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Normalized whitespace and indentation in the matlab toolbox

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This commit is contained in:
Ray Speth 2012-03-15 19:52:58 +00:00
parent b159a8f20b
commit 790d40b00c
278 changed files with 1399 additions and 1584 deletions
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52
interfaces/matlab/toolbox/1D/@Domain1D/Domain1D.m
View file

@ -1,42 +1,42 @@
function d = Domain1D(a, b, c, d, e)
% DOMAIN1D - Create a new one-dimensional domain.
% DOMAIN1D - Create a new one-dimensional domain.
%
d.dom_id = -1;
if nargin == 1
d.dom_id = domain_methods(0, a);
d.dom_id = domain_methods(0, a);
elseif nargin == 2
% a stagnation flow
if a == 1
if isa(b,'Solution')
d.dom_id = domain_methods(0, 1, thermo_hndl(b), kinetics_hndl(b), ...
trans_hndl(b), 1);
% a stagnation flow
if a == 1
if isa(b,'Solution')
d.dom_id = domain_methods(0, 1, thermo_hndl(b), kinetics_hndl(b), ...
trans_hndl(b), 1);
else
error('Wrong argument type. Expecting instance of class Solution.');
end
elseif a == 6
if isa(b,'Interface')
d.dom_id = domain_methods(0, 6, kinetics_hndl(b));
else
error('Wrong argument type. Expecting instance of class Interface.');
end
else
error('Wrong argument type. Expecting instance of class Solution.');
error('wrong object type');
end
elseif a == 6
if isa(b,'Interface')
d.dom_id = domain_methods(0, 6, kinetics_hndl(b));
else
error('Wrong argument type. Expecting instance of class Interface.');
end
else
error('wrong object type');
end
elseif nargin == 3
if a == 1
if isa(b,'Solution')
d.dom_id = domain_methods(0, 1, thermo_hndl(b), kinetics_hndl(b), ...
trans_hndl(b), c);
if a == 1
if isa(b,'Solution')
d.dom_id = domain_methods(0, 1, thermo_hndl(b), kinetics_hndl(b), ...
trans_hndl(b), c);
else
error('Wrong argument type. Expecting instance of class Solution.');
end
else
error('Wrong argument type. Expecting instance of class Solution.');
error('unknown domain type');
end
else
error('unknown domain type');
end
end
if d.dom_id < 0
error(geterr);
error(geterr);
end
d.domain_type = a;
d = class(d, 'Domain1D');

9
interfaces/matlab/toolbox/1D/@Domain1D/componentIndex.m
View file

@ -1,9 +1,8 @@
function n = componentIndex(d, name)
% COMPONENTINDEX -
%
% COMPONENTINDEX -
%
if isa(name,'double')
n = name;
n = name;
else
n = domain_methods(d.dom_id, 18, name);
n = domain_methods(d.dom_id, 18, name);
end

4
interfaces/matlab/toolbox/1D/@Domain1D/componentName.m
View file

@ -1,7 +1,7 @@
function s = componentName(d, n)
% COMPONENTNAME - Name of component n.
%
%
m = length(n);
for i = 1:m
s{i} = domain_methods(d.dom_id, 40, n(i));
s{i} = domain_methods(d.dom_id, 40, n(i));
end

2
interfaces/matlab/toolbox/1D/@Domain1D/disableEnergy.m
View file

@ -1,4 +1,4 @@
function d = disableEnergy(d)
% ENABLEENERGY - enable the energy equation
%
%
domain_methods(d.dom_id, 66, 0);

2
interfaces/matlab/toolbox/1D/@Domain1D/domainIndex.m
View file

@ -1,6 +1,6 @@
function i = domainIndex(d)
% DOMAININDEX - domain index.
%
%
% This function returns an integer flag denoting the location
% of the domain, beginning with 1 at the left.
%

2
interfaces/matlab/toolbox/1D/@Domain1D/domainType.m
View file

@ -1,6 +1,6 @@
function i = domainType(d)
% DOMAINTYPE - Type of domain.
%
%
% This function returns an integer flag denoting the domain
% type.
i = domain_methods(d.dom_id, 12);

2
interfaces/matlab/toolbox/1D/@Domain1D/domain_hndl.m
View file

@ -1,5 +1,5 @@
function n = domain_hndl(d)
% DOMAIN_HNDL - Integer used to access kernel object.
%
%
n = d.dom_id;

20
interfaces/matlab/toolbox/1D/@Domain1D/gridPoints.m
View file

@ -1,15 +1,13 @@
function zz = gridPoints(d, n)
% GRID -
%
% GRID -
%
if nargin == 1
for i = 1:nPoints(d)
zz(i) = domain_methods(d.dom_id, 19, i);
end
for i = 1:nPoints(d)
zz(i) = domain_methods(d.dom_id, 19, i);
end
else
m = length(n);
for i = 1:m
zz(i) = domain_methods(d.dom_id, 19, n(i));
end
m = length(n);
for i = 1:m
zz(i) = domain_methods(d.dom_id, 19, n(i));
end
end

7
interfaces/matlab/toolbox/1D/@Domain1D/isFlow.m
View file

@ -1,10 +1,9 @@
function a = isFlow(d)
% ISFLOW - Returns 1 if the domain is a flow domain, and 0 otherwise.
%
%
t = domainType(d);
if t == 50
a = 1;
a = 1;
else
a = 0;
a = 0;
end

1
interfaces/matlab/toolbox/1D/@Domain1D/isInlet.m
View file

@ -7,4 +7,3 @@ if t == 104
else
a = 0;
end

7
interfaces/matlab/toolbox/1D/@Domain1D/isSurface.m
View file

@ -1,10 +1,9 @@
function a = isSurface(d)
% ISSURFACE - Returns 1 if the domain is a surface, and 0 otherwise.
%
%
t = domainType(d);
if t == 102
a = 1;
a = 1;
else
a = 0;
a = 0;
end

5
interfaces/matlab/toolbox/1D/@Domain1D/massFlux.m
View file

@ -1,5 +1,4 @@
function mdot = massFlux(d)
% MASSFLUX -
%
% MASSFLUX -
%
mdot = domain_methods(d.dom_id, 17);

9
interfaces/matlab/toolbox/1D/@Domain1D/massFraction.m
View file

@ -1,17 +1,16 @@
function y = massFraction(d, k)
% MASSFRACTION - Mass fraction of species k.
%
%
% This method returns the mass fraction of species k, where
% k is the integer index of the species in the flow domain
% to which the boundary domain is attached.
%
if domainIndex(d) == 0
error('no flow domain attached!')
error('no flow domain attached!')
end
if isInlet(d)
y = domain_methods(d.dom_id,16,k-1);
y = domain_methods(d.dom_id,16,k-1);
else
error('not yet...');
error('not yet...');
end

2
interfaces/matlab/toolbox/1D/@Domain1D/nComponents.m
View file

@ -1,4 +1,4 @@
function n = nComponents(d)
% NCOMPONENTS - number of components
%
%
n = domain_methods(d.dom_id, 11);

1
interfaces/matlab/toolbox/1D/@Domain1D/nPoints.m
View file

@ -2,4 +2,3 @@ function npts = nPoints(d)
% NPOINTS - Number of grid points.
%
npts = domain_methods(d.dom_id, 14);

12
interfaces/matlab/toolbox/1D/@Domain1D/private/domain_methods.m
View file

@ -1,15 +1,15 @@
function v = domain_methods(n, job, a, b, c, d)
%
if nargin == 2
v = ctmethods(90, n, job);
v = ctmethods(90, n, job);
elseif nargin == 3
v = ctmethods(90, n, job, a);
v = ctmethods(90, n, job, a);
elseif nargin == 4
v = ctmethods(90, n, job, a, b);
v = ctmethods(90, n, job, a, b);
elseif nargin == 5
v = ctmethods(90, n, job, a, b, c);
v = ctmethods(90, n, job, a, b, c);
elseif nargin == 6
v = ctmethods(90, n, job, a, b, c, d);
v = ctmethods(90, n, job, a, b, c, d);
elseif nargin == 7
v = ctmethods(90, n, job, a, b, c, d, e);
v = ctmethods(90, n, job, a, b, c, d, e);
end

