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Merge pull request #28 from the-virtual-brain/NeuroML
DSL2.0 for CUDA and python models
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| <Lems | ||
| xmlns="http://www.neuroml.org/lems/0.7.4" | ||
| xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" | ||
| xsi:schemaLocation="http://www.neuroml.org/lems/0.7.4 ../../LEMS/Schemas/LEMS/LEMS_v0.7.4.xsd" | ||
| description="A number of ComponentTypes for rate based/population models. | ||
| Base type of any cell/population which has a (dimensionless) rate _R. | ||
| Epileptor 2-D (phase plane) oscillator."> | ||
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| <ComponentType name="Epileptor_2D" | ||
| description="Rate based 2D oscillator for TVB" | ||
| value=""> | ||
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| <Constant name="a" symbol="float32" dimension="" value="1.0" description="Coefficient of the cubic term in the first state-variable."/> | ||
| <Constant name="b" symbol="float32" dimension="" value="3.0" description="Coefficient of the squared term in the first state-variable."/> | ||
| <Constant name="c" symbol="float32" dimension="" value="1.0" description="Additive coefficient for the second state-variable x_{2}, called :math:`y_{0}` in Jirsa paper."/> | ||
| <Constant name="d" symbol="float32" dimension="" value="5.0" description="Coefficient of the squared term in the second state-variable x_{2}."/> | ||
| <Constant name="r" symbol="float32" dimension="lo=0.0, hi=0.001, step=0.00005" value="0.00035" description="Temporal scaling in the slow state-variable, called :math:`1\\tau_{0}` in Jirsa paper (see class Epileptor)."/> | ||
| <Constant name="s" symbol="float32" dimension="" value="4.0" description="Linear coefficient in the third state variable"/> | ||
| <Constant name="x0" symbol="float32" dimension="lo=-3.0, hi=-1.0, step=0.1" value="-1.6" description="Epileptogenicity parameter."/> | ||
| <Constant name="Iext" symbol="float32" dimension="lo=1.5, hi=5.0, step=0.1" value="3.1" description="External input current to the first state-variable."/> | ||
| <Constant name="slope" symbol="float32" dimension="lo=-16.0, hi=6.0, step=0.1" value="0." description="Linear coefficient in the first state-variable."/> | ||
| <Constant name="Iext2" symbol="float32" dimension="lo=0.0, hi=1.0, step=0.05" value="3.1" description="External input current to the first state-variable."/> | ||
| <Constant name="tau" symbol="float32" dimension="" value="10.0" description="Temporal scaling coefficient in fifth state variable."/> | ||
| <Constant name="aa" symbol="float32" dimension="" value="6.0" description="Linear coefficient in fifth state variable."/> | ||
| <Constant name="bb" symbol="float32" dimension="" value="2.0" description="Linear coefficient of lowpass excitatory coupling in fourth state variable."/> | ||
| <Constant name="Kvf" symbol="float32" dimension="lo=0.0, hi=4.0, step=0.5" value="0.0" description="Coupling scaling on a very fast time scale."/> | ||
| <Constant name="Kf" symbol="float32" dimension="lo=0.0, hi=4.0, step=0.5" value="0.0" description="Correspond to the coupling scaling on a fast time scale."/> | ||
| <Constant name="Ks" symbol="float32" dimension="lo=-4.0, hi=4.0, step=0.1" value="0.0" description="Permittivity coupling, that is from the fast time scale toward the slow time scale."/> | ||
| <Constant name="tt" symbol="float32" dimension="lo=0.001, hi=1.0, step=0.001" value="1.0" description="Time scaling of the whole system to the system in real time."/> | ||
| <Constant name="modification" symbol="bool" dimension="" value="1.0" description="When modification is True, then use nonlinear influence on z. The default value is False, i.e., linear influence."/> | ||
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| <!-- Parameters will be assumed to be swept. sweep data will be matched by order of entry --> | ||
| <Parameter name="global_coupling" dimension="float" /> | ||
| <Parameter name="global_speed" dimension="float" /> | ||
| <Parameter name="x0" dimension="float" /> | ||
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| <Dynamics> | ||
| <StateVariable name="x1" dimension="-2., 1." exposure=""/> | ||
| <StateVariable name="y1" dimension="-20., 2."/> | ||
| <StateVariable name="z" dimension="-2.0, 5.0" exposure=""/> | ||
| <StateVariable name="x2" dimension="-2., 0."/> | ||
| <StateVariable name="y2" dimension="0., 2." exposure=""/> | ||
| <StateVariable name="g" dimension="-1, 1."/> | ||
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| <!-- <DerivedVariable name="coupling_value" exposure="c_0" value="0.0" reduce="add"/>--> | ||
| <!-- Per state variable specifiable noise factor --> | ||
