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/* Ergo, version 3.8.2, a program for linear scaling electronic structure
* calculations.
* Copyright (C) 2023 Elias Rudberg, Emanuel H. Rubensson, Pawel Salek,
* and Anastasia Kruchinina.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*
* Primary academic reference:
* Ergo: An open-source program for linear-scaling electronic structure
* calculations,
* Elias Rudberg, Emanuel H. Rubensson, Pawel Salek, and Anastasia
* Kruchinina,
* SoftwareX 7, 107 (2018),
* <http://dx.doi.org/10.1016/j.softx.2018.03.005>
*
* For further information about Ergo, see <http://www.ergoscf.org>.
*/
/** @file box_system.cc
@brief BoxSystem class representing a hierarchical data structure
of boxes in 3D space (an oct-tree).
The idea is that you have a list of items at different points in space,
and you want a hierarchical system of boxes containing those items.
You give a list of items, and the function create_box_system will
create a system of boxes for you.
@author: Elias Rudberg <em>responsible</em>
*/
#include <cmath>
#include <stdlib.h>
#include <vector>
#include "box_system.h"
#include "output.h"
#include "memorymanag.h"
#include "utilities.h"
#include "mat_gblas.h"
BoxSystem::BoxSystem()
{
boxList = NULL;
}
BoxSystem::~BoxSystem()
{
if(boxList)
delete [] boxList;
}
/** Creates the box system.
@param itemList list of items to create the box structure for.
@param noOfItems their number.
@param toplevelBoxSize
*/
int
BoxSystem::create_box_system(box_item_struct* itemList,
int noOfItems,
ergo_real toplevelBoxSize)
{
// Allocate resultBoxList with just one item to begin with,
// It will be expanded later as needed.
int maxNoOfBoxes = 1;
boxList = new box_struct_basic[maxNoOfBoxes];
// create "mother box" containing all distrs.
int currBoxIndex = 0;
if(currBoxIndex >= maxNoOfBoxes)
{
do_output(LOG_CAT_ERROR, LOG_AREA_INTEGRALS, "error in create_box_system: (currBoxIndex >= maxNoOfBoxes)");
return -1;
}
box_struct_basic* motherBox = &boxList[currBoxIndex];
currBoxIndex++;
// first get dimensions of box
const ergo_real HUGE_NUMBER = 888888888;
ergo_real xminList[3];
ergo_real xmaxList[3];
ergo_real xdiffList[3];
for(int kk = 0; kk < 3; kk++)
{
xminList[kk] = HUGE_NUMBER;
xmaxList[kk] = -HUGE_NUMBER;
}
for(int i = 0; i < noOfItems; i++)
{
for(int kk = 0; kk < 3; kk++)
{
ergo_real x = itemList[i].centerCoords[kk];
if(x < xminList[kk])
xminList[kk] = x;
if(x > xmaxList[kk])
xmaxList[kk] = x;
}
} // END FOR i
int bestCoordIndex = 0;
for(int kk = 0; kk < 3; kk++)
{
xdiffList[kk] = xmaxList[kk] - xminList[kk];
if(xdiffList[kk] > xdiffList[bestCoordIndex])
bestCoordIndex = kk;
}
for(int kk = 0; kk < 3; kk++) {
if(xdiffList[kk] < 0) {
do_output(LOG_CAT_ERROR, LOG_AREA_INTEGRALS, "error in create_box_system: (xdiffList[kk] < 0).");
do_output(LOG_CAT_ERROR, LOG_AREA_INTEGRALS, "error in create_box_system: kk = %d, xdiffList[kk] = %9.4g < 0.\n", kk, xdiffList[kk]);
return -1;
}
}
ergo_real largestDiff = xdiffList[bestCoordIndex];
// compute number of levels and size of mother box
int numberOfLevels = 1;
ergo_real width = toplevelBoxSize;
while(width < largestDiff)
{
width *= 2;
numberOfLevels++;
}
if(numberOfLevels >= MAX_NO_OF_BOX_LEVELS)
{
do_output(LOG_CAT_ERROR, LOG_AREA_INTEGRALS, "error in create_box_system: (numberOfLevels >= MAX_NO_OF_BOX_LEVELS)");
do_output(LOG_CAT_ERROR, LOG_AREA_INTEGRALS, "error in create_box_system: numberOfLevels = %d, MAX_NO_OF_BOX_LEVELS = %d.", numberOfLevels, (int)MAX_NO_OF_BOX_LEVELS);
do_output(LOG_CAT_ERROR, LOG_AREA_INTEGRALS, "error in create_box_system: toplevelBoxSize = %7.3g, largestDiff = %7.3g.", (double)toplevelBoxSize, (double)largestDiff);
return -1;
}
motherBox->width = width;
// Set center of mother box.