116
interfaces/matlab/toolbox/1D/@Domain1D/set.m
View file

@ -1,8 +1,8 @@
function a = set(a,varargin)
% SET - Set properties.
%
% The properties that may be set are
%
% The properties that may be set are
%
% Either the full property name or the symbol may be
% specified. For the extensive properties (V,H,U,S), the values
% must be given per unit mass. H, U, and S must be set in
@ -25,62 +25,62 @@ function a = set(a,varargin)
%
property_argin = varargin;
while length(property_argin) >= 2,
prop = property_argin{1};
val = property_argin{2};
property_argin = property_argin(3:end);
switch prop
case 'Temperature'
setTemperature(a,val);
case 'T'
setTemperature(a,val);
case 'MassFractions'
setMassFractions(a,val);
case 'Y'
setMassFractions(a,val);
case 'mdot'
setMdot(a,val);
case 'MassFlux'
setMdot(a,val);
case 'P'
setPressure(a,val);
case 'Pressure'
setPressure(a,val);
case 'tol'
sz = size(val);
if sz == nComponents(a)
setTolerances(a, val(1,:), val(2,:));
elseif length(val) == 2
setTolerances(a, 'default', val(1), val(2));
else
error('wrong array size for error tolerances');
end
case 'tol-time'
sz = size(val);
if sz == nComponents(a)
setTolerances(a, val(1,:), val(2,:));
elseif length(val) == 2
rt = val(1);
at = val(2);
setTolerances(a, 'default', rt, at, 'ts');
else
error('wrong array size for error tolerances');
end
case 'grid'
setupGrid(a, val);
case 'bounds'
setBounds(a, val(1,:), val(2,:));
case 'X'
setMoleFractions(a, val);
case 'MoleFractions'
setMoleFractions(a, val);
case 'T_fixed'
setFixedTempProfile(a, val);
case 'ID'
setID(a, val);
otherwise
error(['unknown property ' char(prop)]);
end
prop = property_argin{1};
val = property_argin{2};
property_argin = property_argin(3:end);
switch prop
case 'Temperature'
setTemperature(a,val);
case 'T'
setTemperature(a,val);
case 'MassFractions'
setMassFractions(a,val);
case 'Y'
setMassFractions(a,val);
case 'mdot'
setMdot(a,val);
case 'MassFlux'
setMdot(a,val);
case 'P'
setPressure(a,val);
case 'Pressure'
setPressure(a,val);
case 'tol'
sz = size(val);
if sz == nComponents(a)
setTolerances(a, val(1,:), val(2,:));
elseif length(val) == 2
setTolerances(a, 'default', val(1), val(2));
else
error('wrong array size for error tolerances');
end
case 'tol-time'
sz = size(val);
if sz == nComponents(a)
setTolerances(a, val(1,:), val(2,:));
elseif length(val) == 2
rt = val(1);
at = val(2);
setTolerances(a, 'default', rt, at, 'ts');
else
error('wrong array size for error tolerances');
end
case 'grid'
setupGrid(a, val);
case 'bounds'
setBounds(a, val(1,:), val(2,:));
case 'X'
setMoleFractions(a, val);
case 'MoleFractions'
setMoleFractions(a, val);
case 'T_fixed'
setFixedTempProfile(a, val);
case 'ID'
setID(a, val);
otherwise
error(['unknown property ' char(prop)]);
end
end

4
interfaces/matlab/toolbox/1D/@Domain1D/setBounds.m
View file

@ -1,5 +1,5 @@
function d = setBounds(d, component, lower, upper)
% SETBOUNDS -
%
% SETBOUNDS -
%
n = componentIndex(d,component);
domain_methods(d.dom_id, 51, n, lower, upper);

22
interfaces/matlab/toolbox/1D/@Domain1D/setCoverageEqs.m
View file

@ -1,20 +1,20 @@
function d = setCoverageEqs(d,onoff)
% SETCOVERAGEEQS - Enable or disable solving the coverage equations.
%
%
if d.domain_type ~= 6
error('Wrong domain type. Expected a reacting surface domain.')
error('Wrong domain type. Expected a reacting surface domain.')
end
ion = -1;
if isa(onoff,'char')
if strcmp(onoff,'on') | strcmp(onoff,'yes')
ion = 1;
elseif strcmp(onoff,'off') | strcmp(onoff,'no')
ion = 0;
else
error(strcat('unknown option: ',onoff))
end
if strcmp(onoff,'on') | strcmp(onoff,'yes')
ion = 1;
elseif strcmp(onoff,'off') | strcmp(onoff,'no')
ion = 0;
else
error(strcat('unknown option: ',onoff))
end
elseif isa(onoff,'numeric')
ion = onoff;
ion = onoff;
end
domain_methods(d.dom_id, 120, ion);
domain_methods(d.dom_id, 120, ion);

2
interfaces/matlab/toolbox/1D/@Domain1D/setID.m
View file

@ -1,4 +1,4 @@
function d = setID(d, id)
% SETID - Set the ID tag for the domain.
%
%
domain_methods(d.dom_id, 54, id);

4
interfaces/matlab/toolbox/1D/@Domain1D/setMdot.m
View file

@ -1,4 +1,4 @@
function d = setMdot(d, mdot)
% SETMDOT -
%
% SETMDOT -
%
domain_methods(d.dom_id, 60, mdot);

4
interfaces/matlab/toolbox/1D/@Domain1D/setMoleFractions.m
View file

@ -1,4 +1,4 @@
function d = setMoleFractions(d, x)
% SETMOLEFRACTIONS -
%
% SETMOLEFRACTIONS -
%
domain_methods(d.dom_id, 62, x);

5
interfaces/matlab/toolbox/1D/@Domain1D/setPressure.m
View file

@ -1,5 +1,4 @@
function d = setPressure(d, p)
% SETPRESSURE -
%
% SETPRESSURE -
%
domain_methods(d.dom_id, 63, p);

7
interfaces/matlab/toolbox/1D/@Domain1D/setProfile.m
View file

@ -1,9 +1,8 @@
function d = setProfile(d, n, p)
% SETPROFILE -
%
% SETPROFILE -
%
if d.stack == 0
error('install domain in stack before calling setProfile.');
error('install domain in stack before calling setProfile.');
end
setProfile(d.stack,domainIndex(d),n,p);

2
interfaces/matlab/toolbox/1D/@Domain1D/setTemperature.m
View file

@ -1,4 +1,4 @@
function d = setTemperature(d, t)
% SETTEMPERATURE - Set the temperature [K].
%
%
domain_methods(d.dom_id, 61, t);

50
interfaces/matlab/toolbox/1D/@Domain1D/setTolerances.m
View file

@ -1,35 +1,35 @@
function d = setTolerances(d, component, rtol, atol, typ)
% SETTOLERANCES -
%
% SETTOLERANCES -
%
ityp = 0;
if nargin == 5
switch typ
case 'ts'
ityp = -1;
case 'time'
ityp = -1;
case 'ss'
ityp = 1;
case 'steady'
ityp = 1;
end
switch typ
case 'ts'
ityp = -1;
case 'time'
ityp = -1;
case 'ss'
ityp = 1;
case 'steady'
ityp = 1;
end
end
if strcmp(component,'default')
nc = nComponents(d);
for ii = 1:nc
domain_methods(d.dom_id, 52, ii, rtol, atol, ityp);
end
return
nc = nComponents(d);
for ii = 1:nc
domain_methods(d.dom_id, 52, ii, rtol, atol, ityp);
end
return
end
if iscell(component)
nc = length(component);
for ii = 1:nc
n = componentIndex(d, component{ii});
domain_methods(d.dom_id, 52, n, rtol, atol, ityp);
end
nc = length(component);
for ii = 1:nc
n = componentIndex(d, component{ii});
domain_methods(d.dom_id, 52, n, rtol, atol, ityp);
end
else
n = componentIndex(d, component);
domain_methods(d.dom_id, 52, n, rtol, atol, ityp);
n = componentIndex(d, component);
domain_methods(d.dom_id, 52, n, rtol, atol, ityp);
end

5
interfaces/matlab/toolbox/1D/@Domain1D/setupGrid.m
View file

@ -1,5 +1,4 @@
function d = setupGrid(d, grid)
% SETUPGRID -
%
% SETUPGRID -
%
domain_methods(d.dom_id, 53, grid);

3
interfaces/matlab/toolbox/1D/@Domain1D/temperature.m
View file

@ -1,5 +1,4 @@
function t = temperature(d)
% TEMPERATURE - Temperature [K].
%
%
t = domain_methods(d.dom_id, 15);

20
interfaces/matlab/toolbox/1D/@Domain1D/z.m
View file

@ -1,15 +1,13 @@
function zz = z(d, n)
% GRID -
%
% GRID -
%
if nargin == 1
for i = 1:nPoints(d)
zz(i) = domain_methods(d.dom_id, 19, i);
end
for i = 1:nPoints(d)
zz(i) = domain_methods(d.dom_id, 19, i);
end
else
m = length(n);
for i = 1:m
zz(i) = domain_methods(d.dom_id, 19, n(i));
end
m = length(n);
for i = 1:m
zz(i) = domain_methods(d.dom_id, 19, n(i));
end
end

