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Code generation: unit scaling for rate computation is the other way round #1241

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Jul 3, 2024
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Code generation: unit scaling for rate computation is the other way round #1241

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f85e4b8
Analyser: properly scale the computation of a rate.
agarny Jul 3, 2024
48c7137
Addressed spelling issue.
agarny Jul 3, 2024
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2 changes: 2 additions & 0 deletions .codespellexclude
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Expand Up @@ -13,3 +13,5 @@
if (index < pFunc()->mErrors.size()) {
issue = pFunc()->mIssues.at(pFunc()->mErrors.at(index));
return pFunc()->mErrors.size();
identity and expression, level of experience, education, socio-economic status,
"W3C MathML DTD error: Element apply content does not follow the DTD, expecting (csymbol | ci | cn | apply | reln | lambda | condition | declare | sep | semantics | annotation | annotation-xml | integers | reals | rationals | naturalnumbers | complexes | primes | exponentiale | imaginaryi | notanumber | true | false | emptyset | pi | eulergamma | infinity | interval | list | matrix | matrixrow | set | vector | piecewise | lowlimit | uplimit | bvar | degree | logbase | momentabout | domainofapplication | inverse | ident | domain | codomain | image | abs | conjugate | exp | factorial | arg | real | imaginary | floor | ceiling | not | ln | sin | cos | tan | sec | csc | cot | sinh | cosh | tanh | sech | csch | coth | arcsin | arccos | arctan | arccosh | arccot | arccoth | arccsc | arccsch | arcsec | arcsech | arcsinh | arctanh | determinant | transpose | card | quotient | divide | power | rem | implies | vectorproduct | scalarproduct | outerproduct | setdiff | fn | compose | plus | times | max | min | gcd | lcm | and | or | xor | union | intersect | cartesianproduct | mean | sdev | variance | median | mode | selector | root | minus | log | int | diff | partialdiff | divergence | grad | curl | laplacian | sum | product | limit | moment | exists | forall | neq | factorof | in | notin | notsubset | notprsubset | tendsto | eq | leq | lt | geq | gt | equivalent | approx | subset | prsubset | mi | mn | mo | mtext | ms | mspace | mrow | mfrac | msqrt | mroot | menclose | mstyle | merror | mpadded | mphantom | mfenced | msub | msup | msubsup | munder | mover | munderover | mmultiscripts | mtable | mtr | mlabeledtr | mtd | maligngroup | malignmark | maction)*, got (CDATA bvar ).",
2 changes: 1 addition & 1 deletion src/analyser.cpp
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Expand Up @@ -2453,7 +2453,7 @@ void Analyser::AnalyserImpl::scaleEquationAst(const AnalyserEquationAstPtr &ast)
auto astGrandparent = astParent->parent();

if (astGrandparent->mPimpl->mType == AnalyserEquationAst::Type::EQUALITY) {
scaleAst(astGrandparent->mPimpl->mOwnedRightChild, astGrandparent, 1.0 / scalingFactor);
scaleAst(astGrandparent->mPimpl->mOwnedRightChild, astGrandparent, scalingFactor);
} else {
scaleAst(astParent, astGrandparent, 1.0 / scalingFactor);
}
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11 changes: 7 additions & 4 deletions tests/resources/generator/cellml_unit_scaling_voi_indirect/model.c
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Expand Up @@ -8,14 +8,15 @@
const char VERSION[] = "0.5.0";
const char LIBCELLML_VERSION[] = "0.5.0";

const size_t STATE_COUNT = 2;
const size_t STATE_COUNT = 3;
const size_t VARIABLE_COUNT = 0;

const VariableInfo VOI_INFO = {"t", "ms", "environment", VARIABLE_OF_INTEGRATION};
const VariableInfo VOI_INFO = {"t", "second", "environment", VARIABLE_OF_INTEGRATION};

const VariableInfo STATE_INFO[] = {
{"x", "mM", "t_in_ms", STATE},
{"x", "mM", "t_in_s", STATE}
{"x", "metre", "t_in_s", STATE},
{"x", "metre", "t_in_ms", STATE},
{"x", "metre", "t_in_ks", STATE}
};

const VariableInfo VARIABLE_INFO[] = {
Expand Down Expand Up @@ -52,6 +53,7 @@ void initialiseVariables(double *states, double *rates, double *variables)
{
states[0] = 3.0;
states[1] = 7.0;
states[2] = 11.0;
}

void computeComputedConstants(double *variables)
Expand All @@ -62,6 +64,7 @@ void computeRates(double voi, double *states, double *rates, double *variables)
{
rates[0] = 5.0;
rates[1] = 1000.0*9.0;
rates[2] = 0.001*13.0;
}