for(int kk = 0; kk < 3; kk++)
motherBox->centerCoords[kk] = xminList[kk] + motherBox->width / 2;
motherBox->firstItemIndex = 0;
motherBox->noOfItems = noOfItems;
// OK, mother box done.
// Now create boxes on other levels, one level at a time.
this->levelList[0].noOfBoxes = 1;
this->levelList[0].startIndexInBoxList = 0;
int* itemIndexBucketList[2][2][2];
for(int ix = 0; ix < 2; ix++)
for(int iy = 0; iy < 2; iy++)
for(int iz = 0; iz < 2; iz++)
itemIndexBucketList[ix][iy][iz] = new int[noOfItems];
int itemCounterList[2][2][2];
// Allocate temporary itemList for use when reordering items.
std::vector<box_item_struct> itemListTemp(noOfItems);
for(int levelNumber = 1; levelNumber < numberOfLevels; levelNumber++)
{
levelList[levelNumber].startIndexInBoxList = currBoxIndex;
int currLevelNoOfBoxes_1 = 0;
// go through boxes of previous level, and create new boxes at this level if needed.
// We go through boxes of previous level twice, the first time to check how many
// new boxes must be allocated.
int startIndex = levelList[levelNumber-1].startIndexInBoxList;
for(int i = startIndex; i < startIndex + levelList[levelNumber-1].noOfBoxes; i++)
{
// now resultBoxList[i] is the box whose children we are creating.
boxList[i].firstChildBoxIndex = currBoxIndex;
int noOfChildren = 0;
if(boxList[i].noOfItems == 0)
{
do_output(LOG_CAT_ERROR, LOG_AREA_INTEGRALS, "ERROR: (boxList[i].noOfItems == 0)");
return -1;
}
// create 2*2*2 = 8 new boxes
for(int ix = 0; ix < 2; ix++)
for(int iy = 0; iy < 2; iy++)
for(int iz = 0; iz < 2; iz++)
{
itemCounterList[ix][iy][iz] = 0;
} // END FOR ix iy iz
// now go through the points of the parent box to decide which of the 8 children each point belongs to.
for(int j = boxList[i].firstItemIndex; j < boxList[i].firstItemIndex + boxList[i].noOfItems; j++)
{
int ix = 0;
int iy = 0;
int iz = 0;
if(itemList[j].centerCoords[0] > boxList[i].centerCoords[0])
ix = 1;
if(itemList[j].centerCoords[1] > boxList[i].centerCoords[1])
iy = 1;
if(itemList[j].centerCoords[2] > boxList[i].centerCoords[2])
iz = 1;
itemCounterList[ix][iy][iz]++;
} // END FOR j
// OK, all items counted, counters updated to indicate how many items
// belong to each of the 8 candidate child boxes.
// Now count new boxes.
for(int ix = 0; ix < 2; ix++)
for(int iy = 0; iy < 2; iy++)
for(int iz = 0; iz < 2; iz++)
{
if(itemCounterList[ix][iy][iz] > 0)
{
currLevelNoOfBoxes_1++;
noOfChildren++;
} // END IF (itemCounterList[ix][iy][iz] > 0)
} // END FOR ix iy iz
} // END FOR i
// OK, now we know how many new boxes are needed.
int maxNoOfBoxesNew = maxNoOfBoxes + currLevelNoOfBoxes_1;
box_struct_basic* boxListNew = new box_struct_basic[maxNoOfBoxesNew];
// copy previous contents of resultBoxList
memcpy(boxListNew, boxList, maxNoOfBoxes*sizeof(box_struct_basic));
// free old list, and set pointer to new list instead.
