diff --git a/erpnext/controllers/buying_controller.py b/erpnext/controllers/buying_controller.py
index cf57658..fc912c9 100644
--- a/erpnext/controllers/buying_controller.py
+++ b/erpnext/controllers/buying_controller.py
@@ -269,7 +269,7 @@
 			# get raw materials rate
 			if self.doctype == "Purchase Receipt":
 				from erpnext.stock.utils import get_incoming_rate
-				item_rate = get_incoming_rate({
+				rm.rate = get_incoming_rate({
 					"item_code": bom_item.item_code,
 					"warehouse": self.supplier_warehouse,
 					"posting_date": self.posting_date,
@@ -277,10 +277,9 @@
 					"qty": -1 * required_qty,
 					"serial_no": rm.serial_no
 				})
-				if not item_rate:
-					from erpnext.controllers.stock_controller import get_valuation_rate
-					item_rate = get_valuation_rate(bom_item.item_code, self.supplier_warehouse)
-				rm.rate = item_rate or bom_item.rate
+				if not rm.rate:
+					from erpnext.stock.stock_ledger import get_valuation_rate
+					rm.rate = get_valuation_rate(bom_item.item_code, self.supplier_warehouse)
 			else:
 				rm.rate = bom_item.rate
 
diff --git a/erpnext/controllers/stock_controller.py b/erpnext/controllers/stock_controller.py
index a72a3d0..d7c7a43 100644
--- a/erpnext/controllers/stock_controller.py
+++ b/erpnext/controllers/stock_controller.py
@@ -49,17 +49,12 @@
 
 						self.check_expense_account(detail)
 
-						stock_value_difference = flt(sle.stock_value_difference, 2)
-						if not stock_value_difference:
-							valuation_rate = get_valuation_rate(sle.item_code, sle.warehouse)
-							stock_value_difference = flt(sle.actual_qty)*flt(valuation_rate)
-
 						gl_list.append(self.get_gl_dict({
 							"account": warehouse_account[sle.warehouse],
 							"against": detail.expense_account,
 							"cost_center": detail.cost_center,
 							"remarks": self.get("remarks") or "Accounting Entry for Stock",
-							"debit": stock_value_difference
+							"debit": flt(sle.stock_value_difference, 2)
 						}))
 
 						# to target warehouse / expense account
@@ -68,7 +63,7 @@
 							"against": warehouse_account[sle.warehouse],
 							"cost_center": detail.cost_center,
 							"remarks": self.get("remarks") or "Accounting Entry for Stock",
-							"credit": stock_value_difference
+							"credit": flt(sle.stock_value_difference, 2)
 						}))
 					elif sle.warehouse not in warehouse_with_no_account:
 						warehouse_with_no_account.append(sle.warehouse)
@@ -300,26 +295,3 @@
 	if cint(frappe.defaults.get_global_default("auto_accounting_for_stock")) and not allow_negative_stock:
 		if cint(frappe.db.get_value("Stock Settings", None, "allow_negative_stock")):
 			frappe.throw(_("Negative stock is not allowed in case of Perpetual Inventory, please disable it from Stock Settings"))
-
-def get_valuation_rate(item_code, warehouse):
-	last_valuation_rate = frappe.db.sql("""select valuation_rate
-		from `tabStock Ledger Entry`
-		where item_code = %s and warehouse = %s
-		and ifnull(valuation_rate, 0) > 0
-		order by posting_date desc, posting_time desc, name desc limit 1""", (item_code, warehouse))
-
-	if not last_valuation_rate:
-		last_valuation_rate = frappe.db.sql("""select valuation_rate
-			from `tabStock Ledger Entry`
-			where item_code = %s and ifnull(valuation_rate, 0) > 0
-			order by posting_date desc, posting_time desc, name desc limit 1""", item_code)
-
-	valuation_rate = flt(last_valuation_rate[0][0]) if last_valuation_rate else 0
-
-	if not valuation_rate:
-		valuation_rate = frappe.db.get_value("Item Price", {"item_code": item_code, "buying": 1}, "price_list_rate")
-
-	if not valuation_rate:
-		frappe.throw(_("Purchase rate for item: {0} not found, which is required to book accounting entry. Please mention item price against a buying price list.").format(item_code))
-
-	return valuation_rate
diff --git a/erpnext/stock/doctype/stock_settings/stock_settings.py b/erpnext/stock/doctype/stock_settings/stock_settings.py
index 95ace86..12ab0c9 100644
--- a/erpnext/stock/doctype/stock_settings/stock_settings.py
+++ b/erpnext/stock/doctype/stock_settings/stock_settings.py
@@ -12,9 +12,6 @@
 class StockSettings(Document):
 
