briling · briling · Mar 20, 2026 · Mar 19, 2026 · Mar 19, 2026 · Mar 19, 2026
diff --git a/.github/CHANGELOG.md b/.github/CHANGELOG.md
@@ -3,6 +3,7 @@
 ### New features
 
 * Add partial extended xyz support (https://github.com/briling/v/pull/18)
+* Read and print lattice parameters to/from extxyz header (#39)
 * Add `j` hotkey to jump to a frame inside and CLI option `frame:%d` to start with a specific frame (https://github.com/briling/v/pull/5)
 * Add `bmax` CLI argument for max. bond length (920202b)
 * Add `com` and `exitcom` CLI argument for `gui:0` and on-exit command sequences, respectively
@@ -17,6 +18,7 @@
 * Read molecules from the standard input (#28)
 * Show infrared intensities and mode masses (#35)
 * Improve the text-in-corner look (de242c7, #36)
+* Add `u` to the headless mode (#37)
 * Improve data structures and code readability
 
 ### Fixes
@@ -28,7 +30,6 @@
 * Fix text blinking when playing animation (80cae88, #36)
 
 ### Coming in the next version:
-* extended xyz (#16, #17)
 * high-symmetry determination bugs (#21)
 * how to build on mac (#34)
 

diff --git a/README.md b/README.md
@@ -45,13 +45,14 @@ To build:
 ```
 ./v file [file2 ... fileN] [options]
 ```
-A filename `-` stands for the standard input.
+A filename `-` stands for the standard input (xyz files only).
 
 Show the reference:
 ```
 ./v
 ```
 
+### Options
 <details open><summary><strong>Command-line options</strong></summary>
 
 |                          |                                                               |
@@ -81,6 +82,7 @@ Show the reference:
 
 </details>
 
+### Keyboard
 <details open><summary><strong>Keyboard reference</strong></summary>
 
 |                                |                                                           |
@@ -120,15 +122,17 @@ Show the reference:
 
 </details>
 
-<details open><summary><strong>Mouse (in development)</strong></summary>
+### Mouse
+
 One can also use the mouse to rotate the molecule and zoom in/out.
-</details>
 
-<details open><summary><strong>Headless mode (in development)</strong></summary>
+### Additional commands
 
-If run in the headless mode with `gui:0`, the symbols from the standard input are processed 
+#### Headless mode
+
+If run in the headless mode with `gui:0`, the symbols from the standard input are processed
 as if the corresponding keys were pressed in the normal mode.
-Right now, only `p`, `x`, `z`, and `.` are available.
+Right now, `p`, `x`, `z`, `u`, and `.` are available.
 Command-line option `com:%s` overrides the standard input.
 These examples are equivalent:
 ```
@@ -142,8 +146,60 @@ D*h
 D*h
 ```
 
+#### Normal mode
+In the normal mode, the symbols from the CLI option `exitcom:` are executed immediately before closing.
+For example,
+```
+./v mol/mol0001.xyz exitcom:z
+```
+automatically prints the last xyz coordinates when the user closes the window.
+
+
+
+
+### Boundary conditions
+Two types of boundary conditions are recognized:
+* PBC (3D)
+* spherical confinement
+
+#### PBC
+PBC can be read from the xyz [file header](https://ase-lib.org/ase/io/formatoptions.html#extxyz)
+by specifying `Lattice="ax ay az bx by bz cx cy cz"`:
+```
+./v mol/MOL_3525.ext.xyz
+```
+Currently, only the PBC in all three dimensions are supported.
+
+The same can be passed via the command-line, in which case it overrides the one from the file:
+```
+./v mol/MOL_3525.xyz cell:8.929542,0,0,4.197206,8.892922,0,0.480945,2.324788,10.016044
+```
+For orthogonal/cubic cell:
+```
+./v mol/1372_D02.340_1.out bonds:0 cell:20.23,20.23,20.23
+./v mol/1372_D02.340_1.out bonds:0 cell:20.23
+```
+In Bohr instead of Å:
+```
+./v mol/1372_D02.340_1.out bonds:0 cell:b10.7
+```
+Finally, to disable the cell from the file:
+```
+./v mol/MOL_3525.ext.xyz cell:0
+```
+
+#### Spherical confinement
+Spherical confinement can be specified from the command-line by the following:
+```
+./v mol/mol0001.xyz shell:2     #  sphere with r = 2 Å is put around the molecule
+./v mol/mol0001.xyz shell:b4    #  sphere with r = 2 Bohr
+./v mol/mol0001.xyz shell:2,3   #  spheres with r = 2 and 3 Å (e.g., soft and hard boundaries)
+./v mol/mol0001.xyz shell:b4,5  #  spheres with r = 4 and 5 Bohr
+```
+
 </details>
 
