got medyan process running!

README.md

@@ -14,6 +14,12 @@ Install conda: https://docs.conda.io/en/latest/miniconda.html
 
 Using conda, you can run `conda env create -f env.yml`, which will create a conda environment called `vivarium_models` with all the required dependencies (including ReaDDy) installed.
 
+To update:
+
+```
+
+```
+
 ### MEDYAN
 
 To install MEDYAN:

env.yml

@@ -2,8 +2,8 @@ name: vivarium_models
 channels:
   - conda-forge
 dependencies:
-  - python=3.8
+  - python=3.9.6
   - readdy/label/dev::readdy
   - pip
   - pip:
-    - "-e .[dev]"
+    - "-e .[dev]"

in/filaments/filament-system.txt

@@ -0,0 +1,209 @@
+##################################################
+### Important notes:
+### 1. Units in MEDYAN are nm, second, pN, and pN*nm
+##################################################
+
+##################################################
+### PART I: Basic simulation parameters
+### Carefully check this section before running
+##################################################
+
+### 1. Set network sizes and shape
+# Set the number of compartments in x, y and z directions
+# Network size = compartment size (500nm by default) * (NX, NY, NZ)
+
+NX:                          2
+NY:                          2
+NZ:                          4
+
+# Define network boundary geometry (CUBIC, SPHERICAL, CYLINDER)
+
+BOUNDARYSHAPE:               CUBIC
+
+# Set diameter for SPHERICAL or CYLINDER type
+# CUBIC: No need to set, boundary is the same as network size
+
+BOUNDARYDIAMETER:	     
+
+### 2. Set total running time 
+
+RUNTIME:                     1.0
+
+### 3. Output simulation results every SNAPSHOTTIME
+
+SNAPSHOTTIME:                1.0
+
+### 4. Set chemistry input file name
+
+CHEMISTRYFILE:               chemistryinput.txt
+
+### 5. Initialize filaments
+# Option 1: Random generation
+# Set the number of filament and 
+# filament length (in number of cylinders)
+# FILAMENTTYPE: use 0 if only one type of filaments
+
+NUMFILAMENTS:                0
+FILAMENTLENGTH:              1
+FILAMENTTYPE:                0
+
+# Option 2: Initialize by setting input filament file
+
+FILAMENTFILE:                filaments.txt
+
+
+####################################################
+### PART II: Force field information
+### Based on: actin filament, non-muscle myosin II,
+### 	      alpha-actinin, Arp2/3
+### Changes not recommended unless using a different
+### species or have a different parameter source
+####################################################
+
+### 1. Minimize system energy every MINIMIZATIONTIME
+# Use a lower value if: 1. simulation fails or generates warnings
+#                       2. has very fast chemical reactions
+# Recommend value: 0.001 - 0.05
+# Please use the same value for NEIGHBORLISTTIME
+
+MINIMIZATIONTIME:             0.05
+NEIGHBORLISTTIME:             0.05
+
+### 2. Actin filaments 
+
+# Stretching: Popov et al, 2016, PLoS Comp Biol
+
+FSTRETCHINGFFTYPE:            HARMONIC
+FSTRETCHINGK:                 100.0
+
+# Bending: Ott et al, 1993, Phys Rev E
+
+FBENDINGFFTYPE:               COSINE
+FBENDINGK:                    672.0
+FBENDINGTHETA:                0.0
+
+# Volume exclusion: Popov et al, 2016, PLoS Comp Biol
+
+VOLUMEFFTYPE:                 REPULSION
+VOLUMECUTOFF:                 27.0
+VOLUMEK:                      1E5
+
+# Dynamic rate model - Brownian Ratchet: 
+# Footer et al, PNAS, 2007
+
+DFPOLYMERIZATIONTYPE: 	      BROWRATCHET
+DFPOLYMERIZATIONLEN:          2.7
+
+### 3. Non-muscle myosin IIA motor
+
+# Stretching: Vilfan, Biophys J, 2010  
+
+MSTRETCHINGFFTYPE:            HARMONIC
+MSTRETCHINGK:                 2.5
+
+# Number of heads: 
+
+NUMMOTORHEADSMIN:             15 
+NUMMOTORHEADSMAX:             30 
+
+# Step size: 
+
+MOTORSTEPSIZE:                6.0
+
+# Dynamic rate - motor catch-bond:
+# Erdmann et al, JCP, 2013
+
+DMUNBINDINGTYPE:              LOWDUTYCATCH 
+DMUNBINDINGFORCE:             12.62
+
+# Dynamic rate - motor walking
+# Komianos & Papoian, PRX, 2018
+# Tunable parameters based on different studies
+# recommended values 24pN - 100 pN
+
+DMWALKINGTYPE:                LOWDUTYSTALL
+DMWALKINGFORCE:               90.0
+
+### 4. Alpha-actinin crosslinker
+
+# Stretching: Didonna et al, Phys Rev E, 2007
+
+LSTRETCHINGFFTYPE:            HARMONIC
+LSTRETCHINGK:                 8.0
+
+# Dynamic rate - linker slip-bond:
+# Ferrer et al, PNAS, 2008
+
+DLUNBINDINGTYPE:              SLIP
+DLUNBINDINGLEN:               0.24
+
+### 4. Arp2/3 brancher
+# 4 force fields: Popov et al, Plos Comp Biol, 2016
+# No reliable literature values for this FF
+
+BRSTRETCHINGFFTYPE:           HARMONIC
+BRSTRETCHINGK:                100.0
+BRSTRETCHINGL:                6.0
+
+BRBENDINGFFTYPE:              COSINE
+BRBENDINGK:                   10.0
+BRBENDINGTHETA:               1.22
+
+BRDIHEDRALFFTYPE:             COSINE
+BRDIHEDRALK:                  10.0
+
+BRPOSITIONFFTYPE:             COSINE
+BRPOSITIONK:                  20.0 
+
+### 5. Boundary 
+# Repulsion: Popov et al, 2016, PLoS Comp Biol
+
+BOUNDARYFFTYPE:               REPULSIONEXP
+BOUNDARYCUTOFF:               300.0
+BOUNDARYINTERACTIONK:         41.0
+BOUNDARYSCREENLENGTH:         2.7
+
+##################################################
+### PART III: Advanced settings
+### Changes not recommended 
+##################################################
+
+### 1. Cylinder setup
+
+MONOMERSIZE:                   2.7
+CYLINDERSIZE:                  108.0
+
+### 2. Algorithm 
+# Minimization
+
+CONJUGATEGRADIENT:             POLAKRIBIERE
+GRADIENTTOLERANCE:             5.0
+MAXDISTANCE:                   1.0
+LAMBDAMAX:                     0.01
+
+# Chemistry
+
+CALGORITHM:                    NRM
+
+### 3. Number of binding site per 108nm cylinder
+
+NUMBINDINGSITES:               4
+
+### 4. The number of filament type
+# I.e. actin filament, microtubule, intermediate filament
+
+NUMFILAMENTTYPES:              1
+
+### 5. The compartment size
+# Based on Kuramoto length, see Popov et al., PLoS Comp Biol, 2016 
+# Some chemical reaction rates are scaled based on compartment size
+
+COMPARTMENTSIZEX:              500.0
+COMPARTMENTSIZEY:              500.0
+COMPARTMENTSIZEZ:              500.0
+
+### 6. Others: DO NOT CHANGE
+
+NDIM:                          3
+PROJECTIONTYPE:                STRAIGHT
+SAMEFILBINDINGSKIP:            100

