Changed 'dipole' to 'voxel' in most of the code comments, help and error messages.

Standard output and command line options are kept intact for now.

Author: myurkin

misc/near_field/README.md

@@ -1,3 +1,3 @@
-The NearField program allows to compute the near-field on an arbitrary (i.e. not related to the grid used for the dipole) set of points, using dipoles stored by ADDA.
+The NearField program allows to compute the near-field on an arbitrary (i.e. not related to the voxel grid used for the simulations) set of points, using polarizations stored by ADDA.
 
 Compilation and usage are described in [nearfield_manual.txt](nearfield_manual.txt). 64-bit Windows executables are available in the corresponding [ADDA package](https://github.com/adda-team/adda/releases).

misc/pip/README.md

@@ -10,10 +10,10 @@ pip [<grid> [<filename>]]
 ```
 
 Executable is named `pip`, it accepts up tp two command line parameters: 
-- `<grid>` - maximum shape size (number of dipoles) along the largest dimension that is determined automatically. If omitted, the default value of 80 is used (and further arguments cannot be used).
+- `<grid>` - maximum shape size (number of voxels) along the largest dimension that is determined automatically. If omitted, the default value of 80 is used (and further arguments cannot be used).
 - `<filename>`. Input shape is read from `<filename>.obj` and DDSCAT7 shape is saved into `<filename>.dat`. If omitted, PIP will use the default filename `shape` (read `shape.obj` and save `shape.dat`). If `<filename>` includes extension, then it will be used for input file (instead of `.obj`).
 
-It should be possible to read other 3D formats, which are supported by routines in `ivread_wr.f90` - see comments in the source files. However, only `.obj` format is sufficiently tested. Also limited testing has been performed for `.dxf`, `.stl`, and `.wrl` formats. Multiple materials in input files (at least, for `.obj` and `.wrl` formats) are transformed into multiple domains in the output file. Should work for very large number of dipoles (limited only by memory and computational time).
+It should be possible to read other 3D formats, which are supported by routines in `ivread_wr.f90` - see comments in the source files. However, only `.obj` format is sufficiently tested. Also limited testing has been performed for `.dxf`, `.stl`, and `.wrl` formats. Multiple materials in input files (at least, for `.obj` and `.wrl` formats) are transformed into multiple domains in the output file. Should work for very large number of voxels (limited only by memory and computational time).
 
 Existing limitations:
 * For poorly tested input formats, it is potentially possible that the materials will not be properly recognized, leading to too much materials and errors in voxelization. Then there is a backup option to produce single-domain output file. For that change the value of `logical, parameter :: ignore_mat` in `FEM-Geo-Wr.f90` to `.true.`. 

src/ADDAmain.c

@@ -78,7 +78,7 @@ int main(int argc,char **argv)
 	ParseParameters(argc,argv);
 	D("Reading command line finished");
 	VariablesInterconnect(); // also initializes beam
-	// Initialize box's; get number of dipoles; set some variables
+	// Initialize box's; get number of voxels; set some variables
 	InitShape();
 	D("Initialization of shape finished");
 	FinalizeSymmetry(); // finalize symmetries and check for possible conflicts of symmetries with other options

src/CalculateE.c

@@ -627,7 +627,7 @@ static void CalcScatPlane(const enum incpol which,const enum Eftype type)
 static void StoreFields(const enum incpol which,doublecomplex * restrict cmplxF,
 	double * restrict realF,const char * restrict fname_preffix,const char * restrict tmpl UOIP,
 	const char * restrict field_name,const char * restrict fullname)
-/* Write any fields on each dipole to file (internal fields, incident beam, polarization, etc.). Accepts both complex
+/* Write any fields at each voxel to file (internal fields, incident beam, polarization, etc.). Accepts both complex
  * and real fields. Processes the one, which is not null.
  *
  * All processors should write the 'field' to temporary file. These files are named by template 'tmpl' and afterwards
@@ -706,11 +706,11 @@ static void ParticleToBeamRF(double vec[static restrict 3])