void computeVariables(double voi, double *states, double *rates, double *variables)
Expand Down
60 changes: 42 additions & 18 deletions tests/resources/generator/cellml_unit_scaling_voi_indirect/model.cellml
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@@ -1,29 +1,50 @@
<?xml version='1.0' encoding='UTF-8'?>
<model name="my_model" xmlns="http://www.cellml.org/cellml/2.0#" xmlns:cellml="http://www.cellml.org/cellml/2.0#">
<!-- Define the VOI as being time (expressed in milliseconds). Then:
- Use the VOI as-is (i.e. time expressed in milliseconds) in a component to compute an ODE; and
- Use a scaled version of the VOI (here, time expressed in seconds) in a component to compute another ODE. -->
<!-- Define the VOI as being time (expressed in seconds). Then:
- Use the VOI as-is (i.e. time expressed in seconds) in a component to compute an ODE;
- Use a scaled version of the VOI (here, time expressed in milliseconds) in a component to compute another ODE
- Use a scaled version of the VOI (here, time expressed in kiloseconds) in a component to compute another ODE. -->
<units name="ms">
<unit prefix="milli" units="second"/>
</units>
<units name="mM">
<unit prefix="milli" units="mole"/>
<unit exponent="-1" units="litre"/>
<units name="ks">
<unit prefix="kilo" units="second"/>
</units>
<units name="mM_per_s">
<unit units="mM"/>
<units name="m_per_s">
<unit units="metre"/>
<unit exponent="-1" units="second"/>
</units>
<units name="mM_per_ms">
<unit units="mM"/>
<units name="m_per_ms">
<unit units="metre"/>
<unit exponent="-1" units="ms"/>
</units>
<units name="m_per_ks">
<unit units="metre"/>
<unit exponent="-1" units="ks"/>
</units>
<component name="environment">
<variable interface="public" name="t" units="ms"/>
<variable interface="public" name="t" units="second"/>
</component>
<component name="t_in_s">
<variable interface="public" name="t" units="second"/>
<variable initial_value="3" name="x" units="metre"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>x</ci>
</apply>
<cn cellml:units="m_per_s">5</cn>
</apply>
</math>
</component>
<component name="t_in_ms">
<variable interface="public" name="t" units="ms"/>
<variable initial_value="3" name="x" units="mM"/>
<variable initial_value="7" name="x" units="metre"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
Expand All @@ -34,13 +55,13 @@
</bvar>
<ci>x</ci>
</apply>
<cn cellml:units="mM_per_ms">5</cn>
<cn cellml:units="m_per_ms">9</cn>
</apply>
</math>
</component>
<component name="t_in_s">
<variable interface="public" name="t" units="second"/>
<variable initial_value="7" name="x" units="mM"/>
<component name="t_in_ks">
<variable interface="public" name="t" units="ks"/>
<variable initial_value="11" name="x" units="metre"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
Expand All @@ -51,14 +72,17 @@
</bvar>
<ci>x</ci>
</apply>
<cn cellml:units="mM_per_s">9</cn>
<cn cellml:units="m_per_ks">13</cn>
</apply>
</math>
</component>
<connection component_1="environment" component_2="t_in_s">
<map_variables variable_1="t" variable_2="t"/>
</connection>
<connection component_1="environment" component_2="t_in_ms">
<map_variables variable_1="t" variable_2="t"/>
</connection>
<connection component_1="environment" component_2="t_in_s">
<connection component_1="environment" component_2="t_in_ks">
<map_variables variable_1="t" variable_2="t"/>
</connection>
</model>
2 changes: 1 addition & 1 deletion tests/resources/generator/cellml_unit_scaling_voi_indirect/model.h
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Expand Up @@ -20,7 +20,7 @@ typedef enum {

typedef struct {
char name[2];
char units[3];
char units[7];
char component[12];
VariableType type;
} VariableInfo;
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11 changes: 7 additions & 4 deletions tests/resources/generator/cellml_unit_scaling_voi_indirect/model.py
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Expand Up @@ -7,7 +7,7 @@
__version__ = "0.4.0"
LIBCELLML_VERSION = "0.5.0"

STATE_COUNT = 2
STATE_COUNT = 3
VARIABLE_COUNT = 0


Expand All @@ -19,11 +19,12 @@ class VariableType(Enum):
ALGEBRAIC = 4


VOI_INFO = {"name": "t", "units": "ms", "component": "environment", "type": VariableType.VARIABLE_OF_INTEGRATION}
VOI_INFO = {"name": "t", "units": "second", "component": "environment", "type": VariableType.VARIABLE_OF_INTEGRATION}

STATE_INFO = [
{"name": "x", "units": "mM", "component": "t_in_ms", "type": VariableType.STATE},
{"name": "x", "units": "mM", "component": "t_in_s", "type": VariableType.STATE}
{"name": "x", "units": "metre", "component": "t_in_s", "type": VariableType.STATE},
{"name": "x", "units": "metre", "component": "t_in_ms", "type": VariableType.STATE},
{"name": "x", "units": "metre", "component": "t_in_ks", "type": VariableType.STATE}
]

VARIABLE_INFO = [
Expand All @@ -41,6 +42,7 @@ def create_variables_array():
def initialise_variables(states, rates, variables):
states[0] = 3.0
states[1] = 7.0
states[2] = 11.0


def compute_computed_constants(variables):
Expand All @@ -50,6 +52,7 @@ def compute_computed_constants(variables):
def compute_rates(voi, states, rates, variables):
rates[0] = 5.0
rates[1] = 1000.0*9.0
rates[2] = 0.001*13.0


def compute_variables(voi, states, rates, variables):
Expand Down