Anisotropic particle

Gay-Berne model

Uniaxial GB interaction

class GBForce(all_info, nlist, r_cut)

The constructor of a method of Gay-Berne force.

Parameters:
  • all_info (AllInfo) – The system information.
  • nlist (NeighborList) – The neighbor list.
  • r_cut (float) – The cut-off radius.
setParams(string type1, string type2, float epsilon0, float sigma0, float nu, float mu, float sigma_e, float sigma_s, float epsilon_e, float epsilon_s, float Ps)

specifies the GB force parameters with type1, type2, epsilon0, sigma0, nu, mu, end-to-end length (sigma_e), side-by-side length (sigma_s), end-to-end energy (epsilon_e), side-by-side energy (epsilon_s), Ps.

Example:

gb = galamost.GBForce(all_info, neighbor_list, 10.0)
gb.setParams('A', 'A' , 1.5, 1.5, 1.0, 2.0,3.0, 1.0, 0.5, 3.0, 1.0)
# sets parameters: type1, type2, epsilon0, sigma0, nu, mu, sigma_e,
# sigma_s, epsilon_e, epsilon_s, Ps.
app.add(gb)

Bond force of uniaxial GB particles

class BondForceAni(all_info)

The constructor of a method of bond force calculation of anisotropic particles.

Parameters:all_info (AllInfo) – The system information.
setParams(string bondtype, float Kbond, float rbond, float Kangle, float dangle)

specifies the bond force parameters with bond type, bond spring constant, end-to-end length of GB particle, angle spring constant, equilibrium angle degree.

Example:

bondani = galamost.BondForceAni(all_info)
bondani.setParams('A-A', 100.0 , 4.498, 30.0, 0.0)
app.add(bondani)

Biaxial GB interaction

class PBGBForce(all_info, nlist)

The constructor of a method of Gay-Berne force.

Parameters:
setGUM(float gamma, float nu, float mu)

specifies the GB force parameters with gamma, nu, mu.

setParams(string type1, string type2, float epsilon, float sigma, float r_cut)

specifies the GB force parameters with type1, type2, epsilon, sigma, cutoff radius.

setAspheres(string filename)

specifies the file for shape parameters.

setPatches(string filename)

specifies the file for Patch parameters.

Example:

pbgb = galamost.PBGBForce(all_info, neighbor_list)
pbgb.setGUM(1.0, 3.0, 1.0);#(gamma, niu, miu)
pbgb.setParams('B', 'B' , 1.0, 1.0, 5.0)#(,,epsilon, sigma, rcut)
pbgb.setParams('A', 'A' , 1.0, 1.0, 5.0)#(,,epsilon, sigma, rcut)
pbgb.setParams('A', 'B' , 2.0, 1.0, 5.0)#(,,epsilon, sigma, rcut)
pbgb.setAspheres('patch.log')#(,a,b,c,eia_one,eib_one,eic_one)
pbgb.setPatches('patch.log')
app.add(pbgb)

File ‘patch.log’:

<Patches>
B 2                             #particle type, patch number
p1 60  0         0   1          #patch type, beta(degree) which is half of the opening angle-
p1 60  0         0   -1         #of the attractive patch, patch position(x, y, z) in unit vector
</Patches>
<PatchParams>
p1 p1 88.0 0.5                  #patch type, patch type, alpha_A, and gamma_epsilon
</PatchParams>
<Aspheres>
A 1.0 1.0 1.0 3.0 3.0 3.0       #a,b,c,eia_one,eib_one,eic_one
B 1.0 1.0 3.0 1.0 1.0 0.2       #a,b,c,eia_one,eib_one,eic_one
</Aspheres>

Soft anisotropic model

Janus particle model

class LzwForce(all_info, nlist, r_cut)

The constructor of a method of LZW force calculation.

Parameters:
  • all_info (AllInfo) – The system information.
  • nlist (NeighborList) – The neighbor list.
  • r_cut (float) – The cut-off radius.
setParams(string type1, string type2, float alphaR, float mu, float nu, float alphaA, float beta)

specifies the LZW force parameters with type1, type2, alphaR, mu, nu, alphaA, and beta.

setMethod(string method)

chooses a method of ‘Disk’, ‘Janus’, ABAtriJanus’, ‘BABtriJanus’.

Example:

lzw = galamost.LzwForce(all_info, neighbor_list, 1.0)
lzw.setParams('A', 'A' , 396.0, 1.0, 0.5, 88.0,60.0/180.0*3.1415926)
lzw.setMethod('ABAtriJanus')
# sets method with the choice of ABAtriJanus.
app.add(lzw)

Thermostat for Janus particle model

class BerendsenAniNvt(AllInfo all_info, ParticleSet group, ComputeInfo comp_info, float T, float tauT, float tauR)

The constructor of a Berendsen NVT thermostat for anisotropic particles.