in/filaments/filaments.txt

@@ -0,0 +1 @@
+FILAMENT A -70 0 0 10 0 0

vivarium_models/processes/medyan.py

@@ -1,8 +1,10 @@
 import os
+import numpy as np
 
+from vivarium.core.engine import pf
 from vivarium.core.process import Process
 from vivarium.core.composition import (
-    # simulate_process,
+    simulate_process,
     PROCESS_OUT_DIR,
 )
 from vivarium.plots.simulation_output import plot_simulation_output
@@ -39,6 +41,7 @@ class MedyanProcess(Process):
         "system_template": "filament-system.txt",
         "system_file": "filament-system.txt",
         "filament_file": "filaments.txt",
+        "medyan_executable": "medyan",
     }
 
     def __init__(self, parameters=None):
@@ -63,17 +66,18 @@ def ports_schema(self):
         }
 
     def initial_state(self, config):
-        initial_state = {
-            unique_id: {"type_name": "", "points": points}
-            for unique_id, points in config.get("points", {}).items()
+        initial_filaments = {
+            unique_id: {"type_name": "A", "points": points}
+            for unique_id, points in config.get("filaments", {}).items()
         }
-        return initial_state
+        return {
+            'filaments': initial_filaments}
 
     def next_update(self, timestep, state):
         initial_filaments = state["filaments"]
 
         filament_lines = [
-            filament_to_string(filament["type"], filament["points"])
+            filament_to_string(filament["type_name"], filament["points"])
             for filament in initial_filaments.values()
         ]
 
@@ -87,7 +91,9 @@ def next_update(self, timestep, state):
 
         system_template = self.parameters["system_template"]
         template = env.get_template(system_template)
-        system_text = template.render(filament_file=filament_path)
+        system_text = template.render(
+            filament_file=self.parameters['filament_file'],
+            timestep=timestep)
 
         system_path = input_directory / self.parameters["system_file"]
         with open(system_path, "w") as system_file:
@@ -96,13 +102,15 @@ def next_update(self, timestep, state):
         medyan_command = [
             self.parameters["medyan_executable"],
             "-s",
-            system_file,
+            system_file.name,
             "-i",
-            input_directory,
+            str(input_directory),
             "-o",
             self.parameters["output_directory"],
         ]
 
+        import ipdb; ipdb.set_trace()
+
         medyan_process = subprocess.Popen(medyan_command, stdout=subprocess.PIPE)
         output, error = medyan_process.communicate()
 
@@ -114,7 +122,19 @@ def main():
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)
 
-    output = MedyanProcess.next_update()
+    medyan = MedyanProcess({
+        'medyan_executable': '/home/youdonotexist/Downloads/medyan-4.2.0/build/medyan'})
+    initial_state = {
+        'filaments': {
+            '1': {
+                'type_name': 'A',
+                'points': [
+                    np.array([-70, 0, 0]),
+                    np.array([10, 0, 0])]}}}
+
+    output = simulate_process(medyan, {
+        'initial_state': initial_state,
+        'total_time': 10})
 
     # plot the simulation output
     plot_settings = {}

vivarium_models/templates/filament-system.txt

@@ -27,11 +27,11 @@ BOUNDARYDIAMETER:
 
 ### 2. Set total running time 
 
-RUNTIME:                     100.0
+RUNTIME:                     {{timestep}}
 
 ### 3. Output simulation results every SNAPSHOTTIME
 
-SNAPSHOTTIME:                1.0
+SNAPSHOTTIME:                {{timestep}}
 
 ### 4. Set chemistry input file name