| <DerivedVariable name="sig_x1" exposure="float" value="sqrt(dt) * sqrt(2.0 * 1e-3)" reduce="add"/> | ||
| <DerivedVariable name="sig_y1" exposure="float" value="sqrt(dt) * sqrt(2.0 * 1e-3)" reduce="add"/> | ||
| <DerivedVariable name="sig_z" exposure="float" value="sqrt(dt) * sqrt(2.0 * 1e-3)" reduce="add"/> | ||
| <DerivedVariable name="sig_x2" exposure="float" value="sqrt(dt) * sqrt(2.0 * 1e-3)" reduce="add"/> | ||
| <DerivedVariable name="sig_y2" exposure="float" value="sqrt(dt) * sqrt(2.0 * 1e-3)" reduce="add"/> | ||
| <DerivedVariable name="sig_g" exposure="float" value="0" reduce="add"/> | ||
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| <DerivedVariable name="rec_speed_dt" exposure="float" value="1.0f / global_speed / (dt)" reduce="add"/> | ||
| <!-- <DerivedVariable name="G" exposure="float" value="params" reduce="add"/>--> | ||
| <DerivedVariable name="lc_0" exposure="float" value="0.0"/> | ||
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| <!-- For conditionals use <(=); or >(=) for less- or greater then (equal to) --> | ||
| <!-- Population 1 --> | ||
| <ConditionalDerivedVariable name="if_ydot0" exposure="" dimension="(x1 < 0) * (- a * powf(x1, 2) * b * x1)"/> | ||
| <ConditionalDerivedVariable name="else_ydot0" exposure="" dimension="(x1 >= 0) * (slope - x2 + 0.6 * powf((z - 4.0), 2))"/> | ||
| <TimeDerivative variable="dx1" exposure="" value="tt * (y1 - z + Iext + Kvf * c_pop1 + (if_ydot0 + else_ydot0) )"/> | ||
| <TimeDerivative variable="dy1" exposure="" value="tt * (c - d * powf(x1, 2) - y1)"/> | ||
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| <!-- Energy --> | ||
| <ConditionalDerivedVariable name="if_ydot1" exposure="" dimension="(y1 < 0) * (- 0.1 * powf(Z, 7))"/> | ||
| <ConditionalDerivedVariable name="else_ydot1" exposure="" dimension="0"/> | ||
| <ConditionalDerivedVariable name="ifmod_h" exposure="" dimension="(modification==true)*(x0 + 3. / (1. + exp(-(x1 + 0.5) / 0.1)) "/> | ||
| <ConditionalDerivedVariable name="elsemod_h" exposure="" dimension="(modification==false)*(4 * (x1 - x0) + if_ydot1) )"/> | ||
| <TimeDerivative variable="dz" exposure="" value="tt * (r * ((ifmod_h + elsemod_h)) - z + Ks * c_pop1))"/> | ||
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| <!-- Population 2 --> | ||
| <TimeDerivative variable="dx2" exposure="" value="tt * (-y2 + x2 - powf(x2, 3) + Iext2 + bb * g - 0.3 * (z - 3.5) + Kf * c_pop2)"/> | ||
| <ConditionalDerivedVariable name="if_ydot3" exposure="" dimension="0"/> | ||
| <ConditionalDerivedVariable name="else_ydot3" exposure="" dimension="(x2 >= -0.25) * (aa * (x2 + 0.25))"/> | ||
| <TimeDerivative variable="dy2" exposure="" value="tt * (-y2 + else_ydot3) / tau"/> | ||
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| <!-- Filter --> | ||
| <TimeDerivative variable="dg" exposure="" value="tt * (-0.01 * (g - 0.1 * x1) )"/> | ||
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| </Dynamics> | ||
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| <!-- Exposures are used for observables, for the name enter variable to be observed (usually states) | ||
| and for dimension enter the reduction functionality--> | ||
| <Exposure name="o_x1" dimension="x1"/> | ||
| <Exposure name="o_x2" dimension="x2"/> | ||
| <Exposure name="o_z" dimension="z"/> | ||
| <Exposure name="o_-x1+x2" dimension="-x1 + x2"/> | ||
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| </ComponentType> | ||
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| <ComponentType name="coupling_function_pop1"> | ||
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| <!-- Added function for pre and post synaptic activity. Fixed the power being **, however no parse checks for it--> | ||
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| <Constant name="coupl_a" symbol="float32" dimension="lo=0.0, hi=10., step=0.1" value="1" description="Rescales the connection strength."/> | ||
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| <!-- variable for pre synaptic function, only 1 param is allowed (and should be sufficient)) --> | ||
| <Parameter name="x1_j" dimension=''/> | ||
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| <!-- variables for post synaptic function--> | ||
| <Requirement name="wij" dimension=''/> | ||
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| <Function name="pre" value="sin(x1_j - x1)" description="pre synaptic function for coupling activity"/> | ||
| <Function name="post" value="a" description="post synaptic = a * pre"/> | ||
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| <!-- Handle local coupling result, full expression is c_0 *= 'value'. Name option is hardcoded --> | ||
| <DerivedParameter name="c_pop1" value="global_coupling"/> | ||
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| </ComponentType> | ||
