progress on filament simulation

docs/Smoldyn/SmoldynManual.tex

@@ -3530,9 +3530,13 @@ \section{Statements about filaments}
 
 Start of filament type definition block. The filament type name may be given with $name$, or it may be given afterward with the \ttt{name} statement. If the name has not been used yet for a filament type, then a new filament type is started. Between this instruction and \ttt{end\_filament\_type}, all lines need to pertain to filament types. Parameters of one filament type can be listed in multiple blocks, or parameters for many filament types can be listed in one block.
 
+\item{\ttt{name} $name$}
+
+From within a filament type definition block, this switches to a new filament type and creates it if needed.
+
 \item{\ttt{dynamics} $dynamics$}
 
-Sets the dynamics for the filament type. Options are: ``RigidBeads'', ``RigidSegments'', ``Rouse'', ``Alberts'', ``Nedelec''. These are case-insensitive.
+Sets the dynamics for the filament type. Current options are: ``none'', ``Newton''. These are case-insensitive.
 
 \item{\ttt{biology} $biology$}
 
@@ -3570,17 +3574,13 @@ \section{Statements about filaments}
 
 Viscosity of the surrounding medium.
 
-\item{\ttt{bead\_radius} $value$}
-
-Radius of the beads in these filaments. Used for hydrodynamic calculations.
-
 \item{\ttt{standard\_length} $length$}
 
 Relaxed length of a filament segment. It can change through stretching or compression.
 
 \item{\ttt{standard\_angle} $yaw$ $pitch$ $roll$}
 
-Relaxed angles between adjacent filament segments. When facing toward the filament's front end, yaw represents left-right bending, pitch represents up-down bending, and roll represents rotation about the filament axis.
+Relaxed angles between adjacent filament segments. When facing toward the filament's front end, yaw represents left-right bending, pitch represents up-down bending, and roll represents rotation about the filament axis. For 2D simulations, only enter a single bending angle.
 
 \item{\ttt{force\_length} $value$}
 
@@ -3600,21 +3600,21 @@ \section{Statements about filaments}
 
 \begin{description}
 
-\item{\ttt{random\_filament} $name$ $type$ $segments$ $[x$ $y$ $z]$}
+\item{\ttt{random\_filament} $name$ $type$ $segments$ $[x$ $y$ $z$ $\theta$ $\phi$ $\chi]$ $thickness$}
 
-Create a new filament with random segments. It is named $name$, is of type $type$, has $segments$ number of segments, and, optionally, has its starting location at $(x,y,z)$.
+Create a new filament with random segments. It is named $name$, is of type $type$, has $segments$ number of segments, and, optionally, has its starting location at $(x,y,z)$ and initial yaw-pitch-roll angle $(\theta, \phi, \chi)$. It also has optional thickness $thickness.$.
 
-\item{\ttt{start\_filament} $name$}
+\item{\ttt{start\_filament} $type$ $name$}
 
-Start of filament definition block. The filament name may be given with $name$, or it may be given afterward with the \ttt{name} statement. If the name has not been used yet for a filament, then a new filament is started. Between this instruction and \ttt{end\_filament}, all lines need to pertain to filaments. Parameters of one filament can be listed in multiple blocks, or parameters for many filaments can be listed in one block.
+Start of filament definition block, for a filament of type $type$ and named $name$. If the name has not been used yet for a filament of this type, then a new filament is started. Between this instruction and \ttt{end\_filament}, all lines need to pertain to filaments. Parameters of one filament can be listed in multiple blocks, or parameters for many filaments can be listed in one block.
 
-\item{\ttt{* name} $name$}
+\item{\ttt{new\_filament} $type$ $name$}
 
-Name of the filament for editing. This statement is not required because the filament name can also be given with \ttt{start\_filament}. This statement gives the name of the current filament for editing, and creates a new filament if needed.
+Defines a new filament of type $type$ that is called $name$, but does not start a filament block. This statement is largely redundant with \ttt{start\_filament}.
 
-\item{\ttt{type} $type$}
+\item{\ttt{* name} $type$ $name$}
 
-Filament type, which should already be defined in a filament type block.
+Name of the filament for editing. This statement is not required because the filament name can also be given with \ttt{start\_filament}. This statement gives the name of the current filament for editing, and creates a new filament if needed.
 
