#============================================================*
#             test surface rigid simulation                  *
#============================================================*

# set units
#----------
units
units scale  name = mass   uname = reducedMass   value = 10000.0

# open pdb file
database open name =  head format = pdb file = head_em.pdb 

# read molecule
molecule read  database = head  name = m1  model = 1  type = protein
molecule m1 xform  translation = [ -5.4411 -8.07774 -33.7495 ] 

# create domains
#---------------
domain create head = C[2-700]
#domain head backbone  color = [ 0.7 0 0 ] width = 2 show
#domain head atoms color = [ 0.6 0.6 0.6 ] width = 2 show
domain head atoms color = element show


# read surfaces
#--------------
surface read  name = neck format = pm  file = neck_em_surf5.pm 
#surface read  name = neck format = pm  file = neck_em_surf.pm 
surface neck xform translation = [ -5.4411 -8.07774 -33.7495 ] 
#surface neck color = [ 0.6 0.6 0.6 ]  display = line  show 
#surface neck color = [ 1 0 0]  display = points show 
surface neck color = [ 0.6 0.6 0.6 ]  render = color show 

# create sphere
#--------------
solid create  name = sp1  type = sphere \
              radius = 2.0   \
              point = [ 0.180157 -3.34644 -32.3022 ] \
              axis = [ 0 0 -1 ]  \
              color = [ 0 0 1 ]  \
              display = solid    \
              show = true


# create bodies
#--------------
body create  name = ground    type = ground
body create  name = headBody  type = rigid   domain = head 
body create  name = neckBody  type = rigid   surface = neck 
body create  name = spBody    type = rigid   solid = sp1  


# create joints
#--------------
joint create  name = groundJnt  type = weld   position = [ 0 0 0 ]
joint groundJnt bodies = { ground headBody }
joint groundJnt color = [ 1 1 1 ] msize = 0.1 shading = color show = true

joint create  name = headNeckJnt  type = ball  domain = head  res = C[700]  use = CA
joint headNeckJnt bodies = { headBody neckBody }
joint headNeckJnt color = [ 1 1 0 ] msize = 0.1 shading = color show = true

joint create  name = neckSphereJnt  type = universal \
              position = [ 0.180157 -3.34644 -32.3] \
              axis1 = [ 0 1 0 ]  axis2 = [ 1 0 0 ] \
              force_const1 = 800.0  force_const2 = 800.0  
joint neckSphereJnt bodies = { neckBody spBody }
joint neckSphereJnt color = [ 0 1 0 ] msize = 0.1 shading = color show = true



# create a rigid simulation
#--------------------------
simulation create name = rsim  type = rigid

# add bodies
#-----------
simulation rsim add body = ground
simulation rsim add body = headBody
simulation rsim add body = neckBody 
simulation rsim add body = spBody 

# add joints
#-----------
simulation rsim add joint = groundJnt 
simulation rsim add joint = headNeckJnt
simulation rsim add joint = neckSphereJnt

# set solver
#-----------
simulation rsim solver = ode
simulation rsim solver finite_rotation = on

# add forces
#-----------
force create name = force1           \
             type = explicit         \
             point = [ 0 0 0 ]       \
             direction = [ 8000 0 0 ]  \
             scale = 0.002

simulation rsim add force = force1    \
                    body = spBody \
                    time = { 0 1000 }

# initialize simulation
#----------------------
simulation  rsim   initialize
simulation  rsim   momentum = off 
simulation  state  save_frequency = 10 

graphics  background  color = [ 1 1 1 ]