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| <ComponentType name="coupling_function_pop2"> | ||
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| <!-- Added function for pre and post synaptic activity. Fixed the power being **, however no parse checks for it--> | ||
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| <Constant name="coupl_b" symbol="float32" dimension="lo=0.0, hi=10., step=0.1" value="0.1" description="Rescales the connection strength."/> | ||
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| <!-- variables for pre synaptic function--> | ||
| <Parameter name="y1_j" dimension=''/> | ||
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| <!-- variables for post synaptic function--> | ||
| <Requirement name="wij" dimension=''/> | ||
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| <Function name="pre" value="" description = "pre synaptic function for coupling activity"/> | ||
| <Function name="post" value="" description = "post synaptic function for coupling activity"/> | ||
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| <!-- Handle local coupling result, full expression is c_0 *= 'value'. Name option is hardcoded --> | ||
| <DerivedParameter name="c_pop2" value="g"/> | ||
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| </ComponentType> | ||
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| <ComponentType name="noise"> | ||
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| <!-- Param a--> | ||
| <!-- Related to exposures?--> | ||
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| <!-- StateVariables for certain noises--> | ||
| <!-- parant noise of specific children--> | ||
| <!-- ScalingFunction GFUN; noisescaling--> | ||
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| <!-- dimension field for Constant is being (mis)used for fields required for Float (True or False), domain for float32 (lo, hi, step) or field_type for Attr ('str') ) --> | ||
| <!-- is label more than a short description? --> | ||
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| <Constant name="ntau" symbol="Float" dimension="True" value="0.1" description="The noise correlation time"/> | ||
| <Constant name="noise_seed" symbol="Int" dimension="" value="42" description="A random seed used to initialise the random_stream if it is missing."/> | ||
| <Constant name="random_stream" symbol="Attr" dimension="numpy.random.RandomState" value="0.0" description="An instance of numpy's RandomState associated with this | ||
| specific Noise object. Used when you need to resume a simulation from a state saved to disk"/> | ||
| <!-- <Requirement name="temperature" dimension="temperature"/>--> | ||
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| </ComponentType> | ||
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| <ComponentType name="additive" extends="noise"> | ||
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| <!-- specific child of noise--> | ||
| <Constant name="nsig" symbol="float32" dimension="lo=0.0, hi=10.0, step=0.1" value="1.0" | ||
| description="The noise dispersion, it is the standard deviation of the | ||
| distribution from which the Gaussian random variates are drawn. NOTE: | ||
| Sensible values are typically ~gt 1% of the dynamic range of a Model's | ||
| state variables."/> | ||
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| </ComponentType> | ||
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| <ComponentType name="multiplicative" extends="noise"> | ||
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| <!-- specific https://gitlab.version.fz-juelich.de/diaz1/tvb_dslchild of noise--> | ||
| <Constant name="nsig" symbol="float32" dimension="lo=0.0, hi=10.0, step=0.1" value="1.0" | ||
| description="The noise dispersion, it is the standard deviation of the | ||
| distribution from which the Gaussian random variates are drawn. NOTE: | ||
| Sensible values are typically ~gt 1% of the dynamic range of a Model's | ||
| state variables."/> | ||
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| <Constant name="b" symbol="Attr" dimension="equations.TemporalApplicableEquation" value="0.0" | ||
| description="A function evaluated on the state-variables, the result of which enters as the diffusion coefficient."/> | ||
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| </ComponentType> | ||
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| </Lems> | ||
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| <!--Look at vector representation in XML LEMS--> |
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| <Lems> | ||
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| <Target component="simset"/> | ||
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| <!--<Include file="ex2dims.xml"/>--> | ||