 \item{\ttt{first\_segment} $x$ $y$ $z$ $length$ $angle_0$ $angle_1$ $angle_2$ $[thickness]$}
 

examples/S13_filaments/filament.txt

@@ -1,8 +1,8 @@
 # Filaments
 
-#graphics opengl
-random_seed 2
-graphics opengl_better
+graphics opengl
+#random_seed 2
+#graphics opengl_better
 
 dim 3
 boundaries x 0 100 r
@@ -13,15 +13,15 @@ species red
 
 difc red 3
 
-color red white
+color red red
 
 time_start 0
 time_stop 10000
 time_step 0.01
 
 frame_thickness 0
 
-mol 1 red u u u
+mol 2 red u u u
 
 
 start_filament_type black
@@ -32,18 +32,22 @@ kT 1
 #treadmill_rate 1
 standard_length 5
 standard_angle 0 0 0
-force_length 0
+force_length 1
 force_angle 100 0 0
 end_filament_type
 
 
-start_filament template
-type black
+start_filament black template
 random_segments 5  10 50 1  u u u
+#copy fil2
+#name black fil2
+#translate + 15 15 0
 end_filament
 
 
-#filament template copy fil2
+filament template copy fil2
+filament fil2 translate + 15 15 0
+
 
 /*
 filament template copy fil3

examples/S13_filaments/filament1.txt

@@ -26,14 +26,18 @@ color black
 thickness 2
 polygon edge
 kT 1
-#treadmill_rate 1
-standard_length 5
+treadmill_rate 2
+standard_length 2
 standard_angle 0 0 0
-force_length 0
-force_angle 100 0 0
+force_length 10
+force_angle 5 -1 -1
 end_filament_type
 
-random_filament fil1 tread 5 10 50 1  u u u
+random_filament fil1 tread 10  10 50 1  0 0 0
+random_filament fil2 tread 10  20 50 1  1 0 0
+random_filament fil3 tread 10  10 40 1  -1 0 0
+random_filament fil4 tread 10  30 50 1  2 0 0
+random_filament fil5 tread 10  30 30 1  -1 0 0
 
 
 start_surface bounds

source/Smoldyn/smoldyn.h

@@ -756,15 +756,6 @@ typedef struct latticesuperstruct
 
 /********************************* Filaments ********************************/
 
-enum FilamentDynamics
-{
-    FDnone,
-    FDrigidbeads,
-    FDrigidsegments,
-    FDrouse,
-    FDalberts,
-    FDnedelec
-};
 enum FilamentBiology
 {
     FBactin,
@@ -776,37 +767,38 @@ enum FilamentBiology
     FBnone
 };
 
-typedef struct beadstruct
+enum FilamentDynamics
 {
-    double xyz[3];    // bead coordinates
-    double xyzold[3]; // bead coordinates for prior time
-} * beadptr;
+    FDnone,
+    FDnewton
+};
 
 typedef struct segmentstruct
 {
-    double xyzfront[3]; // Coords. for segment front
-    double xyzback[3];  // Coords. for segment back
-    double len;         // segment length
-    double ypr[3];      // relative ypr angles
-    double dcm[9];      // relative dcm
-    double adcm[9];     // absolute segment orientation
-    double thk;         // thickness of segment
+    struct filamentstruct* fil;				// owning filament
+    int index;                        // self index along filament
+    double xyzfront[3]; 							// Coords. for segment front
+    double xyzback[3]; 								// Coords. for segment back
+    double len;         							// segment length
+    double thk;         							// thickness of segment
+    double ypr[3];      							// relative ypr angles
+    double dcm[9];      							// relative dcm
+    double adcm[9];     							// absolute segment orientation
 } * segmentptr;
 
 typedef struct filamentstruct
 {
-    struct filamenttypestruct* filtype; // filament type structure
-    char* filname;                      // filament name (reference, not owned)
-    int maxbs;                          // number of beads or segments allocated
-    int nbs;                            // number of beads or segments
-    int frontbs;                        // index of front bead or segment
-    beadptr* beads;                     // array of beads if any
+    struct filamenttypestruct* filtype; // owning filament type
+    char* filname;                      // filament name (ref, not owned)
+    int maxseg;                         // number of segments allocated
+    int nseg;                           // number of segments
+    int frontseg;                       // index of front segment
     segmentptr* segments;               // array of segments if any
-    struct filamentstruct* frontend;    // what front attaches to if anything
-    struct filamentstruct* backend;     // what back attaches to if anything
-    int maxbranch;                      // max number of branches off this filament
-    int nbranch;                        // number of branches off this filament
-    int* branchspots;                   // list of bead or segments where branches are
+    struct filamentstruct* frontend;    // what front attaches to
+    struct filamentstruct* backend;     // what back attaches to
+    int maxbranch;                      // max branches off this filament
+    int nbranch;                        // num branches off this filament
+    int* branchspots;                   // segments where branches are
     struct filamentstruct** branches;   // list of branching filaments
     int maxmonomer;                     // number of monomers allocated
     int nmonomer;                       // number of monomers
@@ -817,11 +809,10 @@ typedef struct filamentstruct
 typedef struct filamenttypestruct
 {
     struct filamentsuperstruct* filss; // filament superstructure
-    char* ftname;                      // filament type name (reference, not owned)
+    char* ftname;                      // fil type name (ref, not owned)
+    enum FilamentBiology biology;      // biological name for filaments
     enum FilamentDynamics dynamics;    // dynamics for the filament
-    int isbead;                        // 1 for bead model, 0 for segments
-    enum FilamentBiology biology;      // Biological name for filament type
-    double bundlevalue;                // number of microfilaments in bundle
+    double bundlevalue;                // microfilaments in bundle
     double color[4];                   // filament color
     double edgepts;                    // thickness of edge for drawing
     unsigned int edgestipple[2];       // edge stippling [factor, pattern]
@@ -831,16 +822,17 @@ typedef struct filamenttypestruct
     double stdypr[3];                  // minimum energy bend angle
     double klen;                       // force constant for length
     double kypr[3];                    // force constant for angle
-    double kT;                         // thermodynamic temperature, [0,inf)
+    double kT;                         // thermodynamic temp, [0,inf)
     double treadrate;                  // treadmilling rate constant
     double viscosity;                  // viscosity
-    double filradius;                  // bead or segment radius
-    int maxface;                       // number of filament faces allocated
+    double filradius;                  // segment radius
+    int maxface;                       // filament faces allocated
     int nface;                         // number of filament faces
     char** facename;                   // list of face names
-    double facetwist;                  // twisting rate of faces along filament
+    double facetwist;                  // twisting rate of faces
     int maxfil;                        // maximum number of filaments
     int nfil;                          // actual number of filaments
+    int autonamenum;                   // next number for autoname
     filamentptr* fillist;              // list of filaments
     char** filnames;                   // names of filaments
 } * filamenttypeptr;
@@ -855,44 +847,6 @@ typedef struct filamentsuperstruct
     filamenttypeptr* filtypes; // list of filament types
 } * filamentssptr;
 
