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Compartmental model improvements [WIP] #983

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Compartmental model improvements [WIP] #983

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f8b4f52
initial work to make voltage initialization user-configurable
WillemWybo Nov 7, 2023
5a631a1
fix compilation issues
WillemWybo Nov 7, 2023
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131 changes: 80 additions & 51 deletions ...on/resources_nest_compartmental/cm_neuron/cm_compartmentcurrents_@NEURON_NAME@.cpp.jinja2
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Expand Up @@ -103,11 +103,11 @@ nest::{{ion_channel_name}}{{cm_unique_suffix}}::{{ion_channel_name}}{{cm_unique_
// channel parameter {{variable_type -}}
{%- set variable = variable_info["ASTVariable"] %}
{%- set rhs_expression = variable_info["rhs_expression"] %}
,{{- variable.name }}({{ printer_no_origin.print(rhs_expression) -}})
, {{- variable.name }}({{ printer_no_origin.print(rhs_expression) -}})
{%- endfor %}
{}

nest::{{ion_channel_name}}{{cm_unique_suffix}}::{{ion_channel_name}}{{cm_unique_suffix}}(const DictionaryDatum& channel_params)
nest::{{ion_channel_name}}{{cm_unique_suffix}}::{{ion_channel_name}}{{cm_unique_suffix}}( const DictionaryDatum& channel_params )

{%- for pure_variable_name, variable_info in channel_info["States"].items() %}
// state variable {{pure_variable_name -}}
Expand All @@ -121,71 +121,83 @@ nest::{{ion_channel_name}}{{cm_unique_suffix}}::{{ion_channel_name}}{{cm_unique_
// channel parameter {{variable_type -}}
{%- set variable = variable_info["ASTVariable"] %}
{%- set rhs_expression = variable_info["rhs_expression"] %}
,{{- variable.name }}({{ printer_no_origin.print(rhs_expression) -}})
, {{- variable.name }}({{ printer_no_origin.print(rhs_expression) -}})
{%- endfor %}
// update {{ion_channel_name}} channel parameters
{
{%- for variable_type, variable_info in channel_info["Parameters"].items() %}
{%- set variable = variable_info["ASTVariable"] %}
{%- set dynamic_variable = render_dynamic_channel_variable_name(variable_type, ion_channel_name) %} //have to remove???????????
// {{ion_channel_name}} channel parameter {{dynamic_variable }}
if( channel_params->known( "{{variable.name}}" ) )
{{variable.name}} = getValue< double >( channel_params, "{{variable.name}}" );
{%- endfor %}
{%- for variable_type, variable_info in channel_info["Parameters"].items() %}
{%- set variable = variable_info["ASTVariable"] %}
if( channel_params->known( "{{variable.name}}" ) )
{{variable.name}} = getValue< double >( channel_params, "{{variable.name}}" );
{%- endfor %}
if( channel_params->known( "V_init" ) )
V_init = getValue< double >( channel_params, "V_init" );
}

void
nest::{{ion_channel_name}}{{cm_unique_suffix}}::append_recordables(std::map< Name, double* >* recordables,
const long compartment_idx)
nest::{{ion_channel_name}}{{cm_unique_suffix}}::append_recordables( std::map< Name, double* >* recordables, const long compartment_idx )
{
// add state variables to recordables map
{%- for pure_variable_name, variable_info in channel_info["States"].items() %}
{%- set variable = variable_info["ASTVariable"] %}
( *recordables )[ Name( "{{variable.name}}" + std::to_string(compartment_idx) )] = &{{variable.name}};
{%- endfor %}
( *recordables )[ Name( "i_tot_{{ion_channel_name}}" + std::to_string(compartment_idx) )] = &i_tot_{{ion_channel_name}};
( *recordables )[ Name( "i_tot_{{ion_channel_name}}" + std::to_string(compartment_idx) )] = &i_tot_{{ion_channel_name}};
}

{%- if nest_version.startswith("v2") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2") or nest_version.startswith("v3.3") %}
void nest::{{ion_channel_name}}{{cm_unique_suffix}}::calibrate()
{%- else %}
void nest::{{ion_channel_name}}{{cm_unique_suffix}}::pre_run_hook()
{%- endif %}
{
// initialize all state variables with their asymptotic value for `V_init`
// For now, they are initialized at 0., but this should change
{%- for pure_variable_name, variable_info in channel_info["States"].items() %}
{%- set variable = variable_info["ASTVariable"] %}
{%- set rhs_expression = variable_info["rhs_expression"] %}
{{ variable.name }} = {{ printer_no_origin.print(rhs_expression) }};
{%- endfor %}
}

