do is to merge the nuclear network xml file and an input mass fractions data xml file appropriate for a 1-D multi-zone calculation into a single xml file appropriate as a libnucnet input file. Use xsltproc (which you should have installed during the compilation tutorial):
xsltproc --stringparam initial_mass_frac_doc ../data_pub/initial_mass_fractions_1d.xml ../../xsl_pub/merge_full.xsl ../../data_pub/example_net.xml > ../../data_pub/example_1d.xml
For a network of nuclei with Z <= 10, compute the evolution of the abundances of species in the three input zones for a duration of 100 seconds with a mixing time between zones of 0.01 seconds:
./example44 ../../data_pub/example_1d.xml 0.01 100. 1 "[z <= 10]" > ex44_output.txt
The result is ex44_output.txt
To run without mixing, use a mixing timescale of zero:
./example44 ../../data_pub/example_1d.xml 0. 100. 1 "[z <= 10]" > ex44_no_mixing_output.txt
The result is ex44_no_mixing_output.txt
To run with only mixing, use the mix_flag to set all zone temperatures to zero:
./example44 ../../data_pub/example_1d.xml 0.1 100. 0 "[z <= 10]" > ex44_mixing_only_output.txt
The result is ex44_mixing_only_output.txt