23
interfaces/matlab/toolbox/1D/@Stack/Stack.m
View file

@ -1,25 +1,24 @@
function s = Stack(domains)
%
% STACK - A one-dimensional 'stack' of domains.
%
% STACK - A one-dimensional 'stack' of domains.
%
% A stack object is a container for one-dimensional domains,
% which are instances of class Domain1D. The domains are of two
% types - extended domains, and connector domains.
% types - extended domains, and connector domains.
%
s.stack_id = -1;
s.domains = domains;
if nargin == 1
nd = length(domains);
for n=1:nd
ids(n) = domain_hndl(domains(n));
end
s.stack_id = stack_methods(0, 8, nd, ids);
nd = length(domains);
for n=1:nd
ids(n) = domain_hndl(domains(n));
end
s.stack_id = stack_methods(0, 8, nd, ids);
else
help(Stack);
error('wrong number of parameters');
help(Stack);
error('wrong number of parameters');
end
if s.stack_id < 0
error(geterr);
error(geterr);
end
s = class(s, 'Stack');

5
interfaces/matlab/toolbox/1D/@Stack/display.m
View file

@ -1,10 +1,9 @@
function display(s, fname)
% DISPLAY - show all domains.
% DISPLAY - show all domains.
%
% fname - file to write summary to. If omitted, output is to the screen.
%
if nargin == 1
fname = '-';
fname = '-';
end
stack_methods(s.stack_id, 103, fname);

4
interfaces/matlab/toolbox/1D/@Stack/domainIndex.m
View file

@ -1,7 +1,7 @@
function n = domainIndex(d, name)
% DOMAININDEX - Index of the domain with a specified name.
if isa(name,'double')
n = name
n = name
else
n = stack_methods(d.stack_id, 109, name);
n = stack_methods(d.stack_id, 109, name);
end

2
interfaces/matlab/toolbox/1D/@Stack/grid.m
View file

@ -1,6 +1,6 @@
function z = grid(s, d)
% GRID - the grid in one domain.
%
%
n = domainIndex(s,d);
d = s.domains(n);
z = gridPoints(d);

1
interfaces/matlab/toolbox/1D/@Stack/plotSolution.m
View file

@ -10,4 +10,3 @@ x = solution(s, domain, component);
plot(z, x);
xlabel('z (m)');
ylabel(component);

17
interfaces/matlab/toolbox/1D/@Stack/private/stack_methods.m
View file

@ -6,20 +6,19 @@ function v = stack_methods(n, job, a, b, c, d, e, f)
% and simply calls ctmethods with a flag associated with this class
% as the first parameter, followed by the input arguments.
if nargin == 2
v = ctmethods(90, n, job);
v = ctmethods(90, n, job);
elseif nargin == 3
v = ctmethods(90, n, job, a);
v = ctmethods(90, n, job, a);
elseif nargin == 4
v = ctmethods(90, n, job, a, b);
v = ctmethods(90, n, job, a, b);
elseif nargin == 5
v = ctmethods(90, n, job, a, b, c);
v = ctmethods(90, n, job, a, b, c);
elseif nargin == 6
v = ctmethods(90, n, job, a, b, c, d);
v = ctmethods(90, n, job, a, b, c, d);
elseif nargin == 7
v = ctmethods(90, n, job, a, b, c, d, e);
v = ctmethods(90, n, job, a, b, c, d, e);
elseif nargin == 8
v = ctmethods(90, n, job, a, b, c, d, e, f);
v = ctmethods(90, n, job, a, b, c, d, e, f);
else
error('too many arguments');
error('too many arguments');
end

10
interfaces/matlab/toolbox/1D/@Stack/resid.m
View file

@ -1,7 +1,7 @@
function r = resid(s, domain, rdt, count)
if nargin == 2
rdt = 0.0;
count = 0;
rdt = 0.0;
count = 0;
end
idom = domainIndex(s, domain);
@ -10,7 +10,7 @@ d = s.domains(idom);
r = zeros(nComponents(d), nPoints(d));
stack_methods(s.stack_id, 113, rdt, count);
for m = 1:nComponents(d)
for n = 1:nPoints(d)
r(m,n) = stack_methods(s.stack_id, 31, idom, m, n);
end
for n = 1:nPoints(d)
r(m,n) = stack_methods(s.stack_id, 31, idom, m, n);
end
end

4
interfaces/matlab/toolbox/1D/@Stack/restore.m
View file

@ -1,6 +1,6 @@
function restore(s, fname, id)
% RESTORE - Restore a previously-saved solution.
%
%
% This method can be used to provide an initial guess for the
% solution.
% solution.
stack_methods(s.stack_id, 111, fname, id);

10
interfaces/matlab/toolbox/1D/@Stack/save.m
View file

@ -1,10 +1,10 @@
function saveSoln(s, fname, id, desc)
% SAVE -
%
% SAVE -
%
if nargin == 2
id = 'solution';
desc = '-';
id = 'solution';
desc = '-';
elseif nargin == 3
desc = '-';
desc = '-';
end
stack_methods(s.stack_id, 107, fname, id, desc);

14
interfaces/matlab/toolbox/1D/@Stack/saveSoln.m
View file

@ -1,14 +1,14 @@
function saveSoln(s, fname, id, desc)
% SAVE - Save solution.
%
%
if nargin == 1
fname = 'soln.xml';
id = 'solution';
desc = '--';
fname = 'soln.xml';
id = 'solution';
desc = '--';
elseif nargin == 2
id = 'solution';
desc = '--';
id = 'solution';
desc = '--';
elseif nargin == 3
desc = '--';
desc = '--';
end
stack_methods(s.stack_id, 107, fname, id, desc);

5
interfaces/matlab/toolbox/1D/@Stack/setFlatProfile.m
View file

@ -1,5 +1,4 @@
function setFlatProfile(s, n, comp, v)
% SETFLATPROFILE -
%
% SETFLATPROFILE -
%
stack_methods(s.stack_id, 102, n, comp, v);

6
interfaces/matlab/toolbox/1D/@Stack/setMaxJacAge.m
View file

@ -1,8 +1,8 @@
function setMaxJacAge(s, ss_age, ts_age)
% SETMAXJACAGE - Set the number of times the Jacobian will be used
% SETMAXJACAGE - Set the number of times the Jacobian will be used
% before it is recomputed.
%
%
if nargin == 2
ts_age = ss_age;
ts_age = ss_age;
end
stack_methods(s.stack_id, 114, ss_age, ts_age);

30
interfaces/matlab/toolbox/1D/@Stack/setProfile.m
View file

@ -7,46 +7,44 @@ function setProfile(s, name, comp, p)
% v -- array of values
%
% The solution vector values for this component will be linearly
% interpolated from the discrete function defined by v vs. zr.
% interpolated from the discrete function defined by v vs. zr.
% Note that zr = 0.0 corresponds to the leftmost grid point in
% the specified domain, and zr = 1.0 corresponds to the rightmost
% grid point. This method can be called at any time, but is
% usually used to set the initial guess for the solution.
%
% Example:
%
%
% zr = [0 0.1 0.2 0.4 0.8 1];
% v = [500 650 700 730 800 900];
% setProfile(1, 2, zr, v);
%
if isa(name,'double')
n = name;
n = name;
else
n = domainIndex(s, name);
n = domainIndex(s, name);
end
d = s.domains(n);
if isa(comp,'double') | isa(comp,'cell')
c = comp;
c = comp;
elseif isa(comp,'char')
c = {comp};
c = {comp};
else
error('wrong type');
error('wrong type');
end
np = length(c);
sz = size(p);
if sz(1) == np + 1;
for j = 1:np
ic = componentIndex(d,c{j});
stack_methods(s.stack_id, 101, n, ic, p(1,:), p(j+1,:));
end
for j = 1:np
ic = componentIndex(d,c{j});
stack_methods(s.stack_id, 101, n, ic, p(1,:), p(j+1,:));
end
elseif sz(2) == np + 1;
ic = componentIndex(d,c{j});
stack_methods(s.stack_id, 101, n, ic, p(:,1), p(:,j+1));
ic = componentIndex(d,c{j});
stack_methods(s.stack_id, 101, n, ic, p(:,1), p(:,j+1));
else
error('wrong profile shape');
error('wrong profile shape');
end