| <!--<Include file="hhchannel.xml"/> --> | ||
| <!--<Include file="hhcell.xml"/>--> | ||
| <!--<Include file="hhmodels.xml"/>--> | ||
| <!--<Include file="MultiRunSimulation.xml"/>--> | ||
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| <ComponentType name="TemperatureDependency"> | ||
| <Exposure name="rateFactor" dimension="none"/> | ||
| <Requirement name="temperature" dimension="temperature"/> | ||
| </ComponentType> | ||
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| <ComponentType name="Q10TemperatureDependency" extends="TemperatureDependency" description="Provides a q10 value"> | ||
| <Parameter name="Q10" dimension="none"/> | ||
| <Requirement name="velocity" dimension="speed"/> | ||
| <!-- <Parameter name="baseTemperature" dimension="temperature"/>--> | ||
| <!-- <Constant name="tenC" symbol="" dimension="temperature" value="10"/>--> | ||
| <!-- <Dynamics>--> | ||
| <!-- <DerivedVariable name="rateFactor" exposure="rateFactor" dimension="none"--> | ||
| <!-- value="Q10^((temperature - baseTemperature) / tenC)"/>--> | ||
| <!-- </Dynamics>--> | ||
| </ComponentType> | ||
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| <!-- <ComponentType name="HHGateQ10" extends="HHGate">--> | ||
| <!-- <Child name="temperatureDependency" type="TemperatureDependency"/>--> | ||
| <!-- --> | ||
| <!-- <Dynamics simultaneous="false">--> | ||
| <!-- <StateVariable name="x" dimension="none"/>--> | ||
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| <!-- <DerivedVariable name="rateFactor" dimension="none" select="temperatureDependency/rateFactor" --> | ||
| <!-- reduce="multiply" required="false"/>--> | ||
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| <!-- <DerivedVariable name="rf" dimension="per_time" select="Forward/r"/>--> | ||
| <!-- <DerivedVariable name="rr" dimension="per_time" select="Reverse/r"/> --> | ||
| <!-- --> | ||
| <!-- <TimeDerivative variable="x" value="(1 + ex)^2 / ex * (rateFactor * rf * (1 - q) - rateFactor * rr * q)"/>--> | ||
| <!-- --> | ||
| <!-- <DerivedVariable name="ex" dimension="none" value="exp(x)"/>--> | ||
| <!-- <DerivedVariable name="q" dimension="none" value="ex / (1 + ex)"/>--> | ||
| <!-- <DerivedVariable name="fcond" exposure="fcond" value="q^power"/>--> | ||
| <!-- </Dynamics> --> | ||
| <!--</ComponentType>--> | ||
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| <!--<HHChannel id="naq10" conductance="10pS">--> | ||
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| <!-- <HHGateQ10 id="m" power="3">--> | ||
| <!-- <temperatureDependency type="Q10TemperatureDependency" Q10="3" baseTemperature="32degC" /> --> | ||
| <!-- <Forward type="HHExpLinearRate" rate="1per_ms" midpoint="-40mV" scale="10mV"/>--> | ||
| <!-- <Reverse type="HHExpRate" rate="4per_ms" midpoint="-65mV" scale="-18mV"/>--> | ||
| <!-- </HHGateQ10>--> | ||
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| <!-- <HHGateQ10 id="h" power="1">--> | ||
| <!-- <Forward type="HHExpRate" rate="0.07per_ms" midpoint="-65mV" scale="-20mV"/>--> | ||
| <!-- <Reverse type="HHSigmoidRate" rate="1per_ms" midpoint="-35mV" scale="10mV"/>--> | ||
| <!-- </HHGateQ10>--> | ||
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| <!--</HHChannel>--> | ||
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| <!--<ComponentType name="HHCellT" extends="HHCell">--> | ||
| <!-- <Parameter name="temperature" dimension="temperature"/>--> | ||
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| <!--</ComponentType>--> | ||
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| <!--<HHCellT id="hhcell_1" capacitance="1pF" injection="4pA" v0="-60mV" temperature="22degC">--> | ||
| <!-- <ChannelPopulation id="NaPop" channel="naq10" number="8000" erev="50mV"/>--> | ||
| <!-- <ChannelPopulation id="KPop" channel="k" number="1100" erev="-77mV"/>--> | ||
| <!--</HHCellT>--> | ||
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| <!--<SimulationSet id="simset">--> | ||
| <!-- <Display id="disp1" title="Example 10: Challen kinetics with Q10" xmin="0" xmax="80" ymin="-80" ymax="50"/>--> | ||
| <!-- --> | ||
| <!-- <Simulation id="sim1" length="80ms" step="0.05ms" target="hhcell_1" display="disp1">--> | ||
| <!-- <DisplayList timeScale="1ms" title="">--> | ||
| <!-- <Line id="V" quantity="v" scale="1mV" timeScale="1ms" color="#0000f0"/>--> | ||
| <!-- --> | ||
| <!-- <Line id="Na_q" quantity="NaPop/geff" scale="1nS" timeScale="1ms" color="#f00000"/>--> | ||
| <!-- <Line id="K_q" quantity="KPop/geff" scale="1nS" timeScale="1ms" color="#00f000"/>--> | ||
| <!-- --> | ||
| <!-- --> | ||
| <!-- </DisplayList>--> | ||
| <!-- </Simulation>--> | ||
| <!--</SimulationSet>--> | ||
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| </Lems> |
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| <Lems | ||