-/* OLD FILAMENTS
-typedef struct filamentstruct
-{
-    struct filamentsuperstruct* filss; // filament superstructure
-    char* fname;                       // filament name
-    double color[4];                   // filament color
-    double edgepts;                    // thickness of edge for drawing
-    unsigned int edgestipple[2];       // edge stippling [factor, pattern]
-    enum DrawMode drawmode;            // polygon drawing mode
-    double shiny;                      // shininess
-    int maxseg;                        // number of segments allocated
-    int nseg;                          // number of segments
-    int front;                         // front index
-    int back;                          // back index
-    double** sxyz;                     // Coords. for segment ends [seg][3]
-    double* slen;                      // segment length [seg]
-    double** sypr;                     // relative ypr angles [seg][3]
-    double** sdcm;                     // relative dcm [seg][9]
-    double** sadcm;                    // absolute segment orientation [seg][9]
-    double* sthk;                      // thickness of segment [nmax], [0,inf)
-    double stdlen;                     // minimum energy segment length
-    double stdypr[3];                  // minimum energy bend angle
-    double klen;                       // force constant for length
-    double kypr[3];                    // force constant for angle
-    double kT;                         // thermodynamic temperature, [0,inf)
-    double treadrate;                  // treadmilling rate constant
-} * filamentptr;
-
-typedef struct filamentsuperstruct
-{
-    enum StructCond condition; // structure condition
-    struct simstruct* sim;     // simulation structure
-    int maxfil;                // maximum number of filaments
-    int nfil;                  // actual number of filaments
-    char** fnames;             // filament names
-    filamentptr* fillist;      // list of filaments
-} * filamentssptr;
-*/
 
 /******************************** BioNetGen *********************************/
 

source/Smoldyn/smoldynfuncs.h

@@ -410,17 +410,17 @@ void filssoutput(simptr sim);
 int filcheckparams(simptr sim,int *warnptr);
 
 // filament manipulation
-int filAddRandomSegments(filamentptr fil,int number,const char *xstr,const char *ystr,const char *zstr,const char *thtstr,const char *phistr,const char *chistr,double thickness);
-int filAddRandomBeads(filamentptr fil,int number,const char *xstr,const char *ystr,const char *zstr);
+int filGetFilIndex(simptr sim,const char *name,int *ftptr);
+filamentptr filAddFilament(filamenttypeptr filtype,const char *filname);
+int filAddRandomSegments(filamentptr fil,int number,const char *xstr,const char *ystr,const char *zstr,const char *thtstr, const char* phistr,const char* chistr,double thickness);
 
 // structure set up
 int filenablefilaments(simptr sim);
-filamentptr filAddFilament(filamenttypeptr filtype,filamentptr fil,const char *filname);
 filamenttypeptr filtypereadstring(simptr sim,ParseFilePtr pfp,filamenttypeptr filtype,const char *word,char *line2);
 filamentptr filreadstring(simptr sim,ParseFilePtr pfp,filamentptr fil,filamenttypeptr filtype,const char *word,char *line2);
 int filloadtype(simptr sim,ParseFilePtr *pfpptr,char *line2);
-int filloadfil(simptr sim,ParseFilePtr *pfpptr,char *line2,filamenttypeptr filtype);
-int filsupdate(simptr sim);
+int filloadfil(simptr sim,ParseFilePtr *pfpptr,char *line2);
+int filupdate(simptr sim);
 
 // core simulation functions
 int filDynamics(simptr sim);