13
interfaces/matlab/toolbox/1D/@Stack/setRefineCriteria.m
View file

@ -11,20 +11,19 @@ function d = setRefineCriteria(d, n, ratio, slope, curve, prune)
% will be retained in the grid. If the computed
% slope or curve value is below prune for all
% components, it will be deleted, unless either
% neighboring point is already marked for deletion.
%
% neighboring point is already marked for deletion.
%
if nargin < 3
ratio = 10.0;
ratio = 10.0;
end
if nargin < 4
slope = 0.8;
slope = 0.8;
end
if nargin < 5
curve = 0.8;
curve = 0.8;
end
if nargin < 6
prune = -0.1;
prune = -0.1;
end
stack_methods(d.stack_id, 106, n, ratio, slope, curve, prune);

3
interfaces/matlab/toolbox/1D/@Stack/setValue.m
View file

@ -1,6 +1,6 @@
function setValue(s, n, comp, localPoint, v)
% SETVALUE - Set the value of a single entry in the solution vector.
%
%
% n -- domain number
% comp -- component number
% localPoint -- local index of the grid point in the domain
@ -17,4 +17,3 @@ function setValue(s, n, comp, localPoint, v)
% stack.
%
stack_methods(s.stack_id, 100, n, comp, localPoint, v);

24
interfaces/matlab/toolbox/1D/@Stack/solution.m
View file

@ -3,21 +3,21 @@ function x = solution(s, domain, component)
%
% x = solution(s, 'flow', 'T') returns in vector x the values of
% solution component 'T' in domain 'flow'.
%
%
idom = domainIndex(s, domain);
d = s.domains(idom);
if nargin == 3
icomp = componentIndex(d, component);
for n = 1:nPoints(d)
x(n) = stack_methods(s.stack_id, 30, idom, icomp, n);
end
icomp = componentIndex(d, component);
for n = 1:nPoints(d)
x(n) = stack_methods(s.stack_id, 30, idom, icomp, n);
end
else
nc = nComponents(d);
np = nPoints(d);
for m = 1:nc
for n = 1:np
x(m,n) = stack_methods(s.stack_id, 30, idom, m, n);
end
end
nc = nComponents(d);
np = nPoints(d);
for m = 1:nc
for n = 1:np
x(m,n) = stack_methods(s.stack_id, 30, idom, m, n);
end
end
end

5
interfaces/matlab/toolbox/1D/@Stack/solve.m
View file

@ -1,5 +1,4 @@
function solve(s, loglevel, refine_grid)
% SOLVE -
%
% SOLVE -
%
stack_methods(s.stack_id, 104, loglevel, refine_grid);

16
interfaces/matlab/toolbox/1D/@Stack/subsref.m
View file

@ -1,11 +1,11 @@
function b = subsref(s,index)
% SUBSREF -
% SUBSREF -
switch index.type
case '()'
b = s.domains(index.subs{:});
case '.'
n = domainIndex(s, index.subs);
b = s.domains(n);
otherwise
error('syntax error');
case '()'
b = s.domains(index.subs{:});
case '.'
n = domainIndex(s, index.subs);
b = s.domains(n);
otherwise
error('syntax error');
end

4
interfaces/matlab/toolbox/1D/@Stack/writeStats.m
View file

@ -1,10 +1,8 @@
function writeStats(s)
% WRITESTATS - Print statistics for the current solution.
%
%
% writeStats(s) prints a summary of the number of function and
% Jacobian evaluations for each grid, and the CPU time spent on
% each one.
%
stack_methods(s.stack_id, 108);

2
interfaces/matlab/toolbox/1D/AxiStagnFlow.m
View file

@ -2,5 +2,5 @@ function m = AxiStagnFlow(gas)
% AXISTAGNFLOW - Axisymmetric stagnation flow.
%
% Return a Domain1D instance representing an axisymmetric
% stagnation flow.
% stagnation flow.
m = Domain1D(1, gas);

6
interfaces/matlab/toolbox/1D/AxisymmetricFlow.m
View file

@ -5,7 +5,7 @@ function m = AxisymmetricFlow(gas, id)
%
m = Domain1D(1, gas);
if nargin == 1
setID(m,'flow');
setID(m,'flow');
else
setID(m,id);
end
setID(m,id);
end

6
interfaces/matlab/toolbox/1D/FreeFlame.m
View file

@ -6,7 +6,7 @@ function m = FreeFlame(gas, id)
%
m = Domain1D(1, gas, 2);
if nargin == 1
setID(m,'flame');
setID(m,'flame');
else
setID(m,id);
end
setID(m,id);
end

6
interfaces/matlab/toolbox/1D/Inlet.m
View file

@ -5,9 +5,7 @@ function m = Inlet(id)
% either the leftmost or rightmost domain in a stack.
m = Domain1D(2);
if nargin == 0
setID(m,'inlet');
setID(m,'inlet');
else
setID(m,id);
setID(m,id);
end

6
interfaces/matlab/toolbox/1D/Outlet.m
View file

@ -3,9 +3,7 @@ function m = Outlet(id)
%
m = Domain1D(5);
if nargin == 0
setID(m,'outlet');
setID(m,'outlet');
else
setID(m,id);
setID(m,id);
end

6
interfaces/matlab/toolbox/1D/OutletRes.m
View file

@ -3,9 +3,7 @@ function m = OutletRes(id)
%
m = Domain1D(-2);
if nargin == 0
setID(m,'outletres');
setID(m,'outletres');
else
setID(m,id);
setID(m,id);
end

17
interfaces/matlab/toolbox/1D/Surface.m
View file

@ -2,14 +2,13 @@ function m = Surface(id, surface_mech)
% SURFACE - Return a Domain1D instance representing a non-reacting
% or reacting surface.
if nargin < 2
m = Domain1D(3);
if nargin == 0
setID(m,'surface');
elseif nargin == 1
setID(m,id);
end
m = Domain1D(3);
if nargin == 0
setID(m,'surface');
elseif nargin == 1
setID(m,id);
end
else
m = Domain1D(6, surface_mech)
setID(m,id);
m = Domain1D(6, surface_mech)
setID(m,id);
end

6
interfaces/matlab/toolbox/1D/SymmPlane.m
View file

@ -3,9 +3,7 @@ function m = SymmPlane(id)
%
m = Domain1D(4);
if nargin == 0
setID(m,'symmetry_plane');
setID(m,'symmetry_plane');
else
setID(m,id);
setID(m,id);
end

56
interfaces/matlab/toolbox/1D/npflame_init.m
View file

@ -19,20 +19,20 @@ function flame = npflame_init(gas, left, flow, right, fuel, oxidizer, nuox)
% Check input parameters
if nargin ~= 7
error('wrong number of input arguments.');
error('wrong number of input arguments.');
end
if ~isIdealGas(gas)
error('gas object must represent an ideal gas mixture.');
error('gas object must represent an ideal gas mixture.');
end
if ~isInlet(left)
error('left inlet object of wrong type.');
error('left inlet object of wrong type.');
end
if ~isFlow(flow)
error('flow object of wrong type.');
error('flow object of wrong type.');
end
if ~isInlet(right)
error('right inlet object of wrong type.');
error('right inlet object of wrong type.');
end
% create the container object
@ -60,9 +60,9 @@ tf = temperature(left);
tox = temperature(right);
for n = 1:nsp
yox(n) = massFraction(right,n);
yf(n) = massFraction(left,n);
ystoich(n) = zst*yf(n) + (1.0 - zst)*yox(n);
yox(n) = massFraction(right,n);
yf(n) = massFraction(left,n);
ystoich(n) = zst*yf(n) + (1.0 - zst)*yox(n);
end
set(gas,'T',temperature(left),'P',pressure(gas),'Y',ystoich);
@ -83,23 +83,23 @@ x0 = massFlux(left)*dz/(massFlux(left) + massFlux(right));
nz = nPoints(flow);
for j = 1:nz
x = zz(j);
zeta = f*(x - x0);
zmix = 0.5*(1.0 - erf(zeta));
zm(j) = zmix;
u(j) = a*(x0 - zz(j));
v(j) = a;
if zmix > zst
for n = 1:nsp
y(j,n) = yeq(n) + (zmix - zst)*(yf(n) - yeq(n))/(1.0 - zst);
x = zz(j);
zeta = f*(x - x0);
zmix = 0.5*(1.0 - erf(zeta));
zm(j) = zmix;
u(j) = a*(x0 - zz(j));
v(j) = a;
if zmix > zst
for n = 1:nsp
y(j,n) = yeq(n) + (zmix - zst)*(yf(n) - yeq(n))/(1.0 - zst);
end
t(j) = teq + (tf - teq)*(zmix - zst)/(1.0 - zst);
else
for n = 1:nsp
y(j,n) = yox(n) + zmix*(yeq(n) - yox(n))/zst;
end
t(j) = tox + zmix*(teq - tox)/zst;
end
t(j) = teq + (tf - teq)*(zmix - zst)/(1.0 - zst);
else
for n = 1:nsp
y(j,n) = yox(n) + zmix*(yeq(n) - yox(n))/zst;
end
t(j) = tox + zmix*(teq - tox)/zst;
end
end
zrel = zz/dz;
@ -109,9 +109,9 @@ setProfile(flame, 2, {'u', 'V'}, [zrel; u; v]);
setProfile(flame, 2, 'T', [zrel; t] );
for n = 1:nsp
nm = speciesName(gas,n);
setProfile(flame, 2, nm, [zrel; transpose(y(:,n))])
nm = speciesName(gas,n);
setProfile(flame, 2, nm, [zrel; transpose(y(:,n))])
end
% set minimal grid refinement criteria
setRefineCriteria(flame, 2, 10.0, 0.99, 0.99);
% set minimal grid refinement criteria
setRefineCriteria(flame, 2, 10.0, 0.99, 0.99);