+
 ## Examples [↑](#contents)
 * `mol/C3H6~mCPBA_01x11.qm.out` — geometries + vibrations
 ```
@@ -166,7 +222,7 @@ D*h
 ![Adamantane mode animation](figures/C10H16.qm.out.gif)
 * `mol/1372_D02.340_1.out` — PBC simulation
 ```
-./v mol/1372_D02.340_1.out bonds:0 cell:b10.7,10.7,1.07 font:-*-*-medium-*-*--15-*-*-*-*-*-*-1
+./v mol/1372_D02.340_1.out bonds:0 cell:b10.7 font:-*-*-medium-*-*--15-*-*-*-*-*-*-1
 ```
 ![Atoms in cell with PBC](figures/1372_D02.340_1.out_1087.gif)
 * `mol/mol0001.xyz`, `mol/mol0002.xyz` — `.xyz` files with atomic numbers and atomic symbols
@@ -177,6 +233,9 @@ D*h
 
 * `mol/MOL_3525.xyz` — organic crystal with non-orthogonal cell
 ```
+./v mol/MOL_3525.ext.xyz
+```
+```
 ./v mol/MOL_3525.xyz cell:8.929542,0.0,0.0,4.197206,8.892922,0.0,0.480945,2.324788,10.016044 font:-*-*-medium-*-*--15-*-*-*-*-*-*-1
 ```
 ![Organic crystal cell](figures/MOL_3525.xyz_1.gif)

diff --git a/obj/v/ac3_print.d b/obj/v/ac3_print.d
@@ -1,2 +1,3 @@
 obj/v/ac3_print.o obj-pic/v/ac3_print.o: src/v/ac3_print.c src/v/v.h \
- src/mol/mol.h src/mol/common.h src/v/pars.h src/math/vec3.h
+ src/mol/mol.h src/mol/common.h src/v/pars.h src/math/matrix.h \
+ src/math/vecn.h src/math/vec3.h
diff --git a/obj/v/ac3_read.d b/obj/v/ac3_read.d
@@ -1,3 +1,3 @@
 obj/v/ac3_read.o obj-pic/v/ac3_read.o: src/v/ac3_read.c src/v/v.h \
  src/mol/mol.h src/mol/common.h src/v/pars.h src/math/vecn.h \
- src/math/vec3.h
+ src/math/vec3.h src/math/matrix.h src/math/vecn.h
diff --git a/obj/v/ac3_read_xyz.d b/obj/v/ac3_read_xyz.d
@@ -1,2 +1,2 @@
 obj/v/ac3_read_xyz.o obj-pic/v/ac3_read_xyz.o: src/v/ac3_read_xyz.c \
- src/v/v.h src/mol/mol.h src/mol/common.h src/v/pars.h
+ src/v/v.h src/mol/mol.h src/mol/common.h src/v/pars.h src/math/vecn.h
diff --git a/obj/v/cli.d b/obj/v/cli.d
@@ -1,3 +1,3 @@
 obj/v/cli.o obj-pic/v/cli.o: src/v/cli.c src/v/v.h src/mol/mol.h \
  src/mol/common.h src/v/pars.h src/math/vecn.h src/math/matrix.h \
- src/math/vecn.h src/math/vec3.h
+ src/math/vecn.h
diff --git a/src/v/ac3_draw.c b/src/v/ac3_draw.c
@@ -28,20 +28,20 @@ static int cmpz(const void * p1, const void * p2){
     return  0;
 }
 
-void ac3_draw(atcoord * ac, rendpars rend){
+void ac3_draw(atcoord * ac, rendpars * rend){
   int n = ac->n;
   kzstr * kz = malloc(sizeof(kzstr)*n);
-  int   * ks = (rend.bonds>0) ? malloc(sizeof(int)*n) : NULL;
+  int   * ks = (rend->bonds>0) ? malloc(sizeof(int)*n) : NULL;
 