 //======================================================================================================================
 
 static void CalcIntegralScatQuantities(const enum incpol which)
-/* calculates all the scattering cross sections, normalized and unnormalized asymmetry parameter, and force on the'
- * particle and each dipole. Cext and Cabs are averaged over orientation, if needed.
+/* calculates all the scattering cross sections, normalized and unnormalized asymmetry parameter, and force on the
+ * particle and each voxel. Cext and Cabs are averaged over orientation, if needed.
  */
 {
-	// Scattering force, extinction force and radiation pressure per dipole
+	// Scattering force, extinction force and radiation pressure per voxel
 	double * restrict Frp;
 	double Cext,Cabs,Csca,Cdec, // Cross sections
 	dummy[3],                // asymmetry parameter*Csca
@@ -841,7 +841,7 @@ static void CalcIntegralScatQuantities(const enum incpol which)
 //======================================================================================================================
 
 static void StoreIntFields(const enum incpol which)
-// Write actual internal fields (not exciting) on each dipole to file
+// Write actual internal fields (not exciting) at each voxel to file
 {
 	// calculate fields; e_field=P/(V*chi)=chi_inv*P; for anisotropic - by components
 	nMult_mat(xvec,pvec,chi_inv);
@@ -882,7 +882,7 @@ int CalculateE(const enum incpol which,const enum Eftype type)
 	if (scat_grid) CalcScatGrid(which);
 	// Calculate integral scattering quantities (cross sections, asymmetry parameter, electric forces)
 	if (calc_Cext || calc_Cabs || calc_Csca || calc_asym || calc_mat_force) CalcIntegralScatQuantities(which);
-	// saves internal fields and/or dipole polarizations to text file
+	// saves internal fields and/or dipole (voxel) polarizations to text file
 	if (store_int_field) StoreIntFields(which);
 	if (store_dip_pol) StoreFields(which,pvec,NULL,F_DIPPOL,F_DIPPOL_TMP,"P","Dipole polarizations");
 	return 0;

src/GenerateB.c

@@ -312,7 +312,7 @@ void InitBeam(void)
 
 void GenerateB (const enum incpol which,   // x - or y polarized incident light
                 doublecomplex *restrict b) // the b vector for the incident field
-// generates incident beam at every dipole
+// generates incident beam at every voxel center
 {
 	size_t i,j;
 	doublecomplex psi0,Q,Q2;
@@ -456,7 +456,7 @@ void GenerateB (const enum incpol which,   // x - or y polarized incident light
 			 * interaction it is expected to be singular, so we use an explicit formula for point dipole:
 			 * C0=(8pi/3)*k^4*|p0|^2. Thus we discard the choice of "-int ...", but still the used value should be
 			 * correct for most formulations, e.g. poi, fcd, fcd_st, igt_so. Moreover, it is also logical, since the
-			 * exciting dipole is really point one, in contrast to the dipoles composing the particle.
+			 * exciting dipole is really point one, in contrast to the voxels composing the particle.
 			 */
 			double temp=p0*WaveNum*WaveNum; // in principle, t1=1/k, but we keep a general formula
 			C0dipole=2*FOUR_PI_OVER_THREE*temp*temp;
@@ -651,8 +651,8 @@ void GenerateB (const enum incpol which,   // x - or y polarized incident light
 	/* TO ADD NEW BEAM
 	 * add a case above. Identifier ('B_...') should be defined inside 'enum beam' in const.h. This case should set
 	 * complex vector 'b', describing the incident field in the particle reference frame. It is set inside the cycle for
-	 * each dipole of the particle and is calculated using
-	 * 1) 'DipoleCoord' - array of dipole coordinates;
+	 * each voxel of the particle and is calculated using
+	 * 1) 'DipoleCoord' - array of dipole (voxel) coordinates;
 	 * 2) 'prop' - propagation direction of the incident field;
 	 * 3) 'ex' - direction of incident polarization;
 	 * 4) 'ey' - complementary unity vector of polarization (orthogonal to both 'prop' and 'ex');

src/calculator.c

@@ -72,7 +72,7 @@ doublecomplex * restrict Avecbuffer; // used to hold the result of matrix-vector
 doublecomplex * restrict vec1,* restrict vec2,* restrict vec3,* restrict vec4;
 // used in matvec.c
 #ifdef SPARSE
-doublecomplex * restrict arg_full; // vector to hold argvec for all dipoles
+doublecomplex * restrict arg_full; // vector to hold argvec for all voxels
 #endif
 
 // LOCAL VARIABLES
@@ -472,7 +472,7 @@ static void CoupleConstant(doublecomplex *mrel,const enum incpol which,doublecom