6
interfaces/matlab/toolbox/@FlowDevice/FlowDevice.m
View file

@ -1,15 +1,13 @@
function x = FlowDevice(typ)
%
if nargin == 0
typ = 1;
typ = 1;
end
x.index = flowdevicemethods(0,typ);
if x.index < 0
error(geterr);
error(geterr);
end
x.type = typ;
x.upstream = -1;
x.downstream = -1;
x = class(x,'FlowDevice');

4
interfaces/matlab/toolbox/@FlowDevice/clear.m
View file

@ -1,4 +1,4 @@
function clear(f)
% CLEAR -
%
% CLEAR -
%
flowdevicemethods(1, f.index)

24
interfaces/matlab/toolbox/@FlowDevice/install.m
View file

@ -1,16 +1,16 @@
function install(f, upstream, downstream)
if nargin == 3
if ~isa(upstream,'Reactor') | ~isa(downstream,'Reactor')
error(['Flow devices can only be installed between reactors or' ...
' reservoirs'])
end
i = hndl(upstream);
j = hndl(downstream);
ok = flowdevicemethods(2, f.index, i, j);
if ok < 0
error(geterr)
end
if ~isa(upstream,'Reactor') | ~isa(downstream,'Reactor')
error(['Flow devices can only be installed between reactors or' ...
' reservoirs'])
end
i = hndl(upstream);
j = hndl(downstream);
ok = flowdevicemethods(2, f.index, i, j);
if ok < 0
error(geterr)
end
else
error('install requires 3 arguments')
end
error('install requires 3 arguments')
end

3
interfaces/matlab/toolbox/@FlowDevice/massFlowRate.m
View file

@ -1,5 +1,4 @@
function mdot = massFlowRate(f, time)
% MASSFLOWRATE - mass flow rate in kg/s
%
%
mdot = flowdevicemethods(21, f.index, time);

14
interfaces/matlab/toolbox/@FlowDevice/private/flowdevicemethods.m
View file

@ -1,13 +1,13 @@
function v = flowdevicemethods(n, job, a, b, c, d)
%
%
if nargin == 2
v = ctmethods(80, n, job);
v = ctmethods(80, n, job);
elseif nargin == 3
v = ctmethods(80, n, job, a);
v = ctmethods(80, n, job, a);
elseif nargin == 4
v = ctmethods(80, n, job, a, b);
v = ctmethods(80, n, job, a, b);
elseif nargin == 5
v = ctmethods(80, n, job, a, b, c);
v = ctmethods(80, n, job, a, b, c);
elseif nargin == 6
v = ctmethods(80, n, job, a, b, c, d);
end
v = ctmethods(80, n, job, a, b, c, d);
end

11
interfaces/matlab/toolbox/@FlowDevice/setFunction.m
View file

@ -2,11 +2,10 @@ function setFunction(f, mf)
% SETMASSFLOWRATE -
%
if f.type == 1
k = flowdevicemethods(5, f.index, func_hndl(mf));
if k < 0
error(geterr);
end
k = flowdevicemethods(5, f.index, func_hndl(mf));
if k < 0
error(geterr);
end
else
error('Mass flow rate can only be set for mass flow controllers')
error('Mass flow rate can only be set for mass flow controllers')
end

15
interfaces/matlab/toolbox/@FlowDevice/setMassFlowRate.m
View file

@ -1,12 +1,11 @@
function setMassFlowRate(f, mdot)
% SETMASSFLOWRATE -
%
% SETMASSFLOWRATE -
%
if f.type == 1
k = flowdevicemethods(3, f.index, mdot);
if k < 0
error(geterr);
end
k = flowdevicemethods(3, f.index, mdot);
if k < 0
error(geterr);
end
else
error('Mass flow rate can only be set for mass flow controllers')
error('Mass flow rate can only be set for mass flow controllers')
end

8
interfaces/matlab/toolbox/@FlowDevice/setValveCoeff.m
View file

@ -1,10 +1,10 @@
function setValveCoeff(f, k)
% SETVALVECOEFF - set valve coefficient
%
%
if f.type ~= 3
error('Valve coefficient can only be set for valves')
error('Valve coefficient can only be set for valves')
end
ok = flowdevicemethods(4, f.index, k);
if ok < 0
error(geterr);
end
error(geterr);
end

56
interfaces/matlab/toolbox/@Func/Func.m
View file

@ -1,12 +1,12 @@
function x = Func(typ, n, p)
%
% Func - a class for functors.
%
%
% A functor is an object that behaves like a function. Cantera
% defines a set of functors to use to create arbitrary functions to
% specify things like heat fluxes, piston speeds, etc., in reactor
% network simulations. Of course, they can be used for other things
% too.
% too.
%
% The main feature of a functor class is that it overloads the '()'
% operator to evaluate the function. For example, suppose object
@ -27,7 +27,7 @@ function x = Func(typ, n, p)
% "Func1". See the Cantera C++ documentation for more details.
%
if ~isa(typ, 'char')
error('Function type must be a string')
error('Function type must be a string')
end
x.f1 = 0;
@ -36,41 +36,39 @@ x.coeffs = 0;
itype = -1;
if strcmp(typ, 'polynomial')
itype = 2;
itype = 2;
elseif strcmp(typ,'fourier')
itype = 1;
itype = 1;
elseif strcmp(typ,'arrhenius')
itype = 3;
itype = 3;
elseif strcmp(typ,'gaussian')
itype = 4;
itype = 4;
end
if itype > 0
x.coeffs = p;
x.index = funcmethods(0,itype,n,p);
x.coeffs = p;
x.index = funcmethods(0,itype,n,p);
elseif strcmp(typ,'periodic')
itype = 50;
x.f1 = n;
x.coeffs = p;
x.index = funcmethods(0,itype,n.index,p);
itype = 50;
x.f1 = n;
x.coeffs = p;
x.index = funcmethods(0,itype,n.index,p);
else
if strcmp(typ,'sum')
itype = 20;
elseif strcmp(typ,'diff')
itype = 25;
elseif strcmp(typ,'prod')
itype = 30;
elseif strcmp(typ,'ratio')
itype = 40;
elseif strcmp(typ,'composite')
itype = 60;
end
x.f1 = n;
x.f2 = p;
x.index = funcmethods(0,itype,n.index,p.index);
if strcmp(typ,'sum')
itype = 20;
elseif strcmp(typ,'diff')
itype = 25;
elseif strcmp(typ,'prod')
itype = 30;
elseif strcmp(typ,'ratio')
itype = 40;
elseif strcmp(typ,'composite')
itype = 60;
end
x.f1 = n;
x.f2 = p;
x.index = funcmethods(0,itype,n.index,p.index);
end
x.typ = typ;
x = class(x,'Func');