 	def validate(self):
-		if cint(self.allow_negative_stock) and cint(frappe.defaults.get_global_default("auto_accounting_for_stock")):
-			frappe.throw(_("Negative stock is not allowed in case of Perpetual Inventory"))
-
 		for key in ["item_naming_by", "item_group", "stock_uom", "allow_negative_stock"]:
 			frappe.db.set_default(key, self.get(key, ""))
 
diff --git a/erpnext/stock/stock_ledger.py b/erpnext/stock/stock_ledger.py
index 7dc8d83..0fbf6a8 100644
--- a/erpnext/stock/stock_ledger.py
+++ b/erpnext/stock/stock_ledger.py
@@ -6,7 +6,6 @@
 from frappe import _
 from frappe.utils import cint, flt, cstr, now
 from erpnext.stock.utils import get_valuation_method
-from erpnext.controllers.stock_controller import get_valuation_rate
 import json
 
 # future reposting
@@ -266,7 +265,7 @@
 
 		if new_stock_qty:
 			valuation_rate = new_stock_value / flt(new_stock_qty)
-	elif not valuation_rate:
+	elif not valuation_rate and qty_after_transaction <= 0:
 		valuation_rate = get_valuation_rate(sle.item_code, sle.warehouse)
 
 	return abs(flt(valuation_rate))
@@ -275,9 +274,10 @@
 	incoming_rate = flt(sle.incoming_rate)
 	actual_qty = flt(sle.actual_qty)
 
-	intialize_stock_queue(stock_queue, sle.item_code, sle.warehouse, actual_qty)
-
 	if actual_qty > 0:
+		if not stock_queue:
+			stock_queue.append([0, 0])
+
 		if stock_queue[-1][0] > 0:
 			stock_queue.append([actual_qty, incoming_rate])
 		else:
@@ -289,12 +289,12 @@
 	else:
 		qty_to_pop = abs(actual_qty)
 		while qty_to_pop:
-			intialize_stock_queue(stock_queue, sle.item_code, sle.warehouse, actual_qty)
+			if not stock_queue:
+				stock_queue.append([0, get_valuation_rate(sle.item_code, sle.warehouse)
+					if qty_after_transaction <= 0 else 0])
 
 			batch = stock_queue[0]
 
-			# print qty_to_pop, batch
-
 			if qty_to_pop >= batch[0]:
 				# consume current batch
 				qty_to_pop = qty_to_pop - batch[0]
@@ -318,11 +318,6 @@
 
 	return abs(valuation_rate)
 
-def intialize_stock_queue(stock_queue, item_code, warehouse, actual_qty):
-	if not stock_queue:
-		estimated_val_rate = get_valuation_rate(item_code, warehouse) if actual_qty < 0 else 0
-		stock_queue.append([0, estimated_val_rate])
-
 def _raise_exceptions(args, verbose=1):
 	deficiency = min(e["diff"] for e in _exceptions)
 	msg = _("Negative Stock Error ({6}) for Item {0} in Warehouse {1} on {2} {3} in {4} {5}").format(args["item_code"],
@@ -353,3 +348,26 @@
 		"timestamp(posting_date, posting_time) <= timestamp(%(posting_date)s, %(posting_time)s)"],
 		"desc", "limit 1", for_update=for_update)
 	return sle and sle[0] or {}
+
+def get_valuation_rate(item_code, warehouse):
+	last_valuation_rate = frappe.db.sql("""select valuation_rate
+		from `tabStock Ledger Entry`
+		where item_code = %s and warehouse = %s
+		and ifnull(valuation_rate, 0) > 0
+		order by posting_date desc, posting_time desc, name desc limit 1""", (item_code, warehouse))
+
+	if not last_valuation_rate:
+		last_valuation_rate = frappe.db.sql("""select valuation_rate
+			from `tabStock Ledger Entry`
+			where item_code = %s and ifnull(valuation_rate, 0) > 0
+			order by posting_date desc, posting_time desc, name desc limit 1""", item_code)
+
+	valuation_rate = flt(last_valuation_rate[0][0]) if last_valuation_rate else 0
+
+	if not valuation_rate:
+		valuation_rate = frappe.db.get_value("Item Price", {"item_code": item_code, "buying": 1}, "price_list_rate")
+
+	if not valuation_rate and cint(frappe.db.get_value("Accounts Settings", None, "auto_accounting_for_stock")):
+		frappe.throw(_("Purchase rate for item: {0} not found, which is required to book accounting entry (expense). Please mention item price against a buying price list.").format(item_code))
+
+	return valuation_rate