work on excluded volume reactions

CMakeLists.txt

@@ -513,7 +513,7 @@ endif ()
 
 if (OPTION_PYTHON)
     # Find python before using pybind11. There is a possibility of version mismatch later.
-    find_package(Python3 COMPONENTS Interpreter Development REQUIRED)
+    find_package(Python3 3.10 EXACT COMPONENTS Interpreter Development REQUIRED)
     set(PYBIND11_SOURCE_DIR ${CMAKE_SOURCE_DIR}/source/pybind11)
     add_subdirectory(${PYBIND11_SOURCE_DIR})
     add_subdirectory(${CMAKE_SOURCE_DIR}/source/python)

docs/Smoldyn/SmoldynCodeDoc.tex

@@ -7020,6 +7020,12 @@ \subsection*{Modifications for version 2.72 (released 8/17/23)}
 \item Merged an automated pull request that might fix dependabot alerts about out of date scipy.
 \item Removed \ttt{public std::unary\_function<type,type>} instances from tree\_iterator.hpp (part of NSV code) because this is deprecated.
 
+\subsection*{Modifications for version 2.73 (not released yet)}
+\item Investigated diffusion coefficients in crowded systems. I now believe that the overlap method is better than the reflection method. This is discussed in the reactions chapter of the Smoldyn manual. I changed the default behavior to overlap method.
+\item Added a line to the CMake file. In the Python module section, edited a line to read \ttt{find\_package(Python3 3.10 EXACT COMPONENTS Interpreter Development REQUIRED)}, where the new portion is the Python 3.10 requirement. This prevents an error of \ttt{invalid command 'bdist\_wheel'} because it now uses the same Python version for everything.
+\item Edited Smoldyn/source/pybind11/tests/requirements.txt to simplify the file and hopefully stop warnings from the gitHub dependabot.
+
+
 \end{itemize}
 
 

examples/S8_reactions/bounce/crowding3D.txt

@@ -0,0 +1,56 @@
+# Simple crowded system simulation
+# Values are roughly right for hemoglobin
+# Units are nm and us
+
+define SEED 1
+define NMOL 6112	# 40% volume occupancy
+define HGRADIUS 2.5
+#define BETTERGRAPHICS
+
+ifdefine BETTERGRAPHICS
+  graphics opengl_better
+  light room ambient 0 0 0
+  light 0 position -1 1 1 0
+  light 0 diffuse 0.5 0.5 0.5
+  light 0 ambient 0.5 0.5 0.5
+  light 0 specular 0.5 0.5 0.5
+else
+  graphics opengl
+  graphic_iter 1000
+endif
+
+text_display time
+
+#random_seed SEED
+
+dim 3
+boundaries x 0 100 p
+boundaries y 0 100 p
+boundaries z 0 100 p
+
+species Hg
+
+difc Hg 65
+
+color Hg lightred
+display_size Hg HGRADIUS
+
+time_start 0
+time_stop 20
+time_step 0.0001            # standard value is 0.0001
+
+frame_thickness 2
+
+mol NMOL Hg u u u
+
+reaction r1 Hg + Hg -> Hg + Hg
+binding_radius r1 2*HGRADIUS
+product_placement r1 bounce -1
+
+output_files crowding3Dout.txt crowding3Dmsdout.txt
+output_format csv
+cmd i 10 20 0.5 radialdistribution Hg Hg 20 100 20 crowding3Dout.txt
+cmd i 10 20 0.5 meansqrdisp Hg all crowding3Dmsdout.txt
+
+end_file
+