std::pair< double, double > nest::{{ion_channel_name}}{{cm_unique_suffix}}::f_numstep(const double v_comp{% for ode in channel_info["Dependencies"]["concentrations"] %}, double {{ode.lhs.name}}{% endfor %}
{% for inline in channel_info["Dependencies"]["receptors"] %}, double {{inline.variable_name}}{% endfor %}
{% for inline in channel_info["Dependencies"]["channels"] %}, double {{inline.variable_name}}{% endfor %})
{
double g_val = 0., i_val = 0.;
double g_val = 0., i_val = 0.;

if({%- for key_zero_param in channel_info["RootInlineKeyZeros"] %} {{ key_zero_param }} > 1e-9 && {%- endfor %} true ){
{% if channel_info["ODEs"].items()|length %} double {{ printer_no_origin.print(channel_info["time_resolution_var"]) }} = Time::get_resolution().get_ms(); {% endif %}
if({%- for key_zero_param in channel_info["RootInlineKeyZeros"] %} {{ key_zero_param }} > 1e-9 && {%- endfor %} true ){
{% if channel_info["ODEs"].items()|length %}double {{ printer_no_origin.print(channel_info["time_resolution_var"]) }} = Time::get_resolution().get_ms(); {% endif %}

{%- for ode_variable, ode_info in channel_info["ODEs"].items() %}
{%- for propagator, propagator_info in ode_info["transformed_solutions"][0]["propagators"].items() %}
double {{ propagator }} = {{ printer_no_origin.print(propagator_info["init_expression"]) }};
{%- endfor %}
{%- for state, state_solution_info in ode_info["transformed_solutions"][0]["states"].items() %}
{{state}} = {{ printer_no_origin.print(state_solution_info["update_expression"]) }};
{%- endfor %}
{%- for ode_variable, ode_info in channel_info["ODEs"].items() %}
{%- for propagator, propagator_info in ode_info["transformed_solutions"][0]["propagators"].items() %}
double {{ propagator }} = {{ printer_no_origin.print(propagator_info["init_expression"]) }};
{%- endfor %}
{%- for state, state_solution_info in ode_info["transformed_solutions"][0]["states"].items() %}
{{state}} = {{ printer_no_origin.print(state_solution_info["update_expression"]) }};
{%- endfor %}
{%- endfor %}

{%- set inline_expression = channel_info["root_expression"] %}
{%- set inline_expression_d = channel_info["inline_derivative"] %}
// compute the conductance of the {{ion_channel_name}} channel
this->i_tot_{{ion_channel_name}} = {{ printer_no_origin.print(inline_expression.get_expression()) }};
// derivative
double d_i_tot_dv = {{ printer_no_origin.print(inline_expression_d) }};

g_val = - d_i_tot_dv / 2.;
i_val = this->i_tot_{{ion_channel_name}} - d_i_tot_dv * v_comp / 2.;
}
return std::make_pair(g_val, i_val);
{%- set inline_expression = channel_info["root_expression"] %}
{%- set inline_expression_d = channel_info["inline_derivative"] %}
// compute the conductance of the {{ion_channel_name}} channel
i_tot_{{ion_channel_name}} = {{ printer_no_origin.print(inline_expression.get_expression()) }};
// derivative
double d_i_tot_dv = {{ printer_no_origin.print(inline_expression_d) }};

g_val = - d_i_tot_dv / 2.;
i_val = i_tot_{{ion_channel_name}} - d_i_tot_dv * v_comp / 2.;
}
return std::make_pair(g_val, i_val);
}

{%- for function in channel_info["Functions"] %}
{{render_channel_function(function, ion_channel_name)}}
{%- endfor %}

double nest::{{ion_channel_name}}{{cm_unique_suffix}}::get_current_{{ion_channel_name}}(){
return this->i_tot_{{ion_channel_name}};
return i_tot_{{ion_channel_name}};
}

// {{ion_channel_name}} channel end ///////////////////////////////////////////////////////////
{% endfor %}
////////////////////////////////////////////////////////////////////////////////
Expand Down Expand Up @@ -214,6 +226,8 @@ nest::{{synapse_name}}{{cm_unique_suffix}}::{{synapse_name}}{{cm_unique_suffix}}
if( receptor_params->known( "{{param_name}}" ) )
{{param_name}} = getValue< double >( receptor_params, "{{param_name}}" );
{%- endfor %}
if( receptor_params->known( "V_init" ) )
V_init = getValue< double >( receptor_params, "V_init" );
}

void
Expand All @@ -222,16 +236,16 @@ nest::{{synapse_name}}{{cm_unique_suffix}}::append_recordables(std::map< Name, d
{%- for convolution, convolution_info in synapse_info["convolutions"].items() %}
( *recordables )[ Name( "{{convolution_info["kernel"]["name"]}}" + std::to_string(syn_idx) )] = &{{convolution}};
{%- endfor %}
( *recordables )[ Name( "i_tot_{{synapse_name}}" + std::to_string(syn_idx) )] = &i_tot_{{synapse_name}};
( *recordables )[ Name( "i_tot_{{synapse_name}}" + std::to_string(syn_idx) )] = &i_tot_{{synapse_name}};
}