166
interfaces/matlab/toolbox/@Func/char.m
View file

@ -1,92 +1,92 @@
function s = char(p)
% CHAR -
%
% CHAR -
%
if strcmp(p.typ,'sum')
s = ['(' char(p.f1) ') + (' char(p.f2) ')'];
s = ['(' char(p.f1) ') + (' char(p.f2) ')'];
elseif strcmp(p.typ,'diff')
s = ['(' char(p.f1) ') - (' char(p.f2) ')'];
s = ['(' char(p.f1) ') - (' char(p.f2) ')'];
elseif strcmp(p.typ,'prod')
s = ['(' char(p.f1) ') * (' char(p.f2) ')'];
s = ['(' char(p.f1) ') * (' char(p.f2) ')'];
elseif strcmp(p.typ,'ratio')
s = ['(' char(p.f1) ') / (' char(p.f2) ')'];
s = ['(' char(p.f1) ') / (' char(p.f2) ')'];
elseif all(p.coeffs == 0)
s = '0';
s = '0';
else
if strcmp(p.typ,'polynomial')
d = length(p.coeffs) - 1;
s = [];
nn = 0;
for b = p.coeffs;
cc(d+1-nn) = b;
nn = nn + 1;
if strcmp(p.typ,'polynomial')
d = length(p.coeffs) - 1;
s = [];
nn = 0;
for b = p.coeffs;
cc(d+1-nn) = b;
nn = nn + 1;
end
for a = cc;
if a ~= 0;
if ~isempty(s)
if a > 0
s = [s ' + '];
else
s = [s ' - '];
a = -a;
end
end
if a ~= 1 | d == 0
s = [s num2str(a)];
if d > 0
s = [s '*'];
end
end
if d >= 2
s = [s 'x^' int2str(d)];
elseif d == 1
s = [s 'x'];
end
end
d = d - 1;
end
elseif strcmp(p.typ,'gaussian')
s = num2str(p.coeffs(1));
s = ['Gaussian(' num2str(p.coeffs(1)) ',' ...
num2str(p.coeffs(2)) ',' ...
num2str(p.coeffs(3)) ')'];
elseif strcmp(p.typ,'fourier')
c = reshape(p.coeffs, [],2);
Ao = c(1,1);
w = c(1,2);
A = c(2:end,1);
B = c(2:end,2);
N = size(c,1)-1;
if Ao ~= 0
s = [num2str(Ao/2)];
else
s = '';
end
for n=1:N
if A(n) ~= 0
if A(n) < 0
prefix = ' - ';
elseif s
prefix = ' + ';
else
prefix = '';
end
s = [s prefix num2str(abs(A(n))) '*cos(' num2str(n*w) '*x)'];
end
if B(n) ~= 0
if B(n) < 0
prefix = ' - ';
elseif s
prefix = ' + ';
else
prefix = '';
end
s = [s prefix num2str(abs(B(n))) '*sin(' num2str(n*w) '*x)'];
end
end
else
s = ['*** char not yet implemented for' p.typ ' ***'];
end
for a = cc;
if a ~= 0;
if ~isempty(s)
if a > 0
s = [s ' + '];
else
s = [s ' - '];
a = -a;
end
end
if a ~= 1 | d == 0
s = [s num2str(a)];
if d > 0
s = [s '*'];
end
end
if d >= 2
s = [s 'x^' int2str(d)];
elseif d == 1
s = [s 'x'];
end
end
d = d - 1;
end
elseif strcmp(p.typ,'gaussian')
s = num2str(p.coeffs(1));
s = ['Gaussian(' num2str(p.coeffs(1)) ',' ...
num2str(p.coeffs(2)) ',' ...
num2str(p.coeffs(3)) ')'];
elseif strcmp(p.typ,'fourier')
c = reshape(p.coeffs, [],2);
Ao = c(1,1);
w = c(1,2);
A = c(2:end,1);
B = c(2:end,2);
N = size(c,1)-1;
if Ao ~= 0
s = [num2str(Ao/2)];
else
s = '';
end
for n=1:N
if A(n) ~= 0
if A(n) < 0
prefix = ' - ';
elseif s
prefix = ' + ';
else
prefix = '';
end
s = [s prefix num2str(abs(A(n))) '*cos(' num2str(n*w) '*x)'];
end
if B(n) ~= 0
if B(n) < 0
prefix = ' - ';
elseif s
prefix = ' + ';
else
prefix = '';
end
s = [s prefix num2str(abs(B(n))) '*sin(' num2str(n*w) '*x)'];
end
end
else
s = ['*** char not yet implemented for' p.typ ' ***'];
end
end

3
interfaces/matlab/toolbox/@Func/display.m
View file

@ -1,9 +1,8 @@
function d = display(a)
% DISPLAY -
% DISPLAY -
%
disp(' ');
disp([inputname(1),' = '])
disp(' ');
disp([' ' char(a)])
disp(' ');

4
interfaces/matlab/toolbox/@Func/plus.m
View file

@ -2,7 +2,5 @@ function r = plus(a, b)
%
% PLUS - Return a functor representing the sum of two functors a
% and b.
%
%
r = Func('sum',a,b);

14
interfaces/matlab/toolbox/@Func/private/funcmethods.m
View file

@ -1,13 +1,13 @@
function v = funcmethods(n, job, a, b, c, d)
%
%
if nargin == 2
v = ctmethods(110, n, job);
v = ctmethods(110, n, job);
elseif nargin == 3
v = ctmethods(110, n, job, a);
v = ctmethods(110, n, job, a);
elseif nargin == 4
v = ctmethods(110, n, job, a, b);
v = ctmethods(110, n, job, a, b);
elseif nargin == 5
v = ctmethods(110, n, job, a, b, c);
v = ctmethods(110, n, job, a, b, c);
elseif nargin == 6
v = ctmethods(110, n, job, a, b, c, d);
end
v = ctmethods(110, n, job, a, b, c, d);
end

5
interfaces/matlab/toolbox/@Func/rdivide.m
View file

@ -1,5 +1,4 @@
function r = rdivide(a,b)
% RDIVIDE -
%
% RDIVIDE -
%
r = Func('ratio',a,b);

16
interfaces/matlab/toolbox/@Func/subsref.m
View file

@ -1,11 +1,11 @@
function b = subsref(a,s)
% SUBSREF
% SUBSREF
switch s.type
case '()'
ind = s.subs{:};
for k = 1:length(ind)
b(k) = funcmethods(2,a.index,ind(k));
end
otherwise
error('Specify value for x as p(x)')
case '()'
ind = s.subs{:};
for k = 1:length(ind)
b(k) = funcmethods(2,a.index,ind(k));
end
otherwise
error('Specify value for x as p(x)')
end

5
interfaces/matlab/toolbox/@Func/times.m
View file

@ -1,5 +1,4 @@
function r = times(a,b)
% TIMES -
%
% TIMES -
%
r = Func('prod',a,b);

12
interfaces/matlab/toolbox/@Interface/Interface.m
View file

@ -5,19 +5,17 @@ doc = XML_Node('doc',src);
node = findByID(doc,id);
t = ThermoPhase(node);
if nargin == 2
k = Kinetics(node,t);
k = Kinetics(node,t);
elseif nargin == 3
k = Kinetics(node,t,p1);
k = Kinetics(node,t,p1);
elseif nargin == 4
k = Kinetics(node,t,p1,p2);
k = Kinetics(node,t,p1,p2);
elseif nargin == 5
k = Kinetics(node,t,p1,p2,p3);
k = Kinetics(node,t,p1,p2,p3);
elseif nargin == 6
k = Kinetics(node,t,p1,p2,p3,p4);
k = Kinetics(node,t,p1,p2,p3,p4);
end
s.kin = k;
s.th = t;
s = class(s,'Interface',t,k);

22
interfaces/matlab/toolbox/@Interface/concentrations.m
View file

@ -1,17 +1,15 @@
function c = concentrations(s)
% CONCENTRATIONS - Surface concentrations
%
%
c = surfmethods(thermo_hndl(s), 101);
if nargout == 0
figure
set(gcf,'Name','Concentrations')
bar(c);
colormap(summer);
nm = speciesNames(s);
legend(nm);
xlabel('Species Number');
ylabel('Concentration [kmol/m2]');
title('Surface Species Concentrations');
figure
set(gcf,'Name','Concentrations')
bar(c);
colormap(summer);
nm = speciesNames(s);
legend(nm);
xlabel('Species Number');
ylabel('Concentration [kmol/m2]');
title('Surface Species Concentrations');
end

22
interfaces/matlab/toolbox/@Interface/coverages.m
View file

@ -1,17 +1,15 @@
function c = coverages(s)
% COVERAGES - Surface coverages
%
%
c = surfmethods(thermo_hndl(s), 101);
if nargout == 0
figure
set(gcf,'Name','Coverages')
bar(c);
colormap(summer);
nm = speciesNames(s);
legend(nm);
xlabel('Species Number');
ylabel('Coverage');
title('Surface Species Coverages');
figure
set(gcf,'Name','Coverages')
bar(c);
colormap(summer);
nm = speciesNames(s);
legend(nm);
xlabel('Species Number');
ylabel('Coverage');
title('Surface Species Coverages');
end