examples/S94_archive/Andrews_Arkin_2010/Bar29.txt

@@ -0,0 +1,159 @@
+# Bar1 Smoldyn simulation
+# by Steve Andrews, 11/30/09
+# Ref: Andrews, Addy, Brent, Arkin, "Detailed simulations of cell biology with Smoldyn 2.1", PLoS Comp. Biol. 2010
+# This file is Bar29.txt, from Bar28.txt
+# This is Bar1+, 1 target cell, no Bar1 adsorption
+# Units: microns and seconds
+
+define WITHBAR1
+
+# *** output file ***
+define	OUTFILE1	FILEROOTout.txt
+define	OUTFILE2	FILEROOTout2.txt
+
+# *** time ***
+define TIMEEND 4500
+
+# *** boundaries ***
+define	XLO	-12
+define	XHI	12
+define	YLO	-12
+define	YHI	12
+define	ZLO	-12
+define	ZHI	12
+
+# *** model parameters ***
+define	NGPCR	6622	# number of GPCR
+define	K1t	250	# target alpha production rate
+define	K1c	12.5	# challenger alpha production rate
+define	K4	100	# Bar1 production rate in um^-2/s
+define	K5	5.15	# Bar1-alpha reaction rate, diff. limit is 10.3 um^3/s
+define	K6	0.008303	# alpha binding to GPCR, *** 2x
+define	K7	0.02	# alpha unbinding from GPCR, *** 2x
+
+graphics opengl
+graphic_iter 10000
+frame_thickness 0
+accuracy 10
+
+dim 3
+species Bar1 alpha GPCR GPCRalpha
+max_mol 300000
+boxsize 0.5
+
+molecule_lists list3 list4 list1 list2 list5
+
+mol_list alpha(fsoln) list1
+mol_list alpha(up) list2
+mol_list GPCR(up) list3
+mol_list GPCRalpha(up) list4
+mol_list Bar1(fsoln) list5
+mol_list Bar1(up) list2
+
+difc Bar1(fsoln) 27
+difc alpha(fsoln) 132
+
+color Bar1(fsoln) 0 1 0
+color Bar1(front) 0 1 0
+color alpha(fsoln) 0 0 0
+color GPCR(up) 0 0 1
+color GPCRalpha(up) 1 0 0.2
+
+display_size alpha(fsoln) 1
+display_size alpha(up) 0
+display_size Bar1(all) 1
+display_size GPCR(up) 2
+display_size GPCRalpha(up) 2
+
+time_start 0
+time_stop TIMEEND
+time_step 0.02
+
+boundaries 0 XLO XHI
+boundaries 1 YLO YHI
+boundaries 2 ZLO ZHI
+
+max_surface 5
+
+start_surface sides
+polygon both none
+unbounded_emitter front Bar1 K4 0 0 0
+unbounded_emitter front alpha K1t 5.5 0 0
+unbounded_emitter front alpha K1c 2.75 4.7632 0
+unbounded_emitter front alpha K1c -2.75 4.7632 0
+unbounded_emitter front alpha K1c -5.5 0 0
+unbounded_emitter front alpha K1c -2.75 -4.7632 0
+unbounded_emitter front alpha K1c 2.75 -4.7632 0
+read_file ellipse_12_12.txt
+end_surface
+
+start_surface cell
+action both all reflect
+polygon both face
+color both 0.8 0.8 0.8
+max_panels sphere 1
+panel sphere 0 0 0 2.5 20 20
+end_surface
+
+start_surface alphatarget
+polygon both face
+color both 0.3 0.3 0.3
+max_panels sphere 6
+panel sphere 5.5	0	0 2.5 20 20
+end_surface
+
+start_surface alphachallenge
+polygon both face
+color both 0.5 0.5 0.5
+max_panels sphere 6
+panel sphere 2.75	4.7632	0 2.5 20 20
+panel sphere -2.75	4.7632	0 2.5 20 20
+panel sphere -5.5	0	0 2.5 20 20
+panel sphere -2.75	-4.7632	0 2.5 20 20
+panel sphere 2.75	-4.7632	0 2.5 20 20
+end_surface
+
+surface_mol NGPCR GPCR(up) cell all all
+
+reaction_surface alphatarget	rxn1t	0 -> alpha(fsoln)	K1t	# alpha production
+reaction_surface alphachallenge	rxn1c	0 -> alpha(fsoln)	K1c	# alpha production
+
+ifdefine WITHBAR1
+  reaction_surface cell		rxn4	0 -> Bar1(fsoln)	K4	# Bar1 production
+  reaction rxn5	Bar1(fsoln) + alpha(fsoln) -> Bar1(fsoln)	K5	# Bar1 protease on alpha
+endif
+
+reaction rxn6	GPCR(up) + alpha(fsoln) -> GPCRalpha(up)	K6	# GPCR-alpha binding
+reaction rxn7	GPCRalpha(up) -> GPCR(up) + alpha(fsoln)	K7	# GPCR-alpha unbinding
+product_placement rxn7 pgemmax 0.2
+
+cmd @ 0 set reaction_rate rxn1t 15.625
+cmd @ 500 set reaction_rate rxn1t 31.25
+cmd @ 1000 set reaction_rate rxn1t 62.5
+cmd @ 1500 set reaction_rate rxn1t 125
+cmd @ 2000 set reaction_rate rxn1t 250
+cmd @ 2500 set reaction_rate rxn1t 500
+cmd @ 3000 set reaction_rate rxn1t 1000
+cmd @ 3500 set reaction_rate rxn1t 2000
+cmd @ 4000 set reaction_rate rxn1t 4000
+
+cmd @ 0 set reaction_rate rxn1c 0.78125
+cmd @ 500 set reaction_rate rxn1c 1.5625
+cmd @ 1000 set reaction_rate rxn1c 3.125
+cmd @ 1500 set reaction_rate rxn1c 6.25
+cmd @ 2000 set reaction_rate rxn1c 12.5
+cmd @ 2500 set reaction_rate rxn1c 25
+cmd @ 3000 set reaction_rate rxn1c 50.0
+cmd @ 3500 set reaction_rate rxn1c 100.0
+cmd @ 4000 set reaction_rate rxn1c 200.0
+
+output_files stdout OUTFILE1 OUTFILE2
+
+cmd B molcountheader stdout
+cmd B molcountheader OUTFILE2
+cmd i 0 TIMEEND 2 molcount stdout
+cmd i 0 TIMEEND 2 molcount OUTFILE2
+cmd i 0 TIMEEND 2 molmoments GPCRalpha(up) OUTFILE1
+
+end_file
+