delete [] boxList;
boxList = boxListNew;
maxNoOfBoxes = maxNoOfBoxesNew;
// Now go through level again, this time creating new boxes and reordering items.
int currLevelNoOfBoxes_2 = 0;
for(int i = startIndex; i < startIndex + levelList[levelNumber-1].noOfBoxes; i++)
{
// now resultBoxList[i] is the box whose children we are creating.
boxList[i].firstChildBoxIndex = currBoxIndex;
int noOfChildren = 0;
if(boxList[i].noOfItems == 0)
{
do_output(LOG_CAT_ERROR, LOG_AREA_INTEGRALS, "ERROR: (resultBoxList[i].noOfItems == 0)");
return -1;
}
// create 2*2*2 = 8 new boxes
box_struct_basic tempBoxList[2][2][2];
for(int ix = 0; ix < 2; ix++)
for(int iy = 0; iy < 2; iy++)
for(int iz = 0; iz < 2; iz++)
{
ergo_real newWidth = boxList[i].width / 2;
ergo_real x = boxList[i].centerCoords[0] + (ix*2-1)*0.5*newWidth;
ergo_real y = boxList[i].centerCoords[1] + (iy*2-1)*0.5*newWidth;
ergo_real z = boxList[i].centerCoords[2] + (iz*2-1)*0.5*newWidth;
tempBoxList[ix][iy][iz].centerCoords[0] = x;
tempBoxList[ix][iy][iz].centerCoords[1] = y;
tempBoxList[ix][iy][iz].centerCoords[2] = z;
tempBoxList[ix][iy][iz].width = newWidth;
itemCounterList[ix][iy][iz] = 0;
} // END FOR ix iy iz
// now go through the points of the parent box to decide which of the 8 children each point belongs to.
for(int j = boxList[i].firstItemIndex; j < boxList[i].firstItemIndex + boxList[i].noOfItems; j++)
{
int ix = 0;
int iy = 0;
int iz = 0;
if(itemList[j].centerCoords[0] > boxList[i].centerCoords[0])
ix = 1;
if(itemList[j].centerCoords[1] > boxList[i].centerCoords[1])
iy = 1;
if(itemList[j].centerCoords[2] > boxList[i].centerCoords[2])
iz = 1;
itemIndexBucketList[ix][iy][iz][itemCounterList[ix][iy][iz]] = j;
itemCounterList[ix][iy][iz]++;
} // END FOR j
// OK, all items copied to itemBucketList.
// Now add new boxes, and order the items accordingly.
int currStartIndex = boxList[i].firstItemIndex;
for(int ix = 0; ix < 2; ix++)
for(int iy = 0; iy < 2; iy++)
for(int iz = 0; iz < 2; iz++)
{
if(itemCounterList[ix][iy][iz] > 0)
{
if(currBoxIndex >= maxNoOfBoxes)
{
do_output(LOG_CAT_ERROR, LOG_AREA_INTEGRALS, "error in create_box_system: (currBoxIndex >= maxNoOfBoxes)");
return -1;
}
boxList[currBoxIndex] = tempBoxList[ix][iy][iz];
boxList[currBoxIndex].firstItemIndex = currStartIndex;
boxList[currBoxIndex].noOfItems = itemCounterList[ix][iy][iz];
for(int k = 0; k < itemCounterList[ix][iy][iz]; k++)
itemListTemp[currStartIndex+k] = itemList[itemIndexBucketList[ix][iy][iz][k]];
currStartIndex += itemCounterList[ix][iy][iz];
currBoxIndex++;
currLevelNoOfBoxes_2++;
noOfChildren++;
} // END IF (itemCounterList[ix][iy][iz] > 0)
} // END FOR ix iy iz
boxList[i].noOfChildBoxes = noOfChildren;
} // END FOR i
if(currLevelNoOfBoxes_2 != currLevelNoOfBoxes_1)
{
do_output(LOG_CAT_ERROR, LOG_AREA_INTEGRALS, "error in create_box_system: (currLevelNoOfBoxes_2 != currLevelNoOfBoxes_1)");
return -1;
}
levelList[levelNumber].noOfBoxes = currLevelNoOfBoxes_2;
memcpy(itemList, &itemListTemp[0], noOfItems*sizeof(box_item_struct));
} // END FOR levelNumber
// OK, boxes created.