17
interfaces/matlab/toolbox/@Interface/private/surfmethods.m
View file

@ -6,20 +6,19 @@ function v = surfmethods(n, job, a, b, c, d, e, f)
% and simply calls ctmethods with a flag associated with this class
% as the first parameter, followed by the input arguments.
if nargin == 2
v = ctmethods(100, n, job);
v = ctmethods(100, n, job);
elseif nargin == 3
v = ctmethods(100, n, job, a);
v = ctmethods(100, n, job, a);
elseif nargin == 4
v = ctmethods(100, n, job, a, b);
v = ctmethods(100, n, job, a, b);
elseif nargin == 5
v = ctmethods(100, n, job, a, b, c);
v = ctmethods(100, n, job, a, b, c);
elseif nargin == 6
v = ctmethods(100, n, job, a, b, c, d);
v = ctmethods(100, n, job, a, b, c, d);
elseif nargin == 7
v = ctmethods(100, n, job, a, b, c, d, e);
v = ctmethods(100, n, job, a, b, c, d, e);
elseif nargin == 8
v = ctmethods(100, n, job, a, b, c, d, e, f);
v = ctmethods(100, n, job, a, b, c, d, e, f);
else
error('too many arguments');
error('too many arguments');
end

20
interfaces/matlab/toolbox/@Interface/setCoverages.m
View file

@ -1,17 +1,13 @@
function setCoverages(s,cov)
% SETCOVERAGES - set surface coverages
%
%
if isa(cov,'double')
sz = length(cov);
if sz == nSpecies(s)
surfmethods(thermo_hndl(s), 3, cov);
else
error('wrong size for coverage array');
end
sz = length(cov);
if sz == nSpecies(s)
surfmethods(thermo_hndl(s), 3, cov);
else
error('wrong size for coverage array');
end
elseif isa(cov,'char')
surfmethods(thermo_hndl(s), 5, cov);
surfmethods(thermo_hndl(s), 5, cov);
end

42
interfaces/matlab/toolbox/@Kinetics/Kinetics.m
View file

@ -1,10 +1,10 @@
function k = Kinetics(r, ph, neighbor1, neighbor2, neighbor3, neighbor4)
%
% KINETICS - Kinetics class constructor.
% KINETICS - Kinetics class constructor.
%
% Class Kinetics represents kinetics managers, which are classes
% that manage reaction mechanisms. The reaction mechanism
% attributes are specified in a CTML file.
% attributes are specified in a CTML file.
%
% indices for bulk phases in a heterogeneous mechanism.
@ -17,42 +17,42 @@ ineighbor4 = -1;
% if only one argument is supplied, and it is an instance of
% 'Kinetics', return a copy of this instance
if nargin == 1
if isa(r,'Kinetics')
k = r;
return
else
error('wrong number of arguments')
end
if isa(r,'Kinetics')
k = r;
return
else
error('wrong number of arguments')
end
end
% if more than one arguement, first one must be an XML_Node
% instance representing the XML tree
if ~isa(r,'XML_Node')
error('first argument must be an XML_Node object')
error('first argument must be an XML_Node object')
end
k.owner = 1;
ixml = hndl(r);
% get the integer indices used to find the stored objects
% representing the phases participating in the mechanism.
% representing the phases participating in the mechanism.
iphase = thermo_hndl(ph);
if nargin > 2
ineighbor1 = thermo_hndl(neighbor1);
if nargin > 3
ineighbor2 = thermo_hndl(neighbor2);
if nargin > 4
ineighbor3 = thermo_hndl(neighbor3);
if nargin > 5
ineighbor4 = thermo_hndl(neighbor4);
end
ineighbor1 = thermo_hndl(neighbor1);
if nargin > 3
ineighbor2 = thermo_hndl(neighbor2);
if nargin > 4
ineighbor3 = thermo_hndl(neighbor3);
if nargin > 5
ineighbor4 = thermo_hndl(neighbor4);
end
end
end
end
end
k.id = kinetics_get(ixml,0,iphase,ineighbor1,ineighbor2,ineighbor3, ...
ineighbor4);
ineighbor4);
if k.id < 0
error(geterr);
error(geterr);
end
k = class(k,'Kinetics');

3
interfaces/matlab/toolbox/@Kinetics/advanceCoverages.m
View file

@ -1,5 +1,4 @@
function advanceCoverages(k, dt)
% ADVANCECOVERAGES - advance the surface coverages forward in time holding the bulk phase concentrations fixed.
%
%
kinetics_set(k.id, 5, 0, dt);

3
interfaces/matlab/toolbox/@Kinetics/clear.m
View file

@ -1,5 +1,4 @@
function clear(k)
% CLEAR - delete the Kinetics instance.
%
%
kinetics_set(k.id,3);

17
interfaces/matlab/toolbox/@Kinetics/creationRates.m
View file

@ -5,19 +5,16 @@ function cdot = creationRates(a)
%
% Returns a column vector of the creation rates of all
% species. If the output is not assigned to a variable, a
% bar graph is produced.
% bar graph is produced.
%
% See also: destructionRates, netProdRates.
%
cdot = kinetics_get(a.id,21,0);
if nargout == 0
figure
set(gcf,'Name','Creation Rates')
bar(cdot)
xlabel('Species Number')
ylabel('Creation Rate (kmol/m^3-s)')
title('Species Chemical Creation Rates')
figure
set(gcf,'Name','Creation Rates')
bar(cdot)
xlabel('Species Number')
ylabel('Creation Rate (kmol/m^3-s)')
title('Species Chemical Creation Rates')
end

17
interfaces/matlab/toolbox/@Kinetics/destructionRates.m
View file

@ -5,19 +5,16 @@ function ddot = destructionRates(a)
%
% Returns a column vector of the destruction rates of all
% species. If the output is not assigned to a variable, a
% bar graph is produced.
% bar graph is produced.
%
% See also: creationRates, netProdRates.
%
ddot = kinetics_get(a.id,22,0);
if nargout == 0
figure
set(gcf,'Name','Destruction Rates')
bar(ddot)
xlabel('Species Number')
ylabel('Destruction Rate (kmol/m^3/s)')
title('Species Chemical Destruction Rates')
figure
set(gcf,'Name','Destruction Rates')
bar(ddot)
xlabel('Species Number')
ylabel('Destruction Rate (kmol/m^3/s)')
title('Species Chemical Destruction Rates')
end

16
interfaces/matlab/toolbox/@Kinetics/destruction_rates.m
View file

@ -3,18 +3,16 @@ function q = destruction_rates(a)
%
% q = destruction_rates(a)
%
% Returns a column vector of the destruction rates of all species.
% Returns a column vector of the destruction rates of all species.
%
% See also: creation_rates, net_production_rates.
%
q = production(a.id,nSpecies(a.ph),1);
if nargout == 0
figure
set(gcf,'Name','Destruction Rates')
bar(q)
xlabel('Species Number')
ylabel('Destruction Rate (kmol/m^3/s)')
title('Species Chemical Destruction Rates')
figure
set(gcf,'Name','Destruction Rates')
bar(q)
xlabel('Species Number')
ylabel('Destruction Rate (kmol/m^3/s)')
title('Species Chemical Destruction Rates')
end

14
interfaces/matlab/toolbox/@Kinetics/equil_Kc.m
View file

@ -11,12 +11,10 @@ function kc = equil_Kc(a)
%
kc = kinetics_get(a.id,14,0);
if nargout == 0
figure
set(gcf,'Name','Equilibrium Constants')
bar(log10(kc))
xlabel('Reaction Number')
ylabel('log_1_0 Kc [kmol, m, s]')
title('Equilibrium Constants Kc')
figure
set(gcf,'Name','Equilibrium Constants')
bar(log10(kc))
xlabel('Reaction Number')
ylabel('log_1_0 Kc [kmol, m, s]')
title('Equilibrium Constants Kc')
end

4
interfaces/matlab/toolbox/@Kinetics/kinetics_hndl.m
View file

@ -1,6 +1,4 @@
function i = kinetics_hndl(k)
% KINETICS_HNDL - integer used to access kernel object
%
%
i = k.id;

3
interfaces/matlab/toolbox/@Kinetics/multiplier.m
View file

@ -6,9 +6,8 @@ function n = multiplier(a,irxn)
% disable reactions. For reversible reactions, it multiplies both
% the forward and reverse rates. By default, the multiplier value
% is 1.0, but it may be set to any other value by calling method
% setMultiplier.
% setMultiplier.
%
% MULTIPLIER(K, IRXN) Multiplier for reaction number IRXN
%
n = kinetics_get(a.id,2,irxn);

1
interfaces/matlab/toolbox/@Kinetics/nReactions.m
View file

@ -2,4 +2,3 @@ function n = nReactions(a)
% NREACTIONS - Number of reactions.
%
n = kinetics_get(a.id,1,0);