 				//see B.T. Draine 'Propagation of Electromagnetic Waves on a Rectangular Lattice of Polarizable Points'
 				// Eq number noted for some lines of code
 				res[i]=3*(mrel[0]*mrel[0]-1)/(mrel[0]*mrel[0]+2); // CM
-				// Eq.(55), corrected value CM for rectangular dipole
+				// Eq.(55), corrected value CM for rectangular voxel
 				res[i]=res[i]/(1+res[i]*draine_precalc_data_array[draine_precalc_data_index].R0[i]);
 				res[i]*=dipvol/FOUR_PI;
 				if (PolRelation==POL_CLDR) {
@@ -525,7 +525,7 @@ static void CoupleConstant(doublecomplex *mrel,const enum incpol which,doublecom
 					res[i]=polMplusRR(2*ONE_THIRD*kd2*(2+kd*INV_PI*log((PI-kd)/(PI+kd))),mrel[i]);
 					break;
 				case POL_IGT_SO: res[i]=polMplusRR(SO_B1*kd2,mrel[i]); break;
-				case POL_LAK: // M=(8pi/3)[(1-ika)exp(ika)-1], a - radius of volume-equivalent (to cubical dipole) sphere
+				case POL_LAK: // M=(8pi/3)[(1-ika)exp(ika)-1], a - radius of volume-equivalent (to a cube) sphere
 					ka=LAK_C*kd;
 					res[i]=polM(2*FOUR_PI_OVER_THREE*((1-I*ka)*imExp(ka)-1),mrel[i]);
 					break;

src/cmplx.h

@@ -107,8 +107,8 @@ static inline doublecomplex imExpM1(const double arg)
 /* exp(i*arg) - 1 (should be used for small argument to avoid precision loss
  * We employ special code only for small arguments, ignoring the case when arg is close to 2piN. The latter can,
  * in principle, be handled by preliminary range reduction as in imExpTable. We do not implement it here, because such
- * case is a "coincidence" - may happen for a single dipole (or a plane of dipoles), while the case of small arg may
- * happen for all dipoles. In the latter case loss of precision affects all computed quantities.
+ * case is a "coincidence" - may happen for a single voxel (or a plane of voxels), while the case of small arg may
+ * happen for all voxels. In the latter case loss of precision affects all computed quantities.
  * The used expression through tan(arg/2) follows from general expression for cexpm1 below.
  */
 {

src/comm.c

@@ -528,7 +528,7 @@ void ParSetup(void)
 	local_x1=gridX;
 #	endif
 	if (local_z1_coer<=local_z0) {
-		LogWarning(EC_INFO,ALL_POS,"No real dipoles are assigned");
+		LogWarning(EC_INFO,ALL_POS,"No real voxels are assigned");
 		local_z1_coer=local_z0;
 	}
 	local_Nz=local_z1-local_z0;
@@ -607,7 +607,7 @@ void ReadField(const char * restrict fname,doublecomplex *restrict field)
 		}
 		else if (i==nvoid_Ndip) { // tests that file doesn't contains extra data rows
 			if (sscanf(linebuf,test_form)!=EOF) LogError(ALL_POS,"Field file %s contains more data rows than number of "
-				"dipoles (%zu) in the particle",fname,nvoid_Ndip);
+				"voxels (%zu) in the particle",fname,nvoid_Ndip);
 		}
 		else { // here local_nvoid_d0 <= i < local_nvoid_d1
 			scanned=sscanf(linebuf,format,buf,buf+1,buf+2,buf+3,buf+4,buf+5);

src/const.h

@@ -177,7 +177,7 @@ enum sh { // shape types
 	SH_CYLINDER,      // cylinder
 	SH_EGG,           // egg
 	SH_ELLIPSOID,     // general ellipsoid
-	SH_LINE,          // line with width of one dipole
+	SH_LINE,          // line with width of one voxel
 	SH_ONION,         // multilayered concentric sphere
 	SH_ONION_ELL,     // multilayered concentric ellipsoid
 	SH_PLATE,         // plate
@@ -212,7 +212,7 @@ enum pol { // which way to calculate coupleconstant
 
 enum scat { // how to calculate scattering quantities
 	SQ_DRAINE, // classical, as Draine
-	SQ_FINDIP, /* Same as Draine, but with correction of radiation energy of a _finite_ dipole when calculating
+	SQ_FINDIP, /* Same as Draine, but with correction of radiation energy of a _finite_ dipole (voxel) when calculating
 	              absorption cross section */
 	SQ_IGT_SO  // Integration of Green's tensor (approximation of second order in kd)
 };
@@ -230,7 +230,7 @@ enum inter { // how to calculate interaction term
 	 * add an identifier starting with 'G_' and a descriptive comment to this list in the alphabetical order.
 	 */
 };
-enum refl { // how to calculate interaction of dipoles through the nearby surface (reflected G)
+enum refl { // how to calculate interaction of voxels through the nearby surface (reflected G)
 	GR_IMG,       // approximate expression based on a single image dipole
 	GR_SOM        // direct evaluation of Sommerfeld integrals
 	/* TO ADD NEW REFLECTION FORMULATION