totNoOfBoxes = currBoxIndex;
noOfLevels = numberOfLevels;
for(int ix = 0; ix < 2; ix++)
for(int iy = 0; iy < 2; iy++)
for(int iz = 0; iz < 2; iz++)
delete [] itemIndexBucketList[ix][iy][iz];
do_output(LOG_CAT_INFO, LOG_AREA_INTEGRALS,
"create_box_system end OK, toplevelBoxSize: %5.1f, #levels: %2i, #boxes at top level: %6i",
(double)toplevelBoxSize, numberOfLevels, levelList[noOfLevels-1].noOfBoxes);
return 0;
}
ergo_real
get_min_distance_from_point_to_box(const ergo_real* boxCenterCoords,
ergo_real halfwidth,
const ergo_real* point)
{
ergo_real dxList[3];
for(int k = 0; k < 3; k++)
{
ergo_real dx = template_blas_fabs(boxCenterCoords[k] - point[k]);
if(dx > halfwidth)
dxList[k] = dx - halfwidth;
else
dxList[k] = 0;
}
ergo_real sum = 0;
for(int k = 0; k < 3; k++)
sum += dxList[k] * dxList[k];
return template_blas_sqrt(sum);
}
int BoxSystem::get_items_near_point_recursive(const box_item_struct* itemList,
const ergo_real* coords,
ergo_real distance,
int* resultOrgIndexList,
int level,
int boxIndex) const
{
const box_struct_basic* box = &boxList[boxIndex];
// Check if this entire box is so far away that it can be skipped.
ergo_real min_distance_from_point_to_box = get_min_distance_from_point_to_box(box->centerCoords, box->width/2, coords);
if(min_distance_from_point_to_box > distance)
return 0;
// No, we could not skip. Take care of box contents.
if(level == noOfLevels-1)
{
// We are at top level.
// Go through all points in box and add the relevant ones to result list.
int count = 0;
for(int i = 0; i < box->noOfItems; i++)
{
const box_item_struct* currItem = &itemList[box->firstItemIndex+i];
ergo_real sum = 0;
for(int coordNo = 0; coordNo < 3; coordNo++)
{
ergo_real d = coords[coordNo] - currItem->centerCoords[coordNo];
sum += d*d;
}
ergo_real currDist = template_blas_sqrt(sum);
if(currDist < distance)
{
// Add to result.
resultOrgIndexList[count] = currItem->originalIndex;
count++;
}
} // END FOR i
return count;
}
// Not top level. Go to next level.
int count = 0;
for(int i = 0; i < box->noOfChildBoxes; i++)
{
int childBoxIndex = box->firstChildBoxIndex + i;
int nNew = get_items_near_point_recursive(itemList,
coords,
distance,
&resultOrgIndexList[count],
level+1,
childBoxIndex);
count += nNew;
}
return count;
}
static int
compare_ints(const void* p1, const void* p2)
{
int i1 = *((int*)p1);
int i2 = *((int*)p2);
if(i1 > i2)
return 1;
if(i1 < i2)
return -1;
return 0;
}
/** Goes through existning box system to find all items within
specified distance from given reference point.
@param itemList the list of items for which the box system was created.
@param coords list of 3 coordinates for reference point.
@param distance the distance to find items within.
@param resultOrgIndexList preallocated list of resulting org indexes.
*/
int BoxSystem::get_items_near_point(const box_item_struct* itemList,
const ergo_real* coords,
ergo_real distance,
int* resultOrgIndexList) const
{
if(!boxList)
{
do_output(LOG_CAT_ERROR, LOG_AREA_INTEGRALS, "error in BoxSystem::get_items_near_point: (!boxList). Must create box system first!");
return -1;
}
int noOfItems = get_items_near_point_recursive(itemList, coords, distance, resultOrgIndexList, 0, levelList[0].startIndexInBoxList);
// sort resultOrgIndexList
qsort(resultOrgIndexList, noOfItems, sizeof(int), compare_ints);
return noOfItems;
}
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