   double resol = world.size * RESOL_SCALE;
-  double r1  = rend.r * resol * rend.scale;
+  double r1  = rend->r * resol * rend->scale;
 
   for(int k=0; k<n; k++){
     kz[k].k = k;
     kz[k].z = ac->r[k*3+2];
   }
   qsort(kz, n, sizeof(kzstr), cmpz);
-  if(rend.bonds>0){
+  if(rend->bonds>0){
     for(int i=0; i<n; i++){
       ks[ kz[i].k ] = i;
     }
@@ -61,19 +61,19 @@ void ac3_draw(atcoord * ac, rendpars rend){
       XDrawArc(world.dis, world.canv, q>0?world.gc_black:world.gc_dot[1], x-r, y-r, 2*r, 2*r, 0, 360*64);
     }
 
-    if(rend.num == 1){
+    if(rend->num == 1){
       char text[16];
       snprintf(text, sizeof(text), "%d", k+1);
       XDRAWSTRING(world.dis, world.canv, world.gc_black, x, y, text, strlen(text));
     }
-    else if(rend.num == -1){
+    else if(rend->num == -1){
       char text[16];
       const char * s = getname(q);
       s ? snprintf(text, sizeof(text), "%s", s) :  snprintf(text, sizeof(text), "%d", q );
       XDRAWSTRING(world.dis, world.canv, world.gc_black, x, y, text, strlen(text));
     }
 
-    if(rend.bonds>0){
+    if(rend->bonds>0){
       for(int j=k*BONDS_MAX; j<(k+1)*BONDS_MAX; j++){
         int k1 = ac->bonds.a[j];
         if(k1 == -1 ){
@@ -92,7 +92,7 @@ void ac3_draw(atcoord * ac, rendpars rend){
         }
         double dd = BOND_OFFSET * r / sqrt(r2d);
         XDrawLine(world.dis, world.canv, world.gc_black, x+dd*dx, y+dd*dy, x1, y1);
-        if(rend.bonds==2){
+        if(rend->bonds==2){
           char text[16];
           snprintf(text, sizeof(text), "%.3lf", ac->bonds.r[j]);
           XDRAWSTRING(world.dis, world.canv, world.gc_black, x+dx/2, y+dy/2, text, strlen(text));

diff --git a/src/v/ac3_print.c b/src/v/ac3_print.c
@@ -1,15 +1,16 @@
 #include "v.h"
+#include "matrix.h"
 #include "vec3.h"
 
-void ac3_print(atcoord * ac, rendpars rend){
+void ac3_print(atcoord * ac, rendpars * rend){
   PRINTOUT(stdout, "$molecule\ncart\n");
   for(int k=0; k<ac->n; k++){
     PRINTOUT(stdout, "%3d   % lf   % lf   % lf",
         ac->q[k],
-        rend.xy0[0] + ac->r[k*3  ],
-        rend.xy0[1] + ac->r[k*3+1],
+        rend->xy0[0] + ac->r[k*3  ],
+        rend->xy0[1] + ac->r[k*3+1],
                  ac->r[k*3+2]);
-    if(rend.bonds>0){
+    if(rend->bonds>0){
       for(int j=0; j<BONDS_MAX; j++){
         int k1 = ac->bonds.a[k*BONDS_MAX+j];