Parameters:
  • all_info (AllInfo) – The system information.
  • group (ParticleSet) – The group of particles.
  • comp_info (ComputeInfo) – The object of calculation of collective information.
  • nlist (NeighborList) – The neighbor list.
  • r_cut (float) – The cut-off radius.
setTau(float tauT, float tauR)

specifies the Berendsen NVT thermostat with tauT and tauR.

setT(float T)

specifies the temperature with a constant value.

setT(Variant vT)

specifies the temperature with a varying value by time step.

Example:

bere = galamost.BerendsenAniNvt(all_info, group, comp_info, 1.0, 0.3, 0.1)
app.add(bere)

Multiple patch particle model

Description:

\begin{eqnarray*} U_{ij}=\left\{ \begin{array}{ll} \frac{\alpha_{ij}^R d_{ij}}{\mu}\left(1-\frac{r_{ij}}{d_{ij}}\right)^\mu- \sum\limits_{\kappa=1}^{M_i}\sum\limits_{\lambda=1}^{M_j} f^\nu \left(\mathbf{n}_{i}^{\kappa}, \mathbf{n}_j^{\lambda}, \mathbf{r}_{ij}\right) \frac{\alpha_{ij}^A d_{ij}}{\mu}\left[\frac{r_{ij}}{d_{ij}}-\left(\frac{r_{ij}}{d_{ij}}\right)^\mu\right] & r_{ij}\leq d_{ij} \\ 0 & r_{ij}> d_{ij}, \end{array} \right. \end{eqnarray*} \begin{eqnarray*} f\left(\mathbf{n}_{i}^{\kappa}, \mathbf{n}_j^{\lambda}, \mathbf{r}_{ij}\right) = \left\{ \begin{array}{ll} \cos\frac{\pi\theta_i^{\kappa}}{2\theta_{m}^{\kappa}}\cos\frac{\pi\theta_j^{\lambda}}{2\theta_{m}^{\lambda}} & \textrm{if $\cos\theta_i^{\kappa}\geq \cos\theta_{m}^{\kappa}$ and $\cos\theta_j^{\lambda} \geq \cos\theta_{m}^{\lambda}$}\\ 0 & \textrm{otherwise}. \end{array} \right. \end{eqnarray*}

The following coefficients must be set per unique pair of particle types:

  • \(\alpha^R\) - alphaR, repulsive strength
  • \(\mu\) - mu, the power (unitless)
  • \(\alpha^A\) - alphaA, attractive strength
  • \(d\) - the diameter defaults to the r_cut (in distance units)
  • \(\nu\) - nu, the angular width of attraction (unitless)
class AniForce(all_info, nlist, r_cut)

The constructor of force calculation of multiple patch particle model.

Parameters:
  • all_info (AllInfo) – The system information.
  • nlist (NeighborList) – The neighbor list.
  • r_cut (float) – The cut-off radius.
setParams(string type1, string type2, float alphaR, float mu)

specifies the force parameters with type1, type2, alphaR, mu.

setPatches(string filename)

specifies the file for Patch parameters.

Example:

ani = galamost.AniForce(all_info, neighbor_list, 1.0)
ani.setParams('A', 'A' , 396.0, 2.0)#(,,alpha_R,mu)
ani.setParams('A', 'B' , 396.0, 2.0)#(,,alpha_R,mu)
ani.setParams('B', 'B' , 396.0, 2.0)#(,,alpha_R,mu)
ani.setPatches('patch-3.log')
app.add(ani)

File ‘patch-3.log’:

<Patches>
A 0                             #particle type, patch number
B 3                             #particle type, patch number
p1 45  0         0   1          #patch type, beta(degree) which is half of the opening angle-
p2 45  0.866025  0   -0.5       #of the attractive patch, patch position(x, y, z) in unit vector
p3 45 -0.866025  0   -0.5
</Patches>
<PatchParams>
p1 p1 220.0 0.5                 #patch type, patch type, alpha_A, and nu
p2 p2 220.0 0.5                 #patch type, patch type, alpha_A, and nu
p3 p3 220.0 0.5                 #patch type, patch type, alpha_A, and nu
p1 p2 220.0 0.5                 #patch type, patch type, alpha_A, and nu
p1 p3 220.0 0.5                 #patch type, patch type, alpha_A, and nu
p2 p3 220.0 0.5                 #patch type, patch type, alpha_A, and nu
</PatchParams>

Thermostat for multiple patch particle model

The motion of anisotropic particles with multiple patches are integrated by rigid body method with a body index in XML file. The solvent particles with a body index of -1 are integrated by normal methods.

Example:

bgroup = galamost.ParticleSet(all_info, 'body')
rigidnvt = galamost.NvtRigid(all_info, bgroup, 1.0, 0.2)
app.add(rigidnvt)

nbgroup = galamost.ParticleSet(all_info,'non_body')
comp_info_nb = galamost.ComputeInfo(all_info, nbgroup)
nh = galamost.NoseHooverNvt(all_info, nbgroup, comp_info_nb, 1.0, 1.0)#( ,temperature, tau)
app.add(nh)