4
interfaces/matlab/toolbox/@Kinetics/nTotalSpecies.m
View file

@ -1,5 +1,5 @@
function nsp = nTotalSpecies(a)
% NTOTALSPECIES - The total number of species, summed over all
% participating phases.
%
% participating phases.
%
nsp = kinetics_get(a.id, 3, 0);

14
interfaces/matlab/toolbox/@Kinetics/netProdRates.m
View file

@ -11,12 +11,10 @@ function wdot = netProdRates(a)
%
wdot = kinetics_get(a.id,23,0);
if nargout == 0
figure
set(gcf,'Name','Production Rates')
bar(wdot)
xlabel('Species Number')
ylabel('Net Production Rate (kmol/m^3/s)')
title('Species Net Chemical Production Rates')
figure
set(gcf,'Name','Production Rates')
bar(wdot)
xlabel('Species Number')
ylabel('Net Production Rate (kmol/m^3/s)')
title('Species Net Chemical Production Rates')
end

20
interfaces/matlab/toolbox/@Kinetics/private/kinetics_get.m
View file

@ -1,18 +1,18 @@
function v = kinetics_get(n, job, a, b, c, d, e, f)
% KINETICS_GET - get kinetics attributes
%
% KINETICS_GET - get kinetics attributes
%
if nargin == 2
v = ctmethods(40, n, job);
v = ctmethods(40, n, job);
elseif nargin == 3
v = ctmethods(40, n, job, a);
v = ctmethods(40, n, job, a);
elseif nargin == 4
v = ctmethods(40, n, job, a, b);
v = ctmethods(40, n, job, a, b);
elseif nargin == 5
v = ctmethods(40, n, job, a, b, c);
v = ctmethods(40, n, job, a, b, c);
elseif nargin == 6
v = ctmethods(40, n, job, a, b, c, d);
v = ctmethods(40, n, job, a, b, c, d);
elseif nargin == 7
v = ctmethods(40, n, job, a, b, c, d, e);
v = ctmethods(40, n, job, a, b, c, d, e);
elseif nargin == 8
v = ctmethods(40, n, job, a, b, c, d, e, f);
end
v = ctmethods(40, n, job, a, b, c, d, e, f);
end

6
interfaces/matlab/toolbox/@Kinetics/private/kinetics_set.m
View file

@ -1,6 +1,4 @@
function kinetics_set(n, job, a, b)
% KINETICS_SET - get kinetics attributes
%
% KINETICS_SET - get kinetics attributes
%
ctmethods(40, n, -job, a, b)

34
interfaces/matlab/toolbox/@Kinetics/reactionEqn.m
View file

@ -2,28 +2,24 @@ function e = reactionEqn(a, irxn)
% reactionEqn Reaction equation of reaction irxn.
%
if nargin == 1
m = nReactions(a);
n = 1;
irxn = [1:m]';
m = nReactions(a);
n = 1;
irxn = [1:m]';
elseif nargin == 2
if isa(irxn,'double')
[m, n] = size(irxn);
else
error('reaction number(s) must be numeric');
end
if isa(irxn,'double')
[m, n] = size(irxn);
else
error('reaction number(s) must be numeric');
end
end
if m == 1 & n == 1
e = kinetics_get(a.id, 31, irxn); % rxnstring(a.id, irxn);
e = kinetics_get(a.id, 31, irxn); % rxnstring(a.id, irxn);
else
e = {};
for i = 1:m
for j = 1:n
e{i,j} = kinetics_get(a.id, 31, irxn(i,j)); % rxnstring(a.id, irxn(i,j));
end
end
e = {};
for i = 1:m
for j = 1:n
e{i,j} = kinetics_get(a.id, 31, irxn(i,j)); % rxnstring(a.id, irxn(i,j));
end
end
end

18
interfaces/matlab/toolbox/@Kinetics/rop.m
View file

@ -5,16 +5,16 @@ function rop = rop(k)
% progress. The first column contains the forward rates of progress,
% and the second column the reverse rates. If this function
% is called with no output argument, a bar graph is produced.
%
f = rop_f(k)
%
f = rop_f(k)
r = rop_r(k)
rop = [f r]
if nargout == 0
figure
set(gcf,'Name','Rates of Progress');
bar(rop);
xlabel('Reaction Number');
ylabel('Rate of Progress [kmol/m^3-s]');
title('Rates of Progress');
legend('Forward', 'Reverse');
figure
set(gcf,'Name','Rates of Progress');
bar(rop);
xlabel('Reaction Number');
ylabel('Rate of Progress [kmol/m^3-s]');
title('Rates of Progress');
legend('Forward', 'Reverse');
end

13
interfaces/matlab/toolbox/@Kinetics/rop_f.m
View file

@ -10,11 +10,10 @@ function q = rop_f(a)
%
q = kinetics_get(a.id,11,0);
if nargout == 0
figure
set(gcf,'Name','Rates of Progress')
bar(q)
xlabel('Reaction Number')
ylabel('Forward Rate of Progress [kmol/m^3]')
title('Forward Rates of Progress')
figure
set(gcf,'Name','Rates of Progress')
bar(q)
xlabel('Reaction Number')
ylabel('Forward Rate of Progress [kmol/m^3]')
title('Forward Rates of Progress')
end

13
interfaces/matlab/toolbox/@Kinetics/rop_net.m
View file

@ -10,11 +10,10 @@ function q = rop_net(a)
%
q = kinetics_get(a.id,13,0);
if nargout == 0
figure
set(gcf,'Name','Rates of Progress')
bar(q)
xlabel('Reaction Number')
ylabel('Net Rate of Progress [kmol/m^3]')
title('Net Rates of Progress')
figure
set(gcf,'Name','Rates of Progress')
bar(q)
xlabel('Reaction Number')
ylabel('Net Rate of Progress [kmol/m^3]')
title('Net Rates of Progress')
end

3
interfaces/matlab/toolbox/@Kinetics/rop_r.m
View file

@ -5,9 +5,8 @@ function q = rop_r(a)
%
% Returns a column vector of the reverse rates of progress
% for all reactions. The value is zero for irreversible
% reactions.
% reactions.
%
% See also: rop_r, rop_net.
%
q = kinetics_get(a.id,12,0);

36
interfaces/matlab/toolbox/@Kinetics/rxnEqs.m
View file

@ -1,29 +1,25 @@
function e = rxnEqs(a, irxn)
% rxnEqs
% rxnEqs
%
if nargin == 1
m = nReactions(a);
n = 1;
irxn = [1:m]'
m = nReactions(a);
n = 1;
irxn = [1:m]'
elseif nargin == 2
if isa(irxn,'double')
[m, n] = size(irxn);
else
error('reaction number(s) must be numeric');
end
if isa(irxn,'double')
[m, n] = size(irxn);
else
error('reaction number(s) must be numeric');
end
end
if m == 1 & n == 1
e = rxnstring(a.id, irxn);
e = rxnstring(a.id, irxn);
else
e = {};
for i = 1:m
for j = 1:n
e{i,j} = rxnstring(a.id, irxn(i,j));
end
end
e = {};
for i = 1:m
for j = 1:n
e{i,j} = rxnstring(a.id, irxn(i,j));
end
end
end

18
interfaces/matlab/toolbox/@Kinetics/setMultiplier.m
View file

@ -7,18 +7,16 @@ function setMultiplier(a,irxn,v)
% see also: MULTIPLIER
%
if nargin == 2
v = irxn;
m = nReactions(a);
irxn = [1:m]';
n = 1;
v = irxn;
m = nReactions(a);
irxn = [1:m]';
n = 1;
else
[m, n] = size(irxn);
[m, n] = size(irxn);
end
for jm = 1:m
for jn = 1:n
kinetics_set(a.id,1,irxn(jm,jn),v);
end
for jn = 1:n
kinetics_set(a.id,1,irxn(jm,jn),v);
end
end

8
interfaces/matlab/toolbox/@Kinetics/stoich_net.m
View file

@ -21,10 +21,10 @@ function nu = stoich_net(a,species,rxns)
% See also: stoich_r, stoich_p.
%
if nargin == 1
nu = stoich_p(a) - stoich_r(a)
nu = stoich_p(a) - stoich_r(a)
elseif nargin == 3
nu = stoich_p(a,species,rxns) - stoich_r(a,species,rxns);
nu = stoich_p(a,species,rxns) - stoich_r(a,species,rxns);
else
error(['syntax error. Type ''help stoich_net'' for more' ...
' information.'])
error(['syntax error. Type ''help stoich_net'' for more' ...
' information.'])
end

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