examples/S94_archive/Andrews_Arkin_2010/MoroneData.txt

@@ -0,0 +1,90 @@
+# Data from Morone et al., 2006.
+# Units are nm
+
+max_panels tri 100
+panel tri 1.639344262	413.9344262	65.57377049	449.1803279
+panel tri 1.639344262	413.9344262	21.31147541	368.852459
+panel tri 65.57377049	449.1803279	55.73770492	391.8032787
+panel tri 21.31147541	368.852459	55.73770492	391.8032787
+panel tri 0	359.8360656	21.31147541	368.852459
+panel tri 21.31147541	368.852459	39.3442623	301.6393443
+panel tri 39.3442623	301.6393443	-4.918032787	254.0983607
+panel tri -4.918032787	254.0983607	63.1147541	237.704918
+panel tri 21.31147541	224.5901639	-6.557377049	159.0163934
+panel tri -4.918032787	254.0983607	56.55737705	196.7213115
+panel tri -6.557377049	159.0163934	20.49180328	135.2459016
+panel tri -5.737704918	113.9344262	52.45901639	159.8360656
+panel tri -5.737704918	113.9344262	148.3606557	0
+panel tri -0.819672131	29.50819672	46.72131148	-0.819672131
+panel tri 46.72131148	-0.819672131	68.03278689	36.8852459
+panel tri 148.3606557	0	130.3278689	95.08196721
+panel tri 130.3278689	95.08196721	95.90163934	142.6229508
+panel tri 95.90163934	142.6229508	52.45901639	159.8360656
+panel tri 52.45901639	159.8360656	56.55737705	196.7213115
+panel tri 56.55737705	196.7213115	145.0819672	246.7213115
+panel tri 145.0819672	246.7213115	336.8852459	245.9016393
+panel tri 95.90163934	142.6229508	113.1147541	154.9180328
+panel tri 56.55737705	196.7213115	113.1147541	154.9180328
+panel tri 63.1147541	237.704918	210.6557377	341.8032787
+panel tri 168.0327869	317.2131148	131.147541	358.1967213
+panel tri 39.3442623	301.6393443	168.0327869	317.2131148
+panel tri 68.03278689	314.7540984	71.31147541	343.442623
+panel tri 55.73770492	391.8032787	111.4754098	349.1803279
+panel tri 111.4754098	349.1803279	114.7540984	315.5737705
+panel tri 86.8852459	259.0163934	75.40983607	295.0819672
+panel tri 119.6721311	391.8032787	195.9016393	430.3278689
+panel tri 195.9016393	430.3278689	231.9672131	431.147541
+panel tri 231.9672131	431.147541	253.2786885	394.2622951
+panel tri 253.2786885	394.2622951	210.6557377	341.8032787
+panel tri 111.4754098	349.1803279	210.6557377	341.8032787
+panel tri 210.6557377	341.8032787	283.6065574	250.8196721
+panel tri 143.442623	273.7704918	281.147541	352.4590164
+panel tri 181.147541	286.8852459	220.4918033	209.8360656
+panel tri 220.4918033	209.8360656	276.2295082	109.8360656
+panel tri 157.3770492	204.0983607	200.8196721	155.7377049
+panel tri 200.8196721	155.7377049	304.0983607	161.4754098
+panel tri 113.1147541	154.9180328	172.1311475	134.4262295
+panel tri 172.1311475	134.4262295	351.6393443	-1.639344262
+panel tri 130.3278689	95.08196721	185.2459016	71.31147541
+panel tri 185.2459016	71.31147541	332.7868852	82.78688525
+panel tri 197.5409836	50	207.3770492	74.59016393
+panel tri 185.2459016	71.31147541	199.1803279	36.8852459
+panel tri 199.1803279	36.8852459	273.7704918	-1.639344262