         if(k1 == -1 ){
@@ -24,8 +25,20 @@ void ac3_print(atcoord * ac, rendpars rend){
   return;
 }
 
-void ac3_print_xyz(atcoord * ac, rendpars rend){
-  PRINTOUT(stdout, "%d\n\n", ac->n);
+void ac3_print_xyz(atcoord * ac, rendpars * rend){
+  PRINTOUT(stdout, "%d\n", ac->n);
+  if(ac->cell.boundary==CELL){
+    double C[9];
+    mx_multmx(3,3,3, C, rend->ac3rmx, ac->cell.rot_to_lab_basis);
+    PRINTOUT(stdout, "Lattice=\"%lf %lf %lf %lf %lf %lf %lf %lf %lf\"\n",
+        C[0], C[3], C[6],
+        C[1], C[4], C[7],
+        C[2], C[5], C[8]);
+  }
+  else{
+    PRINTOUT(stdout, "\n");
+  }
+
   for(int k=0; k<ac->n; k++){
     const char * s = getname(ac->q[k]);
     int ok = s && s[0];
@@ -36,32 +49,32 @@ void ac3_print_xyz(atcoord * ac, rendpars rend){
       PRINTOUT(stdout, " %3d", ac->q[k]);
     }
     PRINTOUT(stdout, "   % lf   % lf   % lf\n",
-        rend.xy0[0] + ac->r[k*3  ],
-        rend.xy0[1] + ac->r[k*3+1],
-                 ac->r[k*3+2]);
+        rend->xy0[0] + ac->r[k*3  ],
+        rend->xy0[1] + ac->r[k*3+1],
+                       ac->r[k*3+2]);
   }
   return;
 }
 
-void ac3_print2fig(atcoord * ac, rendpars rend, double vert[9]){
+void ac3_print2fig(atcoord * ac, rendpars * rend){
   int n = ac->n;
   for(int i=0; i<n; i++){
     PRINTOUT(stdout, "atom %3d% 13.7lf% 13.7lf% 13.7lf\n", ac->q[i],
-        rend.xy0[0] + ac->r[i*3  ],
-        rend.xy0[1] + ac->r[i*3+1],
+        rend->xy0[0] + ac->r[i*3  ],
+        rend->xy0[1] + ac->r[i*3+1],
                  ac->r[i*3+2]);
   }
 
-  if(vert){
+  if(ac->cell.boundary==CELL){
     for(int i=0; i<8; i++){
       double v[3];
-      r3mx(v, vert+3*i, rend.ac3rmx);
+      r3mx(v, ac->cell.vertices+3*i, rend->ac3rmx);
       PRINTOUT(stdout, "atom %3d% 13.7lf% 13.7lf% 13.7lf\n", 0,
-          rend.xy0[0] + v[0], rend.xy0[1] + v[1], v[2]);
+          rend->xy0[0] + v[0], rend->xy0[1] + v[1], v[2]);
     }
   }
 
-  if(rend.bonds>0){
+  if(rend->bonds>0){
     for(int k=0; k<n; k++){
       for(int j=0; j<BONDS_MAX; j++){
         int k1 = ac->bonds.a[k*BONDS_MAX+j];
@@ -75,7 +88,7 @@ void ac3_print2fig(atcoord * ac, rendpars rend, double vert[9]){
     }
   }
 
-  if(vert){
+  if(ac->cell.boundary==CELL){
 #define LINE(I,J)   PRINTOUT(stdout, "bond %3d %3d % 3d\n", (J)+n+1, (I)+n+1, -1)
     for(int i=0; i<8; i+=2){
       LINE(i,i+1); // || z-axis