{%- if nest_version.startswith("v2") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2") or nest_version.startswith("v3.3") %}
void nest::{{synapse_name}}{{cm_unique_suffix}}::calibrate()
{%- else %}
void nest::{{synapse_name}}{{cm_unique_suffix}}::pre_run_hook()
{%- endif %}
{

const double {{render_time_resolution_variable(synapse_info)}} = Time::get_resolution().get_ms();

// set propagators to ode toolbox returned value
Expand Down Expand Up @@ -317,10 +331,9 @@ std::pair< double, double > nest::{{synapse_name}}{{cm_unique_suffix}}::f_numste
}
{%- endfor %}

double nest::{{synapse_name}}{{cm_unique_suffix}}::get_current_{{synapse_name}}(){
return this->i_tot_{{synapse_name}};
}

double nest::{{synapse_name}}{{cm_unique_suffix}}::get_current_{{synapse_name}}(){
return this->i_tot_{{synapse_name}};
}
// {{synapse_name}} synapse end ///////////////////////////////////////////////////////////
{%- endfor %}

Expand Down Expand Up @@ -366,13 +379,15 @@ nest::{{ concentration_name }}{{cm_unique_suffix}}::{{ concentration_name }}{{cm
{%- endfor %}
// update {{ concentration_name }} concentration parameters
{
{%- for variable_type, variable_info in concentration_info["Parameters"].items() %}
{%- set variable = variable_info["ASTVariable"] %}
{%- set dynamic_variable = render_dynamic_channel_variable_name(variable_type, concentration_name) %} //have to remove???????????
// {{ concentration_name }} concentration parameter {{dynamic_variable }}
if( concentration_params->known( "{{variable.name}}" ) )
{{variable.name}} = getValue< double >( concentration_params, "{{variable.name}}" );
{%- endfor %}
{%- for variable_type, variable_info in concentration_info["Parameters"].items() %}
{%- set variable = variable_info["ASTVariable"] %}
{%- set dynamic_variable = render_dynamic_channel_variable_name(variable_type, concentration_name) %}
// {{ concentration_name }} concentration parameter {{dynamic_variable }}
if( concentration_params->known( "{{variable.name}}" ) )
{{variable.name}} = getValue< double >( concentration_params, "{{variable.name}}" );
{%- endfor %}
if( concentration_params->known( "{{ concentration_name }}_init" ) )
{{ concentration_name }}_init = getValue< double >( concentration_params, "{{ concentration_name }}_init" );
}

void
Expand All @@ -384,7 +399,22 @@ nest::{{ concentration_name }}{{cm_unique_suffix}}::append_recordables(std::map<
{%- set variable = variable_info["ASTVariable"] %}
( *recordables )[ Name( "{{variable.name}}" + std::to_string(compartment_idx) )] = &{{variable.name}};
{%- endfor %}
( *recordables )[ Name( "{{concentration_name}}" + std::to_string(compartment_idx) )] = &{{concentration_name}};
( *recordables )[ Name( "{{concentration_name}}" + std::to_string(compartment_idx) )] = &{{concentration_name}};
}

{%- if nest_version.startswith("v2") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2") or nest_version.startswith("v3.3") %}
void nest::{{ concentration_name }}{{cm_unique_suffix}}::calibrate()
{%- else %}
void nest::{{ concentration_name }}{{cm_unique_suffix}}::pre_run_hook()
{%- endif %}
{
// states
{%- for pure_variable_name, variable_info in concentration_info["States"].items() %}
{%- set variable = variable_info["ASTVariable"] %}
{%- set rhs_expression = variable_info["rhs_expression"] %}
{{ variable.name }} = {{ printer_no_origin.print(rhs_expression) }};
{%- endfor %}
{{ concentration_name }} = {{ concentration_name }}_init;
}

void nest::{{ concentration_name }}{{cm_unique_suffix}}::f_numstep(const double v_comp{% for ode in concentration_info["Dependencies"]["concentrations"] %}, double {{ode.lhs.name}}{% endfor %}
Expand Down Expand Up @@ -412,6 +442,5 @@ void nest::{{ concentration_name }}{{cm_unique_suffix}}::f_numstep(const double
double nest::{{concentration_name}}{{cm_unique_suffix}}::get_concentration_{{concentration_name}}(){
return this->{{concentration_name}};
}

// {{concentration_name}} concentration end ///////////////////////////////////////////////////////////
{% endfor %}