| xmlns="http://www.neuroml.org/lems/0.7.4" | ||
| xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" | ||
| xsi:schemaLocation="http://www.neuroml.org/lems/0.7.4 ../../LEMS/Schemas/LEMS/LEMS_v0.7.4.xsd" | ||
| description="A number of ComponentTypes for rate based/population models"> | ||
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| <ComponentType name="Kuramoto" | ||
| description="Base type of any cell/population which has a (dimensionless) rate _R." | ||
| value="none"> | ||
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| <!-- Parameters will be assumed to be swept. sweep data will be matched by order of entry --> | ||
| <Parameter name="global_coupling" dimension='float'/> | ||
| <Parameter name="global_speed" dimension='float'/> | ||
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| <Requirement name="MODEL_LIMIT" dimension="2_pi"/> <!-- put helping functions in util, select wrapping functions. --> | ||
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| <Exposure name="V" dimension="sin(V)"/> | ||
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| <Dynamics> | ||
| <StateVariable name="V" dimension="PI-V, PI"/> | ||
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| <DerivedVariable name="rec_n" dimension="none" value="1.0f / n_node" /> | ||
| <DerivedVariable name="rec_speed_dt" dimension="1/distance" value="1.0f / global_speed / (dt)" /> | ||
| <DerivedVariable name="omega" dimension="MHz" value="60.0 * 2.0 * M_PI_F / 1e3" /> | ||
| <DerivedVariable name="nsig" dimension="none" value="sqrt(dt) * sqrt(2.0 * 1e-5)" /> | ||
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| <TimeDerivative variable="dV" exposure="dV" value="omega * c_0"/> | ||
| </Dynamics> | ||
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| </ComponentType> | ||
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| <ComponentType name="coupling_function"> | ||
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| <!-- Added function for pre and post synaptic activity. Fixed the power being **, however no parse checks for it--> | ||
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| <Constant name="a" symbol="NArray" dimension="lo=0.0, hi=10., step=0.1" value="0.1" description="Rescales the connection strength."/> | ||
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| <!-- variables for pre synaptic function--> | ||
| <Parameter name="V" dimension=''/> | ||
| <Parameter name="V_j" dimension=''/> | ||
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| <!-- variables for post synaptic function--> | ||
| <Requirement name="wij" dimension=''/> | ||
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| <Function name="pre" value="sin(V_j - V)" description = "pre synaptic function for coupling activity"/> | ||
| <Function name="post" value="wij" description = "post synaptic function for coupling activity"/> | ||
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| <!-- Handle local coupling result, full expression is c_0 *= 'value'. Name option is hardcoded --> | ||
| <DerivedParameter name="c_0" value="global_coupling * rec_n"/> | ||
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| </ComponentType> | ||
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| <ComponentType name="noise"> | ||
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| <!-- Param a--> | ||
| <!-- Related to exposures?--> | ||
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| <!-- StateVariables for certain noises--> | ||
| <!-- parant noise of specific children--> | ||
| <!-- ScalingFunction GFUN; noisescaling--> | ||
|
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| <!-- dimension field for Constant is being (mis)used for fields required for Float (True or False), domain for NArray (lo, hi, step) or field_type for Attr ('str') ) --> | ||
| <!-- is label more than a short description? --> | ||
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| <Constant name="ntau" symbol="Float" dimension="True" value="0.1" description="The noise correlation time"/> | ||
| <Constant name="noise_seed" symbol="Int" dimension="" value="42" description="A random seed used to initialise the random_stream if it is missing."/> | ||
| <Constant name="random_stream" symbol="Attr" dimension="numpy.random.RandomState" value="0.0" description="An instance of numpy's RandomState associated with this | ||
| specific Noise object. Used when you need to resume a simulation from a state saved to disk"/> | ||
| <!-- <Requirement name="temperature" dimension="temperature"/>--> | ||
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| </ComponentType> | ||
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| </Lems> |
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