+panel tri 242.6229508	9.016393443	290.9836066	35.24590164
+panel tri 273.7704918	-1.639344262	442.6229508	16.39344262
+panel tri 172.1311475	134.4262295	229.5081967	129.5081967
+panel tri 200.8196721	155.7377049	185.2459016	71.31147541
+panel tri 229.5081967	129.5081967	252.4590164	161.4754098
+panel tri 68.03278689	36.8852459	148.3606557	0
+panel tri 139.3442623	34.42622951	211.4754098	-1.639344262
+panel tri 229.5081967	129.5081967	384.4262295	13.1147541
+panel tri 384.4262295	13.1147541	344.2622951	220.4918033
+panel tri 382.7868852	59.83606557	438.5245902	92.62295082
+panel tri 382.7868852	59.83606557	419.6721311	152.4590164
+panel tri 419.6721311	152.4590164	436.8852459	170.4918033
+panel tri 419.6721311	152.4590164	389.3442623	275.4098361
+panel tri 324.5901639	138.5245902	283.6065574	250.8196721
+panel tri 324.5901639	138.5245902	354.0983607	264.7540984
+panel tri 283.6065574	250.8196721	236.704918	181.9672131
+panel tri 283.6065574	250.8196721	313.9344262	277.8688525
+panel tri 313.9344262	277.8688525	327.0491803	311.4754098
+panel tri 327.0491803	311.4754098	305.7377049	345.9016393
+panel tri 281.147541	352.4590164	435.2459016	333.6065574
+panel tri 281.147541	352.4590164	253.2786885	350
+panel tri 253.2786885	394.2622951	286.0655738	405.7377049
+panel tri 264.7540984	436.8852459	388.5245902	331.147541
+panel tri 286.8852459	435.2459016	388.5245902	331.147541
+panel tri 354.0983607	264.7540984	388.5245902	331.147541
+panel tri 327.0491803	311.4754098	373.7704918	297.5409836
+panel tri 389.3442623	275.4098361	435.2459016	333.6065574
+panel tri 283.6065574	250.8196721	440.1639344	282.7868852
+panel tri 313.9344262	277.8688525	354.0983607	264.7540984
+panel tri 363.1147541	109.8360656	436.8852459	238.5245902
+panel tri 368.852459	350.8196721	436.8852459	401.6393443
+panel tri 311.4754098	440.1639344	437.704918	361.4754098
+panel tri 436.8852459	401.6393443	407.3770492	437.704918
+panel tri 350.8196721	416.3934426	407.3770492	437.704918
+panel tri 113.9344262	227.0491803	143.442623	273.7704918
+panel tri 181.147541	286.8852459	168.0327869	317.2131148
+
+end_file

examples/S94_archive/Andrews_Arkin_2010/benchmark.txt

@@ -0,0 +1,44 @@
+# Michaelis-Menten reaction
+# units: micron and second
+
+graphics none
+
+dim 3
+names E S ES P
+max_mol 11000
+molperbox 3
+accuracy 10
+
+difc E 10
+difc S 10
+difc ES 10
+difc P 10
+
+time_start 0
+time_stop 10
+time_step 0.001
+
+boundaries 0 0 4.4964 p
+boundaries 1 0 4.4964 p
+boundaries 2 0 4.4964 p
+
+molecule_lists Elist Slist ESlist Plist
+mol_list E Elist
+mol_list S Slist
+mol_list ES ESlist
+mol_list P Plist
+
+output_files benchmarkout.txt
+cmd i 0 100 0.01 molcount benchmarkout.txt
+
+# 10 E/vol and 100 S/vol
+mol 909 E u u u
+mol 9091 S u u u
+
+reaction fwd E + S -> ES 0.01
+reaction back ES -> E + S 1
+reaction prod ES -> E + P 1
+product_placement back pgemmax 0.2
+
+end_file
+