Skip to content
Permalink
Browse files

Spell check and grammar check (from 4.0.2)

  • Loading branch information...
jngrad committed Apr 25, 2019
1 parent a160d3e commit 97bb66715cdd8c9e01b56979013a2d602823ece9
@@ -449,7 +449,7 @@ The short ranged part is given by:

.. math :: p^\text{Coulomb, P3M, dir}_{(k,l)}= \frac{1}{4\pi \epsilon_0 \epsilon_r} \frac{1}{2V} \sum_{\vec{n}}^* \sum_{i,j=1}^N q_i q_j \left( \frac{ \mathrm{erfc}(\beta |\vec{r}_j-\vec{r}_i+\vec{n}|)}{|\vec{r}_j-\vec{r}_i+\vec{n}|^3} +\frac{2\beta \pi^{-1/2} \exp(-(\beta |\vec{r}_j-\vec{r}_i+\vec{n}|)^2)}{|\vec{r}_j-\vec{r}_i+\vec{n}|^2} \right) (\vec{r}_j-\vec{r}_i+\vec{n})_k (\vec{r}_j-\vec{r}_i+\vec{n})_l,
where :math:`\beta` is the P3M splitting parameter, :math:`\vec{n}` identifies the periodic images, the asterix denotes that terms with :math:`\vec{n}=\vec{0}` and i=j are omitted.
where :math:`\beta` is the P3M splitting parameter, :math:`\vec{n}` identifies the periodic images, the asterisk denotes that terms with :math:`\vec{n}=\vec{0}` and i=j are omitted.
The long ranged (k-space) part is given by:

.. math :: p^\text{Coulomb, P3M, rec}_{(k,l)}= \frac{1}{4\pi \epsilon_0 \epsilon_r} \frac{1}{2 \pi V^2} \sum_{\vec{k} \neq \vec{0}} \frac{\exp(-\pi^2 \vec{k}^2/\beta^2)}{\vec{k}^2} |S(\vec{k})|^2 \cdot (\delta_{k,l}-2\frac{1+\pi^2\vec{k}^2/\beta^2}{\vec{k}^2} \vec{k}_k \vec{k}_l),
@@ -474,10 +474,10 @@ To use the, e.g., ``ewald`` solver from SCAFACOS as electrostatics solver for y
cutoff to :math:`1.5` and tune the other parameters for an accuracy of
:math:`10^{-3}`, use::

from espressomd.electrostatics import Scafacos
scafacos = Scafacos(prefactor=1, method_name="ewald",
method_params={"ewald_r_cut": 1.5, "tolerance_field": 1e-3})
system.actors.add(scafacos)
from espressomd.electrostatics import Scafacos
scafacos = Scafacos(prefactor=1, method_name="ewald",
method_params={"ewald_r_cut": 1.5, "tolerance_field": 1e-3})
system.actors.add(scafacos)


For details of the various methods and their parameters please refer to
@@ -44,7 +44,7 @@
For the determination of the induced charges only the forces
acting on the induced charges has to be determined. As P3M and the
other Coulomb solvers calculate all mutual forces, the force
other coulomb solvers calculate all mutual forces, the force
calculation was modified to avoid the calculation of the short
range part of the source-source force calculation. For different
particle data organisation schemes this is performed differently.
@@ -124,7 +124,7 @@ typedef struct {
int s_ur[6][3];
/** sizes for send buffers. */
int s_size[6];
/** dimensionof sub meshes to recv. */
/** dimension of sub meshes to recv. */
int r_dim[6][3];
/** left down corners of sub meshes to recv. */
int r_ld[6][3];
@@ -658,7 +658,7 @@ void assign_forces(const CUDA_particle_data *const pdata, const P3MGpuData p,
_cuda_check_errors(block, grid, "assign_forces", __FILE__, __LINE__);
}

/* Init the internal datastructures of the P3M GPU.
/* Init the internal data structures of the P3M GPU.
* Mainly allocation on the device and influence function calculation.
* Be advised: this needs mesh^3*5*sizeof(REAL_TYPE) of device memory.
* We use real to complex FFTs, so the size of the reciprocal mesh
@@ -117,7 +117,7 @@ inline void add_affinity_pair_force(Particle *p1, Particle *p2,
ia_params
->affinity_r0) { // Bond does not exist, we are inside
// of possible bond creation area,
// lets talk about creating a bond
// let's talk about creating a bond
// This implementation creates bond always
for (j = 0; j < 3; j++)
p1->p.bond_site[j] = unfolded_pos[j] - d[j];
@@ -231,7 +231,7 @@ inline void add_affinity_pair_force(Particle *p1, Particle *p2,
ia_params
->affinity_r0) { // Bond does not exist, we are inside
// of possible bond creation area,
// lets talk about creating a bond
// let's talk about creating a bond
double Pon = 1.0 - exp(-ia_params->affinity_Kon * time_step);
// The probability is given by function Pon(x)= 1 - e^(-x) where x is
// Kon*dt.
@@ -326,7 +326,7 @@ inline void add_affinity_pair_force(Particle *p1, Particle *p2,
ia_params
->affinity_r0) { // Bond does not exist, we are inside
// of possible bond creation area,
// lets talk about creating a bond
// let's talk about creating a bond
double Pon = 1.0 - exp(-ia_params->affinity_Kon * time_step);
// The probability is given by function Pon(x)= 1 - e^(-x) where x is
// Kon*dt.
@@ -440,7 +440,7 @@ inline void add_affinity_pair_force(Particle *p1, Particle *p2,
ia_params
->affinity_r0) { // Bond does not exist, we are inside
// of possible bond creation area,
// lets talk about creating a bond
// let's talk about creating a bond
double Pon = 1.0 - exp(-ia_params->affinity_Kon * time_step);
// The probability is given by function Pon(x)= 1 - e^(-x) where x is
// Kon*dt.
@@ -564,7 +564,7 @@ inline void add_affinity_pair_force(Particle *p1, Particle *p2,
ia_params
->affinity_r0) { // Bond does not exist, we are inside
// of possible bond creation area,
// lets talk about creating a bond
// let's talk about creating a bond
double Pon = 1.0 - exp(-ia_params->affinity_Kon * time_step);
// The probability is given by function Pon(x)= 1 - e^(-x) where x is
// Kon*dt.
@@ -688,7 +688,7 @@ inline void add_affinity_pair_force(Particle *p1, Particle *p2,
ia_params
->affinity_r0) { // Bond does not exist, we are inside
// of possible bond creation area,
// lets talk about creating a bond
// let's talk about creating a bond
double Pon = 1.0 - exp(-ia_params->affinity_Kon * time_step);
// The probability is given by function Pon(x)= 1 - e^(-x) where x is
// Kon*dt.
@@ -243,7 +243,7 @@ cdef class ReactionAlgorithm(object):
if(self._params["check_for_electroneutrality"]):
charges = np.array(list(self._params["default_charges"].values()))
if(np.count_nonzero(charges) == 0):
# all partices have zero charge
# all particles have zero charge
# no need to check electroneutrality
return
total_charge_change = 0.0

0 comments on commit 97bb667

Please sign in to comment.
You can’t perform that action at this time.